Cla000461 (gene) Watermelon (97103) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cla000461
Type	gene
Organism	Citrullus. lanatus (Watermelon (97103) v1)
Description	DNA-directed RNA polymerase II subunit E (AHRD V1 **** F2QX94_PICP7); contains Interpro domain(s) IPR014381 DNA-directed RNA polymerase, RPB5 subunit
Location	Chr0 : 1715218 .. 1717021 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDS

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGGTGTTGTCGGAGGAGGAAATCACCAAACTCTTTAGAGTCCGGAAAACTGTGTTGCAGATGTTGAAAGACAGAGGCTACTTTGTTGGAGACTTCGAGCTTGATATGTCAAGAGAACAATTTAAGAAGAAGTTCGGTGAGAGCATGAAAAGAGAAGATCTTGTTATCAATAAATCCATGAGAAATAATAGCTCTGACCAGGTATAGTCTCATACTATACAATGATAATATCATTTATTTAGGCTGCTTTTGATTACTATTTACTTTTTCGTTTTTTAGTTTCTGAAAATTGTGTTTGTTGTTATTATCCAAAAAAAAAGAAAATTGTGTTTGTTGTTTCCCAACTTAATTACCATGATTTTCATTTTCTTAGGTAAACATTTGAATTGTTAGCAAGTTCTAACAACAAAAAAATAAGTTTTTAAAAACTACTTTTCTTTAGTTTTCAAAATTTTATTTAGATTTTGAAAACTCGCAATTAGTTGTGTATTTGAACATGTTTAAACTTTACCTTGTTAAAATGTTGCTGCAAAATTTCCTCAGGAGAAGTTTCTATATGAGTCATTCTCATGTACTTTGACATGAAAAATACTTAACCATCGATCATTGAGTAGTATATAATATTATTTGATAAATTTTTCCAAAACTTTTATGAAGTTTGGTTACAGGGATGTACAGGTTATTTGTTAACCTTTTTATTTATTCCCCTCCTTTTATTTATGACTCTTTTACACAGATATATATTTTCTTTCCTGAAGAGCCGAAGGTTGGTATCAAGACATTGGATACTTATAAAAAACGTATGAAATCAGAGAATGTTTTTAGAGCAATATTGGTTGTTCAACAGAATTTGACCCCCTTTGCTCGTACTTCTATAGGCGAAATATCTTCTAAAGTCCATTTGGAGGTTTTCCAGGTAAAAGTTAAATCTGTAAATAGTTTCTGGAGTCTTTTAATGTCGGATAGAATACAGTAATATTATCATATGCTACAAATTTGATGAGAAATAGAGAGGATGGAAAGAGCCATTTGGTGTCGCTTGCAAATGACTGATCAAATATAATTTATAATACTGAAGTCTACTACTACTACAAGGGCATAGCAATAGTGACAAGCCTGGGTTAAAGAATGGTAATGTTAGTTTGTAATTACTTATGTGATTTCCATTGTCCACATAATTATGCCTACATTCTTATTTTACTAAAGTTAATGTTACCTCTTTGTCACTTTTTGATGCAGGAAGCAGAATTGATGGTTAACATTAAAAATCACGTTCTCATTCCCGAGCACCAGTCCCTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACACAAGTGAGTTTCATCTTTTTTTCTTGAAATACACGAACATTGTGAGAATTTATCTTTCATAAACATGTTGAAATAACCTTTGTAGATTGGCCCGTGGTGGATAAGGGCTATGTAAATAATGTGGGTTTTAGGGAATAAGTTTAAGCAATGATGATCACCTACCTAAGATTTAATATCCTACAAGTTACATTGACAATCAAATATCGTAGGGTTAGGCAGTTGTTTCATTTGAATAGTCGAGATGTGCACAAGTTGGGTTTGACACTCTTGGATACATATTTAAATGTGTTTCTGTTAGTTCCTAAAGTGATTTTGTATTTTTTCTCAGCTACCTCGCATACAGGTTACCGATCCAATTGCTAGATATTATGGGCTGAAGCGTGGACAAGTAGTGAAGATCATCCGACCAAGCGAAACTGCAGGAAGATATGTGACTTATAGATACGTTGTTTGA

mRNA sequence

ATGGTGTTGTCGGAGGAGGAAATCACCAAACTCTTTAGAGTCCGGAAAACTGTGTTGCAGATGTTGAAAGACAGAGGCTACTTTGTTGGAGACTTCGAGCTTGATATGTCAAGAGAACAATTTAAGAAGAAGTTCGGTGAGAGCATGAAAAGAGAAGATCTTGTTATCAATAAATCCATGAGAAATAATAGCTCTGACCAGAATTTGACCCCCTTTGCTCGTACTTCTATAGGCGAAATATCTTCTAAAGTCCATTTGGAGGTTTTCCAGGAAGCAGAATTGATGGTTAACATTAAAAATCACGTTCTCATTCCCGAGCACCAGTCCCTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACACAACTACCTCGCATACAGGTTACCGATCCAATTGCTAGATATTATGGGCTGAAGCGTGGACAAGTAGTGAAGATCATCCGACCAAGCGAAACTGCAGGAAGATATGTGACTTATAGATACGTTGTTTGA

