CmaCh18G005560 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh18G005560
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	Dna-directed rna polymerases i, ii, and iii subunit rpabc1
Location	Cma_Chr18 : 3646798 .. 3648015 (-)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSexon

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

ATGCAAATGTTGAAAGATCGAGGCTACTATGTTGGAGATTTGGACATTGACATGTCAAGAAATCAATTTAGGAATAAGTATGGTGATAATATGAAGAGAGAAGATCTTGTTATCAATAAAGCCATGAGAAATAATAGCTCTGATCAGGTAGAGTTTCATGCTCTACAATGATACTATGAATCCTTAGTGATCCTTTTATTTGTTCCTCTCTTGTTTATGGCTCGTTTCTATAGATATATATATTTTTTCCTGAAGAACCCAAGGTTGGTGTCAAGACGATGAAAACGTATACGAATCGTATGAAATCGGAGAATGTTTTTCGAGCTATATTGGTTGTTCAACAGAATTTGACCCCGTTTGCTCGTACTTGTATAAGCGAAATATCATCTAAATTCCATTTGGAGGTTTTTCAGGTATTGTTTGAGACTATGCTGCAAAAGTTTTGTGATTTCCGTATCATTGTGCTTATAATTGCCATTTTCTACTTGTTGTTGAAGGAAGCTGAATTGATGGTTAATGTTAAAGATCATGTTCTTATTCCTGAGCATCAGCTGTTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACGCAGGTGAGTATCGATTTTTTTCCCGAAAGATACAGAAGTGAACTCATTAAAAAAAGTCCCTTGAAATGTATATTGTTTTTGTGAGATCCTACGTTCGTTGTGGAGGAGAATGAAGCATTCTTTATAAGGGTGTGGAAACATTTTCCTAGCCGATGCTTTTTAAAAACCTTAAGGGGAAGTTGAGAAGTTCAAAAGGGAAAAATCCAAAAATGACAATATCTAAATGGTATTAGAGTTAGACACCGGGCGATGTGCTAGTGAGGAGGCTGAGCCATGAAGGAGGTGGATTGTGAGATCCGGGAGGAGAACGAAACATTCTTTATTTATAAGGGTGTGGAAACCTCTGTCCAGTTGACCCATTTTAAAAGTCTTAAGTGGAAGCTCGTAAGGGGAAAGTAAAAAAAGAACAATATCTGCTAGCAGTGAGCTTAGCTTAGACCGTTACAATTTTGTTCTAACGTAATGTTGTGTTTGTTTGTCTCAGCTACCTCGCATTCAAGTCACTGATCCAATTGCTCGATATTATGGGTTGAAGCGTGGACAAGTTTTGAAGATCATTCGACCAAGTGAGACTGCAGGAAGGTATGTGACTTATAGATATGTTGTTTGA

mRNA sequence

ATGCAAATGTTGAAAGATCGAGGCTACTATGTTGGAGATTTGGACATTGACATGTCAAGAAATCAATTTAGGAATAAGTATGGTGATAATATGAAGAGAGAAGATCTTGTTATCAATAAAGCCATGAGAAATAATAGCTCTGATCAGATATATATATTTTTTCCTGAAGAACCCAAGGTTGGTGTCAAGACGATGAAAACGTATACGAATCGTATGAAATCGGAGAATGTTTTTCGAGCTATATTGGTTGTTCAACAGAATTTGACCCCGTTTGCTCGTACTTGTATAAGCGAAATATCATCTAAATTCCATTTGGAGGTTTTTCAGGAAGCTGAATTGATGGTTAATGTTAAAGATCATGTTCTTATTCCTGAGCATCAGCTGTTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACGCAGCGTGGACAAGTTTTGAAGATCATTCGACCAAGTGAGACTGCAGGAAGGTATGTGACTTATAGATATGTTGTTTGA

Coding sequence (CDS)

