Clc11G06040 (gene) Watermelon (cordophanus) v2

Overview
NameClc11G06040
Typegene
OrganismCitrullus lanatus subsp. cordophanus cv. cordophanus (Watermelon (cordophanus) v2)
DescriptionDNA-directed RNA polymerase II subunit 4
LocationClcChr11: 5912950 .. 5916332 (+)
RNA-Seq ExpressionClc11G06040
SyntenyClc11G06040
Sequences
The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonfive_prime_UTRCDSpolypeptidethree_prime_UTR
Hold the cursor over a type above to highlight its positions in the sequence below.
AATCCTTCTAAAGTAAAAATAGATTTTTTATATAAAAAAAAATTGCACAAATCAATTAAAAAATCTACAGATACATACTTCAACCCACCACTTCAAACAATATTTGATTTTTCTTTTCTCCCTTTCCCCTTCTCCACCACTTCCATTATCGGCCGCCCCTACGCCCCCGCAGTCAATTTTCTTTGTTTCTCCCTGGTCGCCAGCTCGCTGCTACGCTAACCTGCAAAACTCCATCTCTAGGTCTGTCGAAGTTTTTTCTTCCCCTCGTTCTTCTTTATTTACAATTTGATTGTGAATAGAACGATTATTACTTTCTTTAAATGCGTATATTCCTCCAACTCAAGAGGTCTTTTACTCTAGATCACAGGGTCGAATTCGAATCTTCAACCCTTGTCTTTGGTATCTTTTGCAAAATTTATTCTAATTTTTTCATCATATGTTTCACAATTTTCTTGAACTTATTGTAAAATTTAGTGCTAAGCCATTTAGTTAGGGCTCAAAGGCCACTCTCCGTTCCAAAACCTAAAGATTTTATTTTATTTTAAAGCTCATGATTATTCGGCTAATGTAAAATTGATTTGGGCTTCATTAAAATATGAGATCCATCCATCATTTATTTAAAAAAAAATTAAAGATTAACCATGAACAAGTTGAATCGAGTTTCCGTGTCTAGGCTTGCAAAGTATATTAGTAAGTTACTAGCTCATTAATGGAAAACAATGATTAATACTATGAAACATGAGAGTGCCTCCATGTATTTAATGAGTTACATCATGAGGACAATTTCTTAATGTTATAGATTAAAACCATTAAAAGTGAATTGGAGAATCTTTTCTGTCATACTATTCAGATTCTTCTTTTCATCGATTTTAATTTGTATCTATAATTAGTTTTTAACTTGGGCCTCCGAGTTCCGATGCCTTGTAATTTTGTAGGACATAGTTGGGCGAATGTAACTTTTTACTTTGTAGATTTAGTTGTAATCTTTGCTGTACTCTGTTTCCAAATTCTGTAGGTTGATACAAAACTCCAACTTCAAGCATGTCTGGGGAGGAGGAAGAAAATGCTGCTGAGCTTAAAATTGGAGATGGTACAACTATCTATAAATTTATGATTTTTCATCTATATTCAGTGAGATACTAAGTTGCTCGTACTTTTATGGTGATGGGGCTCCTTCATGTATTTGTAAAATTAGAATTTTCTAATCAACTGATGTATTTAATCTTTTATTTTGCTCAAAAAGTTGGAAACTTAATTTATTATGTTATTCCCCATGTCTTATTATATGTATCATCATTACAAATTCTTTGAACCTTCTAGTAGCCAATAGGGAGACTGTTCTTATGTTTTTAACAACGTGTATAGATATAGTTTAGACTGGGGCTTAGACTGGGAATGTGGAGTTAATGTACTAATTTATCTTCCAGCAGTTTTGTAGGTATCGCGGTAATGATCTCTAAGTCCTGAGCGGAGAAAGATACTAAGCTTCCTTGGTTCTTTAAGACCATTCGTTTATGTGATTATATCTTGTAGTCATGTAGTATCTCATAACTTCCTCAGATATTATTGAGTAATTCATAGGCATTATGTAGTGCCTTGTAGGTGGCTGGACACGTTTATCAAAAGACGTTTCTTTTGTATACACCTTCCCATTGTTTTTTATGAAATTGTGTTATTATTTTTCATAATGCGTTCTCGATATTTTGAGCTAGCTCATTTACTACATCAAAGGAATACCTTAATATGTTGTTAAAGGCTCAAAGGACTGGATACTTTGAGTTTTCTTATATGTTTAGGTTTTTCAAATTCTAGATGAAGATGTGTTGTCTATGCAAAATCTGAACTTTTATCTATAATTATTTTGGCGAAAAGATATTCAACTATGGTAAGTTTTTCCATTTTTTATGAATATATGATAATGCAAACTCTAGAACAGCGGAATCTTTGGTTTACATAGATATGTAATTGTTCAAGATTCAAGATCTTGACCCAAACTATTTTGGTGTATATTCTAAGCTGACATTTACTTTGTTTGGTTACTTGCAGAGTTCTTAAAGGCCAAATGTTTAATGAATTGTGAAGTTTCTCTGATTCTTGAACATAAATACGAGCAACTTCAACAAATGTCTGAGGATCCAACGAATCAAGTTTCCCAGTTAGTCTTATGTATATTCATTATCGATTCATGAGTTAATTTAGAGTTTCTCTTGGTTGGTGAGAAAAATATGTAGCTAAATTACGATATTCATTTTATCTTGACATAGAATGACGAGAGATTTTTAATTACAGTCTTATTATGTAGGGTGTTTGAAAAGTCACTACAATATGTGAAACGCTTCAGCCGTTATAAGAACCCTGATGCTGTAAGACAAGTTCGAGAGTATCCTTAAAACTATATACGTTGATGTTTTTCATTTTATGGAATGGTGGGAGAAAAGGCGCCTTTCATTTTTTTGGTTAGTCAAGAACTCTTAGGTTAACTGTTGGGAAATACTTGTTTTGATAGATCGAATCTTAACTGATATACAGAATCCTAAGCAGGTATCAGTTGGCTGAGTTTGAGGTATGTACTAAGCACTTGGTTTAATCAATTTATGTATCATTATTATCTCTTTTTTTTGTGGTGGGGGGGGGGGGGGGGGGGGTGTGAAGATTTATCTCATTAGTCTTGAAATTTGCAGCTTTGTGTTCTTGGCAACCTTTGCCCAGAAACTGTAGAGGAAGCCATTGCTATGGTACCGTCCTTGAAGGTATTTTTTTGTCATTTGCTTGTGACCGATAGTGTAATATTGGTATTTTGTGGAAGTTCGAGTATTTGTCTTTCAACTTTGCATGAACATTCAAGAGATTTTAAAATAGTACTAATAACTTTAAAACTAAGATATAATTCTTTTTCCTTTTCCATTTTTGAAATTGGAGAAAAATTTCAAAAAAAAATTTGTAAACAAAATCTAATTGCTTGGATCATGAATGTTTTTTTTTGGTTGCAGACTAAGGGAAGGGTGCATGACGATGAAGCTATCGAGAAGATGCTGAACGATCTTTCATTAATCAAAAGATTTGAGTAGTTGTCTTCTATATCTTGGATTAAATGTGAATCTATTTCCGAGGCAAAATTGTACCTTATATAGTATAGGATTATGATTTTATGGGTAAGTTTGTAATTGGGATACTCCGCAGTCGGTTACTTGATGTTTCCTTTTGTCTTGGTGGTAGAATGTACTTAATTCTAGATGTGTTATCATGATAAAGTCGAGGTTTTATTTTTATCTTTTTAAAATTATTTATGAGGATTTACTTAATATTTGTTTTCGCCCGAGTTATAAAAGAACTAGATTTTTGTTAAAAGTATATATATACAAAAAATACTCATAAGATTGTGG