Coding sequence (CDS)

ATGGTGTTGTCGGAGGAGGAAATCACCAAACTCTTTAGAGTCCGGAAAACTGTGTTGCAGATGTTGAAAGACAGAGGCTACTTTGTTGGAGACTTCGAGCTTGATATGTCAAGAGAACAATTTAAGAAGAAGTTCGGTGAGAGCATGAAAAGAGAAGATCTTGTTATCAATAAATCCATGAGAAATAATAGCTCTGACCAGAATTTGACCCCCTTTGCTCGTACTTCTATAGGCGAAATATCTTCTAAAGTCCATTTGGAGGTTTTCCAGGAAGCAGAATTGATGGTTAACATTAAAAATCACGTTCTCATTCCCGAGCACCAGTCCCTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACACAACTACCTCGCATACAGGTTACCGATCCAATTGCTAGATATTATGGGCTGAAGCGTGGACAAGTAGTGAAGATCATCCGACCAAGCGAAACTGCAGGAAGATATGTGACTTATAGATACGTTGTTTGA

Protein sequence

MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSMRNNSSDQNLTPFARTSIGEISSKVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGLKRGQVVKIIRPSETAGRYVTYRYVV

Homology

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BLAST of Cla000461 vs. Swiss-Prot
Match: RPB5A_ARATH (DNA-directed RNA polymerases II and IV subunit 5A OS=Arabidopsis thaliana GN=NRPB5A PE=1 SV=1)

HSP 1 Score: 209.5 bits (532), Expect = 2.8e-53
Identity = 117/205 (57.07%), Postives = 134/205 (65.37%), Query Frame = 1


Query: 2   VLSEEEITKLFRVRKTVLQMLKDRGYFVGDFE-----------------------LDMSR 61
           +L+EEE+ +L+R++KT++QML+DRGYF+ D E                       L   R
Sbjct: 1   MLTEEELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKR 60

Query: 62  EQ--------FKKKFGESMKREDLVINKSMRNNSS------DQNLTPFARTSIGEISSKV 121
                     F  +    +K   +  N+    N         QNLTPFART I EISSK 
Sbjct: 61  NDNSDQLYIFFPDEAKVGVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKF 120

Query: 122 HLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGL 170
           HLEVFQEAE++VNIK HVL+PEHQ LT EEKKTLLERYTVKETQLPRIQVTDPIARY+GL
Sbjct: 121 HLEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQLPRIQVTDPIARYFGL 180

[Close]

BLAST of Cla000461 vs. Swiss-Prot
Match: RPAB1_CAEBR (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis briggsae GN=rpb-5 PE=3 SV=1)

HSP 1 Score: 149.1 bits (375), Expect = 4.5e-35
Identity = 95/212 (44.81%), Postives = 115/212 (54.25%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFEL-------------------------- 60
           M   E E  +L+R+RKTVLQM+ DRGY V   EL                          
Sbjct: 1   MADDELETYRLWRIRKTVLQMVHDRGYLVAQEELDQPLETFKETFGDRPSEKKPARSDLT 60

Query: 61  ------DMSREQFKKKFGESMKREDLVINKSMRNNSSDQNL-----------TPFARTSI 120
                 D   +Q    F E  K     I K++     +QN+           TP A+ SI
Sbjct: 61  ILVAHNDDPADQMFVFFPEDTKIGIKTI-KAICQQMQEQNISRAIIVVQTGMTPSAKQSI 120

Query: 121 GEISSKVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDP 170
           G+++ K  LE F EAELMVNI  H L+PEH  +T EEK  LL RY +K++QLPRIQ  DP
Sbjct: 121 GDMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDP 180

[Close]

BLAST of Cla000461 vs. Swiss-Prot
Match: RPAB1_DICDI (DNA-directed RNA polymerases I, II, and III subunit rpabc1 OS=Dictyostelium discoideum GN=polr2e PE=3 SV=2)

HSP 1 Score: 148.3 bits (373), Expect = 7.6e-35
Identity = 92/199 (46.23%), Postives = 116/199 (58.29%), Query Frame = 1