ATGCAAATGTTGAAAGATCGAGGCTACTATGTTGGAGATTTGGACATTGACATGTCAAGAAATCAATTTAGGAATAAGTATGGTGATAATATGAAGAGAGAAGATCTTGTTATCAATAAAGCCATGAGAAATAATAGCTCTGATCAGATATATATATTTTTTCCTGAAGAACCCAAGGTTGGTGTCAAGACGATGAAAACGTATACGAATCGTATGAAATCGGAGAATGTTTTTCGAGCTATATTGGTTGTTCAACAGAATTTGACCCCGTTTGCTCGTACTTGTATAAGCGAAATATCATCTAAATTCCATTTGGAGGTTTTTCAGGAAGCTGAATTGATGGTTAATGTTAAAGATCATGTTCTTATTCCTGAGCATCAGCTGTTGACAAATGAAGAGAAGAAGACGTTGTTGGAGAGGTATACGGTGAAAGAAACGCAGCGTGGACAAGTTTTGAAGATCATTCGACCAAGTGAGACTGCAGGAAGGTATGTGACTTATAGATATGTTGTTTGA

Protein sequence

MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDHVLIPEHQLLTNEEKKTLLERYTVKETQRGQVLKIIRPSETAGRYVTYRYVV

Homology

[Close]

BLAST of CmaCh18G005560 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: 273.9 bits (699), Expect = 1.2e-72
Identity = 140/188 (74.47%), Postives = 159/188 (84.57%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQML+DRGY++ D ++ M++ QF  K+GDNMKREDLV  KA RN++SDQ+YIFFP+E KV
Sbjct: 18  MQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRNDNSDQLYIFFPDEAKV 77

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMK YTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAE++VN+K+H
Sbjct: 78  GVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAEMLVNIKEH 137

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+LT EEKKTLLERYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 138 VLVPEHQVLTTEEKKTLLERYTVKETQLPRIQVTDPIARYFGLKRGQVVKIIRPSETAGR 197

[Close]

BLAST of CmaCh18G005560 vs. Swiss-Prot
Match: RPAB1_PONAB (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=POLR2E PE=2 SV=1)

HSP 1 Score: 164.1 bits (414), Expect = 1.4e-39
Identity = 85/192 (44.27%), Postives = 125/192 (65.10%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNM-----KREDLVINKAMRNNSSDQIYIFFP 60
           MQ+  DRGY V   ++D +  +FR ++GD       +R DL +  A  ++ +DQ+++FFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  EEPKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMV 120
           EEPKVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ K+ LE F + EL++
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query: 121 NVKDHVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPS 171
           N+ +H L+PEH ++T EE   LL RY ++E Q                 RGQV+KIIRPS
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPS 197

[Close]

BLAST of CmaCh18G005560 vs. Swiss-Prot
Match: RPAB1_RAT (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1)

HSP 1 Score: 163.3 bits (412), Expect = 2.3e-39
Identity = 84/192 (43.75%), Postives = 126/192 (65.62%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNM-----KREDLVINKAMRNNSSDQIYIFFP 60
           MQ+  DRGY V   ++D +  +F+ ++GD       +R DL +  A  ++ +DQ+++FFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  EEPKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMV 120
           EEPKVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ K+ LE F + EL++
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query: 121 NVKDHVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPS 171
           N+ +H L+PEH ++T EE   LL RY ++E+Q                 RGQV+KIIRPS
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVARYFGIKRGQVVKIIRPS 197

[Close]

BLAST of CmaCh18G005560 vs. Swiss-Prot
Match: RPAB1_MOUSE (DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus GN=Polr2e PE=1 SV=1)

HSP 1 Score: 163.3 bits (412), Expect = 2.3e-39
Identity = 84/192 (43.75%), Postives = 126/192 (65.62%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNM-----KREDLVINKAMRNNSSDQIYIFFP 60
           MQ+  DRGY V   ++D +  +F+ ++GD       +R DL +  A  ++ +DQ+++FFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  EEPKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMV 120
           EEPKVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ K+ LE F + EL++
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query: 121 NVKDHVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPS 171
           N+ +H L+PEH ++T EE   LL RY ++E+Q                 RGQV+KIIRPS
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVARYFGIKRGQVVKIIRPS 197

[Close]

BLAST of CmaCh18G005560 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: 161.4 bits (407), Expect = 8.8e-39
Identity = 87/193 (45.08%), Postives = 124/193 (64.25%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMK-----REDLVINKAMRNNSSDQIYIFFP 60
           +QM+ DRGY V   ++D     F+ +YGD        R DL I  A  ++ +DQ+++FFP
Sbjct: 19  LQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTILVAHNDDPADQMFVFFP 78

Query: 61  EEPKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMV 120
           E+ K+G+KT+K    +M+ +N+ RAI+VVQ  +TP A+  I +++ K+ LE F EAELMV
Sbjct: 79  EDAKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIGDMAPKYMLEHFLEAELMV 138

Query: 121 NVKDHVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPS 172
           N+ +H L+PEH ++T EEK  LL RY +K++Q                 RGQV+KIIRPS
Sbjct: 139 NITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFGLRRGQVVKIIRPS 198

[Close]

BLAST of CmaCh18G005560 vs. TrEMBL
Match: B9N7D1_POPTR (DNA-directed RNA polymerase family protein OS=Populus trichocarpa GN=POPTR_0006s16660g PE=3 SV=1)

HSP 1 Score: 289.7 bits (740), Expect = 2.4e-75
Identity = 147/188 (78.19%), Postives = 164/188 (87.23%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I M+R QF +KYG+NMKREDLVINK  RN+SSDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEIKMTREQFESKYGNNMKREDLVINKTKRNDSSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EIS+KFHLEVFQEAEL+VN+K+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTKFHLEVFQEAELLVNIKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+L+NEEKKTLLERYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 VLVPEHQVLSNEEKKTLLERYTVKETQLPRIQITDPIARYYGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. TrEMBL
Match: A0A0D2PJI1_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_004G280900 PE=4 SV=1)

HSP 1 Score: 288.9 bits (738), Expect = 4.1e-75
Identity = 146/183 (79.78%), Postives = 163/183 (89.07%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I++S+ QF +KYG+NMKREDLVINK  RN++SDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEINLSKQQFISKYGENMKREDLVINKTKRNDNSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EISSKFHLEVFQEAEL+VNVK+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISSKFHLEVFQEAELLVNVKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ------------RGQVLKIIRPSETAGRYVTYR 172
            L+PEHQ+LTNEEKKTLL RYTVKETQ            RGQV+KIIRPSETAGRY+TYR
Sbjct: 139 ALVPEHQVLTNEEKKTLLHRYTVKETQVSDPIARYFGLKRGQVVKIIRPSETAGRYITYR 198

[Close]

BLAST of CmaCh18G005560 vs. TrEMBL
Match: V4UJN2_9ROSI (Uncharacterized protein OS=Citrus clementina GN=CICLE_v10009504mg PE=3 SV=1)

HSP 1 Score: 287.3 bits (734), Expect = 1.2e-74
Identity = 146/188 (77.66%), Postives = 165/188 (87.77%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQML+DRGY+VGD +I+MS+ QF  K+G+NMKREDLVINKA+RN+SSDQIY+FFP+E KV
Sbjct: 19  MQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS+KFHLEVFQEAEL+VN+K+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+LTNEEKKTLL+RYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 VLVPEHQVLTNEEKKTLLKRYTVKETQLPRIQVTDPIARYYGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. TrEMBL
Match: A0A0B0NU90_GOSAR (Dna-directed rna polymerases i, ii, and iii subunit rpabc1 OS=Gossypium arboreum GN=F383_07135 PE=3 SV=1)

HSP 1 Score: 287.0 bits (733), Expect = 1.6e-74
Identity = 146/188 (77.66%), Postives = 163/188 (86.70%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I++S+ QF +KYG+NMKREDLVINK  RN++SDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEINLSKQQFISKYGENMKREDLVINKTKRNDNSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EISSKFHLEVFQEAEL+VNVK+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISSKFHLEVFQEAELLVNVKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
            L+PEHQ+LTNEEKKTLL RYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 ALVPEHQVLTNEEKKTLLHRYTVKETQLPRIQVSDPIARYFGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. TrEMBL
Match: A0A0D2S793_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_004G280900 PE=3 SV=1)

HSP 1 Score: 287.0 bits (733), Expect = 1.6e-74
Identity = 146/188 (77.66%), Postives = 163/188 (86.70%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I++S+ QF +KYG+NMKREDLVINK  RN++SDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEINLSKQQFISKYGENMKREDLVINKTKRNDNSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EISSKFHLEVFQEAEL+VNVK+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISSKFHLEVFQEAELLVNVKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
            L+PEHQ+LTNEEKKTLL RYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 ALVPEHQVLTNEEKKTLLHRYTVKETQLPRIQVSDPIARYFGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. TAIR10
Match: AT3G22320.1 (AT3G22320.1 Eukaryotic rpb5 RNA polymerase subunit family protein)