mRNA sequence

AATCCTTCTAAAGTAAAAATAGATTTTTTATATAAAAAAAAATTGCACAAATCAATTAAAAAATCTACAGATACATACTTCAACCCACCACTTCAAACAATATTTGATTTTTCTTTTCTCCCTTTCCCCTTCTCCACCACTTCCATTATCGGCCGCCCCTACGCCCCCGCAGTCAATTTTCTTTGTTTCTCCCTGGTCGCCAGCTCGCTGCTACGCTAACCTGCAAAACTCCATCTCTAGGTTGATACAAAACTCCAACTTCAAGCATGTCTGGGGAGGAGGAAGAAAATGCTGCTGAGCTTAAAATTGGAGATGAGTTCTTAAAGGCCAAATGTTTAATGAATTGTGAAGTTTCTCTGATTCTTGAACATAAATACGAGCAACTTCAACAAATGTCTGAGGATCCAACGAATCAAGTTTCCCAGGTGTTTGAAAAGTCACTACAATATGTGAAACGCTTCAGCCGTTATAAGAACCCTGATGCTGTAAGACAAGTTCGAGAAATCCTAAGCAGGTATCAGTTGGCTGAGTTTGAGCTTTGTGTTCTTGGCAACCTTTGCCCAGAAACTGTAGAGGAAGCCATTGCTATGGTACCGTCCTTGAAGACTAAGGGAAGGGTGCATGACGATGAAGCTATCGAGAAGATGCTGAACGATCTTTCATTAATCAAAAGATTTGAGTAGTTGTCTTCTATATCTTGGATTAAATGTGAATCTATTTCCGAGGCAAAATTGTACCTTATATAGTATAGGATTATGATTTTATGGGTAAGTTTGTAATTGGGATACTCCGCAGTCGGTTACTTGATGTTTCCTTTTGTCTTGGTGGTAGAATGTACTTAATTCTAGATGTGTTATCATGATAAAGTCGAGGTTTTATTTTTATCTTTTTAAAATTATTTATGAGGATTTACTTAATATTTGTTTTCGCCCGAGTTATAAAAGAACTAGATTTTTGTTAAAAGTATATATATACAAAAAATACTCATAAGATTGTGG

Coding sequence (CDS)

ATGTCTGGGGAGGAGGAAGAAAATGCTGCTGAGCTTAAAATTGGAGATGAGTTCTTAAAGGCCAAATGTTTAATGAATTGTGAAGTTTCTCTGATTCTTGAACATAAATACGAGCAACTTCAACAAATGTCTGAGGATCCAACGAATCAAGTTTCCCAGGTGTTTGAAAAGTCACTACAATATGTGAAACGCTTCAGCCGTTATAAGAACCCTGATGCTGTAAGACAAGTTCGAGAAATCCTAAGCAGGTATCAGTTGGCTGAGTTTGAGCTTTGTGTTCTTGGCAACCTTTGCCCAGAAACTGTAGAGGAAGCCATTGCTATGGTACCGTCCTTGAAGACTAAGGGAAGGGTGCATGACGATGAAGCTATCGAGAAGATGCTGAACGATCTTTCATTAATCAAAAGATTTGAGTAG

Protein sequence

MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Homology
[Close]
BLAST of Clc11G06040 vs. NCBI nr
Match: XP_038884885.1 (DNA-directed RNA polymerase II subunit 4 [Benincasa hispida])

HSP 1 Score: 271.2 bits (692), Expect = 5.0e-69
Identity = 138/138 (100.00%), Postives = 138/138 (100.00%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIKRFE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

[Close]
BLAST of Clc11G06040 vs. NCBI nr
Match: XP_004138390.1 (DNA-directed RNA polymerase II subunit 4 [Cucumis sativus] >XP_008456795.1 PREDICTED: DNA-directed RNA polymerase II subunit 4 [Cucumis melo] >XP_011656444.1 DNA-directed RNA polymerase II subunit 4 [Cucumis sativus] >KAA0051957.1 DNA-directed RNA polymerase II subunit 4 [Cucumis melo var. makuwa] >KGN45845.1 hypothetical protein Csa_005663 [Cucumis sativus] >TYK04594.1 DNA-directed RNA polymerase II subunit 4 [Cucumis melo var. makuwa])

HSP 1 Score: 270.8 bits (691), Expect = 6.6e-69
Identity = 137/138 (99.28%), Postives = 138/138 (100.00%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIKRFE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