Query: 6   EEITKLFRVRKTVLQMLKDRGYFVG---------DFELDMSREQF-----KK-------- 65
           E+I +L ++RKTVLQML DR Y +           F   +SRE       KK        
Sbjct: 2   EDINRLLQIRKTVLQMLSDREYIITAYEQEYPRESF---VSRENLTMYCVKKDDPTDSIY 61

Query: 66  -------KFGESMKREDLVINKSMRNNSS----DQNLTPFARTSIGEISS--KVHLEVFQ 125
                  K G +  ++ + I K  + N +     QN+TPFA+ ++ E S   K+ LE F 
Sbjct: 62  VFFPDTPKVGVTQIKKYVDIMKDRQANRAIIVVQQNITPFAKQALAEFSQEKKITLEQFN 121

Query: 126 EAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGLKRGQVV 170
           EAEL+VNI +H L+P+H  LT EEK  LL RY +KE+QLPRIQ  DP+ARYYGL RG VV
Sbjct: 122 EAELLVNITHHQLVPKHILLTKEEKLELLTRYKMKESQLPRIQTNDPVARYYGLSRGHVV 181

[Close]

BLAST of Cla000461 vs. Swiss-Prot
Match: RPAB1_SCHPO (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb5 PE=1 SV=1)

HSP 1 Score: 136.3 bits (342), Expect = 3.0e-31
Identity = 84/207 (40.58%), Postives = 115/207 (55.56%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFK------------------ 60
           M   E+ I ++FR  KT  Q++ DRGY V   ELD++ +QFK                  
Sbjct: 1   MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60

Query: 61  -KKFGESMK--------REDLVINKSMR---NNSSDQN-----------LTPFARTSIGE 120
            K   +S K        +E  V  K MR   +   D N           +TP A   I  
Sbjct: 61  AKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIAT 120

Query: 121 ISSKVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIA 167
           ++ +  +E FQE++L+VNI +H L+P+H  L+ +EKK LL+RY ++ETQLPRIQ+ DP+A
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVA 180

[Close]

BLAST of Cla000461 vs. Swiss-Prot
Match: RPAB1_CAEEL (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis elegans GN=rpb-5 PE=3 SV=1)

HSP 1 Score: 136.3 bits (342), Expect = 3.0e-31
Identity = 67/101 (66.34%), Postives = 79/101 (78.22%), Query Frame = 1


Query: 69  LTPFARTSIGEISSKVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQ 128
           +TP A+ SIG+++ K  LE F EAELMVNI  H L+PEH  +T EEK  LL RY +K++Q
Sbjct: 111 MTPSAKQSIGDMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQ 170

Query: 129 LPRIQVTDPIARYYGLKRGQVVKIIRPSETAGRYVTYRYVV 170
           LPRIQ  DP+ARY+GL+RGQVVKIIRPSETAGRY+TYR VV
Sbjct: 171 LPRIQQCDPVARYFGLRRGQVVKIIRPSETAGRYITYRLVV 211

HSP 2 Score: 97.8 bits (242), Expect = 1.2e-19
Identity = 73/211 (34.60%), Postives = 100/211 (47.39%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGE-----SMKREDLV 60
           M   E E  +L+R+RKTVLQM+ DRGY V   ELD   E FK ++G+        R DL 
Sbjct: 1   MADDELETYRLWRIRKTVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLT 60

Query: 61  INKSMRNNSSDQNLTPFAR-TSIGEISSKVHLEVFQEAEL---MVNIKNHVLIPEHQSLT 120
           I  +  ++ +DQ    F     IG  + K   +  QE  +   ++ ++  +     QS+ 
Sbjct: 61  ILVAHNDDPADQMFVFFPEDAKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIG 120

Query: 121 NEEKKTLLERYTVKETQ-----------------------LPRIQVTD----------PI 170
           +   K +LE +   E                         L R ++ D          P+
Sbjct: 121 DMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPV 180

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BLAST of Cla000461 vs. TrEMBL
Match: A0A0A0KF69_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G170410 PE=3 SV=1)

HSP 1 Score: 273.1 bits (697), Expect = 2.3e-70
Identity = 148/207 (71.50%), Postives = 157/207 (75.85%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MV  EEEITKLFRVRKTVLQMLKDRGYFVGDFELDMS+ QFK KFGE+MKREDLVINKS 
Sbjct: 1   MVFPEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSKVQFKNKFGENMKREDLVINKSK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEIS-S 120
           RNNSSDQ                                     NLTPFAR  I E+S S
Sbjct: 61  RNNSSDQIYVFFPEEPKVGIKIVETYVGRMKSENVFRAIFVVQLNLTPFARNKIAELSSS 120