HSP 1 Score: 273.9 bits (699), Expect = 6.9e-74
Identity = 140/188 (74.47%), Postives = 159/188 (84.57%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQML+DRGY++ D ++ M++ QF  K+GDNMKREDLV  KA RN++SDQ+YIFFP+E KV
Sbjct: 18  MQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRNDNSDQLYIFFPDEAKV 77

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMK YTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAE++VN+K+H
Sbjct: 78  GVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAEMLVNIKEH 137

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+LT EEKKTLLERYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 138 VLVPEHQVLTTEEKKTLLERYTVKETQLPRIQVTDPIARYFGLKRGQVVKIIRPSETAGR 197

[Close]

BLAST of CmaCh18G005560 vs. TAIR10
Match: AT5G57980.1 (AT5G57980.1 RNA polymerase II fifth largest subunit, C)

HSP 1 Score: 119.4 bits (298), Expect = 2.2e-27
Identity = 70/192 (36.46%), Postives = 112/192 (58.33%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKR---EDLVINKAMRNNSSDQIYIFFPEE 60
           +QML+DRGY + + D+++ R +F  ++   M +   E L ++     N +D+IY+F+PE 
Sbjct: 19  LQMLRDRGYTIEESDLNLKREEFVQRFCKTMNKVNKEALFVSANKGPNPADKIYVFYPEG 78

Query: 61  PKVGVKTMKTYTN-RMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVN 120
           PKVGV  +K     +M+ + V R I+VV   +T  AR  +SE++    +EVF+EAEL+ N
Sbjct: 79  PKVGVPVIKKEVAIKMRDDKVHRGIVVVPMAITAPARMAVSELNKMLTIEVFEEAELVTN 138

Query: 121 VKDHVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSE 172
           + +H L+ ++ +L ++ KK LL  YTV++TQ                 RGQV+KI R   
Sbjct: 139 ITEHKLVNKYYVLDDQAKKKLLNTYTVQDTQLPRILVTDPLARYYGLKRGQVVKIRRSDA 198

[Close]

BLAST of CmaCh18G005560 vs. TAIR10
Match: AT2G41340.1 (AT2G41340.1 RNA polymerase II fifth largest subunit, D)

HSP 1 Score: 96.3 bits (238), Expect = 2.0e-20
Identity = 67/188 (35.64%), Postives = 106/188 (56.38%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           M+ML+DRGY V D DI++S  QFR  YG++   + L I+   R +SS +I + F     V
Sbjct: 32  MEMLRDRGYDVSDEDINLSLQQFRALYGEHPDVDLLRISAKHRFDSSKKISVVFCGTGIV 91

Query: 61  GVKTMKTYTNRMKS-ENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKD 120
            V  M+     + S EN+   ILV+Q ++T  A   +   S  F +E+F+  +L+VNV  
Sbjct: 92  KVNAMRVIAADVLSRENITGLILVLQSHITNQALKAVELFS--FKVELFEITDLLVNVSK 151

Query: 121 HVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAG 171
           HVL P+HQ+L ++EK++LL++++++E Q                  GQV+K+    E + 
Sbjct: 152 HVLRPKHQVLNDKEKESLLKKFSIEEKQLPRLSSKDPIVRYYGLETGQVMKVTYKDELSE 211

[Close]

BLAST of CmaCh18G005560 vs. TAIR10
Match: AT3G57080.1 (AT3G57080.1 Eukaryotic rpb5 RNA polymerase subunit family protein)

HSP 1 Score: 91.7 bits (226), Expect = 4.8e-19
Identity = 62/188 (32.98%), Postives = 103/188 (54.79%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           +QML+DRGY V D DI++S + FR  YG+    + L I+   R++S+ ++ I F     V
Sbjct: 36  LQMLRDRGYEVSDEDINLSLHDFRTVYGERPDVDRLRISALHRSDSTKKVKIVFFGTSMV 95