[Close]
BLAST of Clc11G06040 vs. NCBI nr
Match: XP_022939401.1 (DNA-directed RNA polymerase II subunit 4-like [Cucurbita moschata] >XP_022939402.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita moschata] >XP_022993195.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita maxima] >XP_022993196.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita maxima] >XP_023549816.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita pepo subsp. pepo] >XP_023549818.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita pepo subsp. pepo] >KAG6578503.1 DNA-directed RNA polymerase II subunit 4, partial [Cucurbita argyrosperma subsp. sororia] >KAG7016067.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 267.3 bits (682), Expect = 7.3e-68
Identity = 135/138 (97.83%), Postives = 137/138 (99.28%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]
BLAST of Clc11G06040 vs. NCBI nr
Match: XP_022133507.1 (DNA-directed RNA polymerase II subunit 4 [Momordica charantia])

HSP 1 Score: 266.2 bits (679), Expect = 1.6e-67
Identity = 135/138 (97.83%), Postives = 136/138 (98.55%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]
BLAST of Clc11G06040 vs. NCBI nr
Match: XP_022954766.1 (DNA-directed RNA polymerase II subunit 4 [Cucurbita moschata] >XP_022954773.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita moschata] >XP_022954778.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita moschata] >XP_022990067.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita maxima] >XP_022990068.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita maxima] >XP_022990070.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita maxima] >XP_023536652.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 265.8 bits (678), Expect = 2.1e-67
Identity = 135/138 (97.83%), Postives = 136/138 (98.55%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLK KGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKAKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match: O48890 (DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana OX=3702 GN=NRPB4 PE=1 SV=1)

HSP 1 Score: 260.0 bits (663), Expect = 1.5e-68
Identity = 130/138 (94.20%), Postives = 135/138 (97.83%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ+SEDP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKFEQLQQISEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA+AMVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSL+KRFE
Sbjct: 121 DEAIEKMLNDLSLVKRFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match: O15514 (DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens OX=9606 GN=POLR2D PE=1 SV=1)

HSP 1 Score: 103.2 bits (256), Expect = 2.4e-21
Identity = 56/137 (40.88%), Postives = 93/137 (67.88%), Query Frame = 0 

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q +  S +   ++S+VF K+L Y
Sbjct: 10  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNY 69

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PSL  +GR  D+
Sbjct: 70  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSL--EGRFEDE 129

Query: 122 EAIEKMLNDLSLIKRFE 139
           E ++++L+D+   + F+
Sbjct: 130 E-LQQILDDIQTKRSFQ 141

[Close]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match: Q9D7M8 (DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus OX=10090 GN=Polr2d PE=1 SV=2)

HSP 1 Score: 103.2 bits (256), Expect = 2.4e-21
Identity = 56/137 (40.88%), Postives = 93/137 (67.88%), Query Frame = 0 

Query: 2   SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQY 61
           +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q +  S +   ++S+VF K+L Y
Sbjct: 10  AGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNY 69

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ A++PSL  +GR  D+
Sbjct: 70  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSL--EGRFEDE 129

Query: 122 EAIEKMLNDLSLIKRFE 139
           E ++++L+D+   + F+
Sbjct: 130 E-LQQILDDIQTKRSFQ 141

[Close]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match: Q54S04 (DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum OX=44689 GN=polr2d PE=3 SV=1)

HSP 1 Score: 93.2 bits (230), Expect = 2.5e-18
Identity = 55/147 (37.41%), Postives = 90/147 (61.22%), Query Frame = 0 

Query: 4   EEEENAAELKIGDEFLKAKCLMNCEVSLILEHK----------YEQ---LQQMSEDPTNQ 63
           +EEE+   LK   +   AK L+N EV+++LEH+          + Q   L  +  +  N 
Sbjct: 12  QEEEDLTTLKFPRDLKDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLYYNSIND 71

Query: 64  VSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVP 123
           + + F K+L Y ++FSRYKN  +++QVR  LS+  L EFE+  L NLCPE  +EA +++P
Sbjct: 72  IIRTFHKTLAYAEKFSRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIP 131