Query: 121 KVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYY 170
           K+HLEVFQE EL+VNIK HVLIPEHQ+LT+EEKKTLL RYTVKETQLPR+QVTDPI+RYY
Sbjct: 121 KLHLEVFQETELLVNIKEHVLIPEHQTLTDEEKKTLLGRYTVKETQLPRMQVTDPISRYY 180

[Close]

BLAST of Cla000461 vs. TrEMBL
Match: W9RWL5_9ROSA (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Morus notabilis GN=L484_003651 PE=3 SV=1)

HSP 1 Score: 271.2 bits (692), Expect = 8.7e-70
Identity = 140/205 (68.29%), Postives = 158/205 (77.07%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVLSE+EIT+LFR+R+TV+QML+DR Y VGDFEL+M++EQF+ K+GE+MKREDL+INKS 
Sbjct: 1   MVLSEDEITRLFRIRRTVMQMLRDRNYLVGDFELNMTKEQFRNKYGENMKREDLIINKSR 60

Query: 61  RNNSSD-------------------------------------QNLTPFARTSIGEISSK 120
           RN+S D                                     QNLTPFART I EIS+K
Sbjct: 61  RNDSPDQIYVFFPEEQKVGVKTMKTYINRMKSENVLRAVLVVQQNLTPFARTCISEISTK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 169
            HLEVFQEAEL+VNIK HVL+PEHQ LTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG
Sbjct: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 180

[Close]

BLAST of Cla000461 vs. TrEMBL
Match: A0A0A0LYM6_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G702030 PE=3 SV=1)

HSP 1 Score: 262.3 bits (669), Expect = 4.0e-67
Identity = 142/206 (68.93%), Postives = 158/206 (76.70%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVLSEEEITKLFR RKTVLQML+DRG+ VGDFEL MSREQFK ++GE+MK+EDLVINKSM
Sbjct: 1   MVLSEEEITKLFRARKTVLQMLRDRGFVVGDFELAMSREQFKNQYGETMKKEDLVINKSM 60

Query: 61  RNNSSD-------------------------------------QNLTPFARTSIGEISSK 120
           RNNSSD                                     + L+ FAR+SI E + K
Sbjct: 61  RNNSSDQIYVFFPEEPKVSVKTVRTYINRMKSDNVFRAILVVQEKLSSFARSSICE-APK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
            HLEVFQEAEL+VNIK+HVLIPEHQ LTNE+KKTLLERYTVK+TQLPR+QVTDPIARYYG
Sbjct: 121 FHLEVFQEAELLVNIKDHVLIPEHQLLTNEDKKTLLERYTVKDTQLPRMQVTDPIARYYG 180

[Close]

BLAST of Cla000461 vs. TrEMBL
Match: A0A0S3TCL1_PHAAN (Uncharacterized protein OS=Vigna angularis var. angularis GN=Vigan.11G248300 PE=3 SV=1)

HSP 1 Score: 260.8 bits (665), Expect = 1.2e-66
Identity = 135/206 (65.53%), Postives = 155/206 (75.24%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVL +EEI++LFR+RKTV+QML+DRG+ VGDFE++MS+ +FK K+GE MKREDLVINKS 
Sbjct: 1   MVLPDEEISRLFRIRKTVMQMLRDRGFLVGDFEINMSKHEFKSKYGEHMKREDLVINKSK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEISSK 120
           ++NS DQ                                     NLTPFART I EISSK
Sbjct: 61  KDNSGDQIYVFFPEEAKVGVKTMKTYTNRMNSENVYRAILVTQTNLTPFARTCISEISSK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
            HLEVFQEAEL+VNIK H L+PEHQ LT+ EKKTL+ERYTVKETQLPRIQVTDP+ARYYG
Sbjct: 121 FHLEVFQEAELLVNIKEHELVPEHQVLTDAEKKTLIERYTVKETQLPRIQVTDPVARYYG 180

[Close]

BLAST of Cla000461 vs. TrEMBL
Match: M5X630_PRUPE (Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa024345mg PE=3 SV=1)

HSP 1 Score: 260.0 bits (663), Expect = 2.0e-66
Identity = 133/206 (64.56%), Postives = 155/206 (75.24%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVL EEEIT+L+RVR+TV+QML+DR Y VGDFE++M+REQFK K+GE+MKREDL INK+ 
Sbjct: 1   MVLPEEEITRLYRVRRTVMQMLRDRKYLVGDFEINMTREQFKAKYGENMKREDLTINKTK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEISSK 120
           RN+S+DQ                                     N+TP ART I EISSK
Sbjct: 61  RNDSTDQLYVFFPEEPKVGVKTIKTYTNRMKSDNVARAILVTQQNMTPMARTCISEISSK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
            H+EVFQE ELMVN+  HVL+PEHQ LTNEEKKTLLERYTVKETQLPRIQ+TDP+A+YYG
Sbjct: 121 FHMEVFQEPELMVNVTEHVLVPEHQLLTNEEKKTLLERYTVKETQLPRIQLTDPVAKYYG 180