Query: 61  GVKTMKTYT-NRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKD 120
            V  +++   + +  E +   ILV+Q ++T  A   I   S  F +E+FQ  +L+VN+  
Sbjct: 96  KVNAIRSVVADILSQETITGLILVLQNHVTNQALKAIELFS--FKVEIFQITDLLVNITK 155

Query: 121 HVLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAG 171
           H L P+HQ+L +EEK TLL++++++E Q                 +GQV+K+    E   
Sbjct: 156 HSLKPQHQVLNDEEKTTLLKKFSIEEKQLPRISKKDAIVRYYGLEKGQVVKVNYRGELTE 215

[Close]

BLAST of CmaCh18G005560 vs. TAIR10
Match: AT3G16680.1 (AT3G16680.1 DNA binding;DNA-directed RNA polymerases)

HSP 1 Score: 81.3 bits (199), Expect = 6.5e-16
Identity = 44/79 (55.70%), Postives = 58/79 (73.42%), Query Frame = 1


Query: 65  MKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSK---FHLEVFQEAELMVNVKDHV 124
           MK Y +++KS NVFRAILVVQ ++  F+R  +  + +    FH+EVFQE EL+VNVK+HV
Sbjct: 1   MKKYIDQLKSANVFRAILVVQ-DIKAFSRQALVFLGAVYPIFHIEVFQEKELIVNVKEHV 60

Query: 125 LIPEHQLLTNEEKKTLLER 141
            +PEHQ LT EEK+  LER
Sbjct: 61  FVPEHQALTTEEKQKFLER 78

[Close]

BLAST of CmaCh18G005560 vs. NCBI nr
Match: gi|566176743|ref|XP_006381734.1| (DNA-directed RNA polymerase family protein [Populus trichocarpa])

HSP 1 Score: 289.7 bits (740), Expect = 3.4e-75
Identity = 147/188 (78.19%), Postives = 164/188 (87.23%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I M+R QF +KYG+NMKREDLVINK  RN+SSDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEIKMTREQFESKYGNNMKREDLVINKTKRNDSSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EIS+KFHLEVFQEAEL+VN+K+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTKFHLEVFQEAELLVNIKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+L+NEEKKTLLERYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 VLVPEHQVLSNEEKKTLLERYTVKETQLPRIQITDPIARYYGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. NCBI nr
Match: gi|743939608|ref|XP_011014255.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A [Populus euphratica])

HSP 1 Score: 289.7 bits (740), Expect = 3.4e-75
Identity = 147/188 (78.19%), Postives = 164/188 (87.23%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I M+R QF +KYG+NMKREDLVINK  RN+SSDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEIKMTREQFESKYGNNMKREDLVINKTKRNDSSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EIS+KFHLEVFQEAEL+VN+K+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTKFHLEVFQEAELLVNIKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+L+NEEKKTLLERYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 VLVPEHQVLSNEEKKTLLERYTVKETQLPRIQITDPIARYYGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. NCBI nr
Match: gi|763759822|gb|KJB27153.1| (hypothetical protein B456_004G280900 [Gossypium raimondii])

HSP 1 Score: 288.9 bits (738), Expect = 5.9e-75
Identity = 146/183 (79.78%), Postives = 163/183 (89.07%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I++S+ QF +KYG+NMKREDLVINK  RN++SDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEINLSKQQFISKYGENMKREDLVINKTKRNDNSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EISSKFHLEVFQEAEL+VNVK+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISSKFHLEVFQEAELLVNVKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ------------RGQVLKIIRPSETAGRYVTYR 172
            L+PEHQ+LTNEEKKTLL RYTVKETQ            RGQV+KIIRPSETAGRY+TYR
Sbjct: 139 ALVPEHQVLTNEEKKTLLHRYTVKETQVSDPIARYFGLKRGQVVKIIRPSETAGRYITYR 198

[Close]

BLAST of CmaCh18G005560 vs. NCBI nr
Match: gi|567918418|ref|XP_006451215.1| (hypothetical protein CICLE_v10009504mg [Citrus clementina])