[Close]

BLAST of Cla000461 vs. TAIR10
Match: AT3G22320.1 (AT3G22320.1 Eukaryotic rpb5 RNA polymerase subunit family protein)

HSP 1 Score: 209.5 bits (532), Expect = 1.6e-54
Identity = 117/205 (57.07%), Postives = 134/205 (65.37%), Query Frame = 1


Query: 2   VLSEEEITKLFRVRKTVLQMLKDRGYFVGDFE-----------------------LDMSR 61
           +L+EEE+ +L+R++KT++QML+DRGYF+ D E                       L   R
Sbjct: 1   MLTEEELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKR 60

Query: 62  EQ--------FKKKFGESMKREDLVINKSMRNNSS------DQNLTPFARTSIGEISSKV 121
                     F  +    +K   +  N+    N         QNLTPFART I EISSK 
Sbjct: 61  NDNSDQLYIFFPDEAKVGVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKF 120

Query: 122 HLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGL 170
           HLEVFQEAE++VNIK HVL+PEHQ LT EEKKTLLERYTVKETQLPRIQVTDPIARY+GL
Sbjct: 121 HLEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQLPRIQVTDPIARYFGL 180

[Close]

BLAST of Cla000461 vs. TAIR10
Match: AT5G57980.1 (AT5G57980.1 RNA polymerase II fifth largest subunit, C)

HSP 1 Score: 125.2 bits (313), Expect = 3.9e-29
Identity = 80/206 (38.83%), Postives = 110/206 (53.40%), Query Frame = 1


Query: 5   EEEITKLFRVRKTVLQMLKDRGY-------------FVGDFELDMSREQFKKKFGESMKR 64
           ++EIT++F+VR+TVLQML+DRGY             FV  F   M++   +  F  + K 
Sbjct: 5   DDEITRIFKVRRTVLQMLRDRGYTIEESDLNLKREEFVQRFCKTMNKVNKEALFVSANKG 64

Query: 65  EDL-----------------VINKSMRNNSSDQN-----------LTPFARTSIGEISSK 124
            +                  VI K +     D             +T  AR ++ E++  
Sbjct: 65  PNPADKIYVFYPEGPKVGVPVIKKEVAIKMRDDKVHRGIVVVPMAITAPARMAVSELNKM 124

Query: 125 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
           + +EVF+EAEL+ NI  H L+ ++  L ++ KK LL  YTV++TQLPRI VTDP+ARYYG
Sbjct: 125 LTIEVFEEAELVTNITEHKLVNKYYVLDDQAKKKLLNTYTVQDTQLPRILVTDPLARYYG 184

[Close]

BLAST of Cla000461 vs. TAIR10
Match: AT2G41340.1 (AT2G41340.1 RNA polymerase II fifth largest subunit, D)

HSP 1 Score: 110.5 bits (275), Expect = 1.0e-24
Identity = 65/201 (32.34%), Postives = 106/201 (52.74%), Query Frame = 1


Query: 4   SEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSMRNN 63
           S  E  K +  R+T ++ML+DRGY V D ++++S +QF+  +GE    + L I+   R +
Sbjct: 17  SSVECHKYYLARRTTMEMLRDRGYDVSDEDINLSLQQFRALYGEHPDVDLLRISAKHRFD 76

Query: 64  SSD---------------------------QNLTPFARTSIGEISSKV---------HLE 123
           SS                            +N+T         I+++           +E
Sbjct: 77  SSKKISVVFCGTGIVKVNAMRVIAADVLSRENITGLILVLQSHITNQALKAVELFSFKVE 136

Query: 124 VFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGLKRG 169
           +F+  +L+VN+  HVL P+HQ L ++EK++LL++++++E QLPR+   DPI RYYGL+ G
Sbjct: 137 LFEITDLLVNVSKHVLRPKHQVLNDKEKESLLKKFSIEEKQLPRLSSKDPIVRYYGLETG 196

[Close]

BLAST of Cla000461 vs. TAIR10
Match: AT3G57080.1 (AT3G57080.1 Eukaryotic rpb5 RNA polymerase subunit family protein)

HSP 1 Score: 94.4 bits (233), Expect = 7.4e-20
Identity = 67/203 (33.00%), Postives = 99/203 (48.77%), Query Frame = 1


Query: 3   LSEEEITKLFRVRKTVLQMLKDRGYFVGD-----------------FELD------MSRE 62
           LS EE  + +  R+  LQML+DRGY V D                  ++D      + R 
Sbjct: 20  LSSEESHRYYLARRNGLQMLRDRGYEVSDEDINLSLHDFRTVYGERPDVDRLRISALHRS 79

Query: 63  QFKKK-----FGESMKREDLVINKSMRNNSSDQNLTPFARTSIGEISSKV---------H 122
              KK     FG SM + +  I   + +  S + +T         ++++           
Sbjct: 80  DSTKKVKIVFFGTSMVKVN-AIRSVVADILSQETITGLILVLQNHVTNQALKAIELFSFK 139

Query: 123 LEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGLK 169
           +E+FQ  +L+VNI  H L P+HQ L +EEK TLL++++++E QLPRI   D I RYYGL+
Sbjct: 140 VEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPRISKKDAIVRYYGLE 199

[Close]

BLAST of Cla000461 vs. TAIR10
Match: AT3G54490.1 (AT3G54490.1 RNA polymerase II fifth largest subunit, E)

HSP 1 Score: 81.6 bits (200), Expect = 5.0e-16
Identity = 58/199 (29.15%), Postives = 87/199 (43.72%), Query Frame = 1


Query: 7   EITKLFRVRKTVLQMLKDRGYFVGDFELDM-----------------------SREQFKK 66
           E  + +  R T  +ML+DRGY V + EL +                        R   KK
Sbjct: 35  ESKRFYLARTTAFEMLRDRGYEVNEAELSLTLSEFRSVFGEKPELERLRICVPLRSDPKK 94

Query: 67  KFGESMKREDLVINKSMR-------NNSSDQNLTPFARTSIGEISSKV------HLEVFQ 126
           K        + +  KS+R       NN     +    ++ +   + K        +E F 
Sbjct: 95  KILVVFMGTEPITVKSVRALHIQISNNVGLHAMILVLQSKMNHFAQKALTTFPFTVETFP 154

Query: 127 EAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYGLKRGQVV 170
             +L+VNI  H+  P+ + L  EEK+ LL ++ +++ QLP +Q  D   RYYGLK+ QVV
Sbjct: 155 IEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLPYLQEKDSFVRYYGLKKKQVV 214

[Close]

BLAST of Cla000461 vs. NCBI nr
Match: gi|659112918|ref|XP_008456369.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like isoform X1 [Cucumis melo])

HSP 1 Score: 280.4 bits (716), Expect = 2.1e-72
Identity = 153/207 (73.91%), Postives = 159/207 (76.81%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MV  EEEITKLFRVRKTVLQMLKDRGYFVGDFELDMS+ QFK KFGE+MKREDLVINKS 
Sbjct: 1   MVFPEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSKAQFKNKFGENMKREDLVINKSK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEIS-S 120
           RNNSSDQ                                     NLTPFAR  I E+S +
Sbjct: 61  RNNSSDQIYVFFPEEPKVGIKIVETYVGRMKSENVFRAIFVVQLNLTPFARNKIAELSST 120

Query: 121 KVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYY 170
           KVHLEVFQEAELMVNIK HVLIPEHQSLT+EEKKTLL RYTVKETQLPR+QVTDPIARYY
Sbjct: 121 KVHLEVFQEAELMVNIKEHVLIPEHQSLTDEEKKTLLGRYTVKETQLPRMQVTDPIARYY 180

[Close]

BLAST of Cla000461 vs. NCBI nr
Match: gi|449450868|ref|XP_004143184.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Cucumis sativus])

HSP 1 Score: 273.1 bits (697), Expect = 3.3e-70
Identity = 148/207 (71.50%), Postives = 157/207 (75.85%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MV  EEEITKLFRVRKTVLQMLKDRGYFVGDFELDMS+ QFK KFGE+MKREDLVINKS 
Sbjct: 1   MVFPEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSKVQFKNKFGENMKREDLVINKSK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEIS-S 120
           RNNSSDQ                                     NLTPFAR  I E+S S
Sbjct: 61  RNNSSDQIYVFFPEEPKVGIKIVETYVGRMKSENVFRAIFVVQLNLTPFARNKIAELSSS 120

Query: 121 KVHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYY 170
           K+HLEVFQE EL+VNIK HVLIPEHQ+LT+EEKKTLL RYTVKETQLPR+QVTDPI+RYY
Sbjct: 121 KLHLEVFQETELLVNIKEHVLIPEHQTLTDEEKKTLLGRYTVKETQLPRMQVTDPISRYY 180