HSP 1 Score: 287.3 bits (734), Expect = 1.7e-74
Identity = 146/188 (77.66%), Postives = 165/188 (87.77%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQML+DRGY+VGD +I+MS+ QF  K+G+NMKREDLVINKA+RN+SSDQIY+FFP+E KV
Sbjct: 19  MQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS+KFHLEVFQEAEL+VN+K+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
           VL+PEHQ+LTNEEKKTLL+RYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 VLVPEHQVLTNEEKKTLLKRYTVKETQLPRIQVTDPIARYYGLKRGQVVKIIRPSETAGR 198

[Close]

BLAST of CmaCh18G005560 vs. NCBI nr
Match: gi|823154629|ref|XP_012477196.1| (PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A [Gossypium raimondii])

HSP 1 Score: 287.0 bits (733), Expect = 2.2e-74
Identity = 146/188 (77.66%), Postives = 163/188 (86.70%), Query Frame = 1


Query: 1   MQMLKDRGYYVGDLDIDMSRNQFRNKYGDNMKREDLVINKAMRNNSSDQIYIFFPEEPKV 60
           MQMLKDRGY+VGD +I++S+ QF +KYG+NMKREDLVINK  RN++SDQIY+FFPEE KV
Sbjct: 19  MQMLKDRGYFVGDFEINLSKQQFISKYGENMKREDLVINKTKRNDNSDQIYVFFPEEAKV 78

Query: 61  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAELMVNVKDH 120
           GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI+EISSKFHLEVFQEAEL+VNVK+H
Sbjct: 79  GVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISSKFHLEVFQEAELLVNVKEH 138

Query: 121 VLIPEHQLLTNEEKKTLLERYTVKETQ-----------------RGQVLKIIRPSETAGR 172
            L+PEHQ+LTNEEKKTLL RYTVKETQ                 RGQV+KIIRPSETAGR
Sbjct: 139 ALVPEHQVLTNEEKKTLLHRYTVKETQLPRIQVSDPIARYFGLKRGQVVKIIRPSETAGR 198

The following BLAST results are available for this feature:

BLAST of CmaCh18G005560 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RPB5A_ARATH	1.2e-72	74.47	DNA-directed RNA polymerases II and IV subunit 5A OS=Arabidopsis thaliana GN=NRP...	[more]
RPAB1_PONAB	1.4e-39	44.27	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=PO...	[more]
RPAB1_RAT	2.3e-39	43.75	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus ...	[more]
RPAB1_MOUSE	2.3e-39	43.75	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus GN=Po...	[more]
RPAB1_CAEEL	8.8e-39	45.08	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis ele...	[more]

BLAST of CmaCh18G005560 vs. TrEMBL


Match Name	E-value	Identity	Description
B9N7D1_POPTR	2.4e-75	78.19	DNA-directed RNA polymerase family protein OS=Populus trichocarpa GN=POPTR_0006s...	[more]
A0A0D2PJI1_GOSRA	4.1e-75	79.78	Uncharacterized protein OS=Gossypium raimondii GN=B456_004G280900 PE=4 SV=1	[more]
V4UJN2_9ROSI	1.2e-74	77.66	Uncharacterized protein OS=Citrus clementina GN=CICLE_v10009504mg PE=3 SV=1	[more]
A0A0B0NU90_GOSAR	1.6e-74	77.66	Dna-directed rna polymerases i, ii, and iii subunit rpabc1 OS=Gossypium arboreum...	[more]
A0A0D2S793_GOSRA	1.6e-74	77.66	Uncharacterized protein OS=Gossypium raimondii GN=B456_004G280900 PE=3 SV=1	[more]

BLAST of CmaCh18G005560 vs. TAIR10


Match Name	E-value	Identity	Description
AT3G22320.1	6.9e-74	74.47	Eukaryotic rpb5 RNA polymerase subunit family protein	[more]
AT5G57980.1	2.2e-27	36.46	RNA polymerase II fifth largest subunit, C	[more]
AT2G41340.1	2.0e-20	35.64	RNA polymerase II fifth largest subunit, D	[more]
AT3G57080.1	4.8e-19	32.98	Eukaryotic rpb5 RNA polymerase subunit family protein	[more]
AT3G16680.1	6.5e-16	55.70	DNA binding;DNA-directed RNA polymerases	[more]