[Close]

BLAST of Cla000461 vs. NCBI nr
Match: gi|703140945|ref|XP_010107375.1| (DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Morus notabilis])

HSP 1 Score: 271.2 bits (692), Expect = 1.2e-69
Identity = 140/205 (68.29%), Postives = 158/205 (77.07%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVLSE+EIT+LFR+R+TV+QML+DR Y VGDFEL+M++EQF+ K+GE+MKREDL+INKS 
Sbjct: 1   MVLSEDEITRLFRIRRTVMQMLRDRNYLVGDFELNMTKEQFRNKYGENMKREDLIINKSR 60

Query: 61  RNNSSD-------------------------------------QNLTPFARTSIGEISSK 120
           RN+S D                                     QNLTPFART I EIS+K
Sbjct: 61  RNDSPDQIYVFFPEEQKVGVKTMKTYINRMKSENVLRAVLVVQQNLTPFARTCISEISTK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 169
            HLEVFQEAEL+VNIK HVL+PEHQ LTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG
Sbjct: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 180

[Close]

BLAST of Cla000461 vs. NCBI nr
Match: gi|1011992460|ref|XP_015949518.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Arachis duranensis])

HSP 1 Score: 265.4 bits (677), Expect = 6.9e-68
Identity = 136/206 (66.02%), Postives = 157/206 (76.21%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVLSEEEI +L+R+RKTV+QML+DR Y VGDFE+ MSRE+F++K+GE+MKREDLVINKS 
Sbjct: 1   MVLSEEEINRLYRIRKTVMQMLRDRDYLVGDFEIKMSREEFRRKYGENMKREDLVINKSK 60

Query: 61  RNNSSDQ-------------------------------------NLTPFARTSIGEISSK 120
           ++NSSDQ                                     NLTPFART I E+S K
Sbjct: 61  KDNSSDQIYVFFPEEAKVGVKTLKTYTNRMNSENVFRAILVCQQNLTPFARTCISEVSQK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
            HLEVFQEAEL++NIK HVL+PEHQ LT+ EKKTL+ERYTVKETQLPRIQVTDP+ARYYG
Sbjct: 121 FHLEVFQEAELLINIKEHVLVPEHQVLTDAEKKTLIERYTVKETQLPRIQVTDPVARYYG 180

[Close]

BLAST of Cla000461 vs. NCBI nr
Match: gi|659118294|ref|XP_008459046.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Cucumis melo])

HSP 1 Score: 264.6 bits (675), Expect = 1.2e-67
Identity = 143/206 (69.42%), Postives = 159/206 (77.18%), Query Frame = 1


Query: 1   MVLSEEEITKLFRVRKTVLQMLKDRGYFVGDFELDMSREQFKKKFGESMKREDLVINKSM 60
           MVLSEEEIT+LFRVRKTVLQML+DRG+ VGDFEL MSREQFK +FGE+MK+ED+VINKSM
Sbjct: 1   MVLSEEEITRLFRVRKTVLQMLRDRGFLVGDFELAMSREQFKNQFGETMKKEDIVINKSM 60

Query: 61  RNNSSD-------------------------------------QNLTPFARTSIGEISSK 120
           RNNSSD                                     + L+ FAR+SI E + K
Sbjct: 61  RNNSSDQIYVFFPEEPKVSVKTVRTYINRMKSDNVFRAILVVQEKLSSFARSSICE-APK 120

Query: 121 VHLEVFQEAELMVNIKNHVLIPEHQSLTNEEKKTLLERYTVKETQLPRIQVTDPIARYYG 170
            HLEVFQEAEL+VNIK+HVLIPEHQ LTNEEKKTLLERYTVK+TQLPR+QVTDPIARYYG
Sbjct: 121 FHLEVFQEAELLVNIKDHVLIPEHQLLTNEEKKTLLERYTVKDTQLPRMQVTDPIARYYG 180

The following BLAST results are available for this feature:

BLAST of Cla000461 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RPB5A_ARATH	2.8e-53	57.07	DNA-directed RNA polymerases II and IV subunit 5A OS=Arabidopsis thaliana GN=NRP...	[more]
RPAB1_CAEBR	4.5e-35	44.81	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis bri...	[more]
RPAB1_DICDI	7.6e-35	46.23	DNA-directed RNA polymerases I, II, and III subunit rpabc1 OS=Dictyostelium disc...	[more]
RPAB1_SCHPO	3.0e-31	40.58	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Schizosaccharomyce...	[more]
RPAB1_CAEEL	3.0e-31	66.34	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis ele...	[more]