BLAST of CmaCh18G005560 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|566176743\|ref\|XP_006381734.1\|	3.4e-75	78.19	DNA-directed RNA polymerase family protein [Populus trichocarpa]	[more]
gi\|743939608\|ref\|XP_011014255.1\|	3.4e-75	78.19	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A [Populus euphratica...	[more]
gi\|763759822\|gb\|KJB27153.1\|	5.9e-75	79.78	hypothetical protein B456_004G280900 [Gossypium raimondii]	[more]
gi\|567918418\|ref\|XP_006451215.1\|	1.7e-74	77.66	hypothetical protein CICLE_v10009504mg [Citrus clementina]	[more]
gi\|823154629\|ref\|XP_012477196.1\|	2.2e-74	77.66	PREDICTED: DNA-directed RNA polymerases II and IV subunit 5A [Gossypium raimondi...	[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
IPR014381	DNA_RNA_pol_RPB5_euk/virus

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:0051604	protein maturation
biological_process	GO:0006626	protein targeting to mitochondrion
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:0005665	DNA-directed RNA polymerase II, core complex
cellular_component	GO:0000418	DNA-directed RNA polymerase IV complex
cellular_component	GO:0005730	nucleolus
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
CmaCh18G005560.1	CmaCh18G005560.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Cucurbita maxima
Date Performed: 2017-05-20


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	PRODOM	PD005155		coord: 122..170 score: 1.
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	GENE3D	G3DSA:3.90.940.20		coord: 116..146 score: 4.0E-9coord: 147..171 score: 1.
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	PFAM	PF01191	RNA_pol_Rpb5_C	coord: 115..147 score: 3.3E-8coord: 146..170 score: 6.
IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	unknown	SSF55287	RPB5-like RNA polymerase subunit	coord: 113..171 score: 1.14
IPR005571	RNA polymerase, Rpb5, N-terminal	GENE3D	G3DSA:3.40.1340.10		coord: 1..115 score: 1.8
IPR005571	RNA polymerase, Rpb5, N-terminal	PFAM	PF03871	RNA_pol_Rpb5_N	coord: 1..72 score: 4.5
IPR005571	RNA polymerase, Rpb5, N-terminal	unknown	SSF53036	Eukaryotic RPB5 N-terminal domain	coord: 1..116 score: 2.35
IPR014381	DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus	PIR	PIRSF000747	RPB5	coord: 1..147 score: 5.0
None	No IPR available	PANTHER	PTHR10535	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	coord: 1..171 score: 2.5

Synteny

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


Gene	Orthologue	Organism	Block
CmaCh18G005560	Cucsa.003940	Cucumber (Gy14) v1	cgycmaB0058
CmaCh18G005560	Csa1G702030	Cucumber (Chinese Long) v2	cmacuB400
CmaCh18G005560	MELO3C021758	Melon (DHL92) v3.5.1	cmameB364
CmaCh18G005560	CSPI01G34500	Wild cucumber (PI 183967)	cmacpiB404
CmaCh18G005560	Lsi02G010460	Bottle gourd (USVL1VR-Ls)	cmalsiB369
CmaCh18G005560	Cp4.1LG09g06850	Cucurbita pepo (Zucchini)	cmacpeB415
CmaCh18G005560	MELO3C021758.2	Melon (DHL92) v3.6.1	cmamedB423
CmaCh18G005560	CsaV3_1G046360	Cucumber (Chinese Long) v3	cmacucB0477
CmaCh18G005560	Cla97C01G009620	Watermelon (97103) v2	cmawmbB394
CmaCh18G005560	Bhi08G000738	Wax gourd	cmawgoB0532
CmaCh18G005560	CsGy1G032960	Cucumber (Gy14) v2	cgybcmaB096
CmaCh18G005560	Carg27042	Silver-seed gourd	carcmaB1314

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh18G005560	Cucurbita maxima (Rimu)	cmacmaB216
CmaCh18G005560	Cucurbita moschata (Rifu)	cmacmoB398
CmaCh18G005560	Cucurbita moschata (Rifu)	cmacmoB407
CmaCh18G005560	Watermelon (Charleston Gray)	cmawcgB342
CmaCh18G005560	Watermelon (97103) v1	cmawmB380
CmaCh18G005560	Watermelon (97103) v1	cmawmB385
CmaCh18G005560	Cucurbita pepo (Zucchini)	cmacpeB438