BLAST of Cla000461 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KF69_CUCSA	2.3e-70	71.50	Uncharacterized protein OS=Cucumis sativus GN=Csa_6G170410 PE=3 SV=1	[more]
W9RWL5_9ROSA	8.7e-70	68.29	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Morus notabilis GN...	[more]
A0A0A0LYM6_CUCSA	4.0e-67	68.93	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G702030 PE=3 SV=1	[more]
A0A0S3TCL1_PHAAN	1.2e-66	65.53	Uncharacterized protein OS=Vigna angularis var. angularis GN=Vigan.11G248300 PE=...	[more]
M5X630_PRUPE	2.0e-66	64.56	Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa024345mg PE=3 SV=1	[more]

BLAST of Cla000461 vs. TAIR10


Match Name	E-value	Identity	Description
AT3G22320.1	1.6e-54	57.07	Eukaryotic rpb5 RNA polymerase subunit family protein	[more]
AT5G57980.1	3.9e-29	38.83	RNA polymerase II fifth largest subunit, C	[more]
AT2G41340.1	1.0e-24	32.34	RNA polymerase II fifth largest subunit, D	[more]
AT3G57080.1	7.4e-20	33.00	Eukaryotic rpb5 RNA polymerase subunit family protein	[more]
AT3G54490.1	5.0e-16	29.15	RNA polymerase II fifth largest subunit, E	[more]

BLAST of Cla000461 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|659112918\|ref\|XP_008456369.1\|	2.1e-72	73.91	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like isoform X1 [Cu...	[more]
gi\|449450868\|ref\|XP_004143184.1\|	3.3e-70	71.50	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Cucumis sativ...	[more]
gi\|703140945\|ref\|XP_010107375.1\|	1.2e-69	68.29	DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Morus notabilis]	[more]
gi\|1011992460\|ref\|XP_015949518.1\|	6.9e-68	66.02	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Arachis duran...	[more]
gi\|659118294\|ref\|XP_008459046.1\|	1.2e-67	69.42	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A-like [Cucumis melo]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR000783	RNA_pol_subH/Rpb5_C
IPR005571	RNA_pol_Rpb5_N
IPR020609	RpoH/RPB5

Vocabulary: **Biological Process**
Term	Definition
GO:0006351	transcription, DNA-templated

Vocabulary: **Molecular Function**
Term	Definition
GO:0003677	DNA binding
GO:0003899	DNA-directed RNA polymerase activity

Vocabulary: **Cellular Component**
Term	Definition
GO:0005634	nucleus

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006144	purine nucleobase metabolic process
biological_process	GO:0006206	pyrimidine nucleobase metabolic process
biological_process	GO:0006351	transcription, DNA-templated
cellular_component	GO:0055029	nuclear DNA-directed RNA polymerase complex
cellular_component	GO:0005730	nucleolus
cellular_component	GO:0044451	nucleoplasm part
cellular_component	GO:0005634	nucleus
molecular_function	GO:0003677	DNA binding
molecular_function	GO:0003899	DNA-directed RNA polymerase activity

Relationships

The following mRNA feature(s) are a part of this gene:


Feature Name	Unique Name	Type
Cla000461	Cla000461.1	mRNA

InterPro

Analysis Name: InterPro Annotations of watermelon (97103)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	PRODOM	PD005155		coord: 103..168 score: 4.0
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	GENE3D	G3DSA:3.90.940.20		coord: 97..169 score: 8.2
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	PFAM	PF01191	RNA_pol_Rpb5_C	coord: 96..168 score: 8.8
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	unknown	SSF55287	RPB5-like RNA polymerase subunit	coord: 94..169 score: 1.57
IPR005571	RNA polymerase, Rpb5, N-terminal	GENE3D	G3DSA:3.40.1340.10		coord: 67..96 score: 4.5E-5coord: 4..64 score: 2.2
IPR005571	RNA polymerase, Rpb5, N-terminal	PFAM	PF03871	RNA_pol_Rpb5_N	coord: 5..75 score: 8.7
IPR005571	RNA polymerase, Rpb5, N-terminal	unknown	SSF53036	Eukaryotic RPB5 N-terminal domain	coord: 5..97 score: 9.15
IPR020609	Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit	HAMAP	MF_00025	RNApol_RpoH_RPB5	coord: 96..169 score: 22
None	No IPR available	PANTHER	PTHR10535	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	coord: 4..169 score: 5.0

Synteny

The following gene(s) are orthologous to this gene:

None

The following gene(s) are paralogous to this gene:

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cla000461	Watermelon (97103) v1	wmwmB001
Cla000461	Watermelon (Charleston Gray)	wcgwmB171