Query: 124 SLKTKGRVHDDEAIEKMLNDLSLIKRF 138
           SLK   ++ DDE ++ +L++LS +++F
Sbjct: 132 SLK---KMEDDE-LQAILDELSNLRKF 154

[Close]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match: Q9VEA5 (DNA-directed RNA polymerase II subunit Rpb4 OS=Drosophila melanogaster OX=7227 GN=Rpb4 PE=2 SV=5)

HSP 1 Score: 88.2 bits (217), Expect = 7.9e-17
Identity = 49/126 (38.89%), Postives = 80/126 (63.49%), Query Frame = 0 

Query: 6   EENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRF 65
           +E+AA+L+   EF  A+ L+  EV ++L+H+  + Q  S D   + S+VF K+  Y   F
Sbjct: 11  DEDAADLQFPKEFENAETLLISEVHMLLDHR--KRQNESADEEQEFSEVFMKTYAYTDSF 70

Query: 66  SRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIE 125
            ++KN + +   R +L + +L +FEL  LGNLCPE  EEA A++PSL  +GR  D+E + 
Sbjct: 71  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSL--EGRFEDEE-LR 130

Query: 126 KMLNDL 132
           ++L+D+
Sbjct: 131 QILDDI 131

[Close]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match: A0A5D3C019 (DNA-directed RNA polymerase II subunit 4 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold409G002310 PE=4 SV=1)

HSP 1 Score: 270.8 bits (691), Expect = 3.2e-69
Identity = 137/138 (99.28%), Postives = 138/138 (100.00%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIKRFE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match: A0A0A0K7V5 (RPOL4c domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_6G014650 PE=4 SV=1)

HSP 1 Score: 270.8 bits (691), Expect = 3.2e-69
Identity = 137/138 (99.28%), Postives = 138/138 (100.00%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIKRFE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match: A0A1S3C4R9 (DNA-directed RNA polymerase II subunit 4 OS=Cucumis melo OX=3656 GN=LOC103496636 PE=4 SV=1)

HSP 1 Score: 270.8 bits (691), Expect = 3.2e-69
Identity = 137/138 (99.28%), Postives = 138/138 (100.00%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIKRFE
Sbjct: 121 DEAIEKMLNDLSLIKRFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match: A0A6J1JVN3 (DNA-directed RNA polymerase II subunit 4-like OS=Cucurbita maxima OX=3661 GN=LOC111489290 PE=4 SV=1)

HSP 1 Score: 267.3 bits (682), Expect = 3.5e-68
Identity = 135/138 (97.83%), Postives = 137/138 (99.28%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match: A0A6J1FFS7 (DNA-directed RNA polymerase II subunit 4-like OS=Cucurbita moschata OX=3662 GN=LOC111445330 PE=4 SV=1)

HSP 1 Score: 267.3 bits (682), Expect = 3.5e-68
Identity = 135/138 (97.83%), Postives = 137/138 (99.28%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSLIK+FE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]
BLAST of Clc11G06040 vs. TAIR 10
Match: AT5G09920.1 (RNA polymerase II, Rpb4, core protein )

HSP 1 Score: 260.0 bits (663), Expect = 1.1e-69
Identity = 130/138 (94.20%), Postives = 135/138 (97.83%), Query Frame = 0 

Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ+SEDP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKFEQLQQISEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120
           YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA+AMVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKRFE 139
           DEAIEKMLNDLSL+KRFE
Sbjct: 121 DEAIEKMLNDLSLVKRFE 138

[Close]
BLAST of Clc11G06040 vs. TAIR 10
Match: AT4G15950.1 (RNA polymerase II, Rpb4, core protein )

HSP 1 Score: 85.9 bits (211), Expect = 2.8e-17
Identity = 45/118 (38.14%), Postives = 76/118 (64.41%), Query Frame = 0 

Query: 21  AKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREI 80
           A+C+M+CE   IL+    QL  +SEDP+ ++   ++++L YV+    Y NP +VR+V E 
Sbjct: 89  AECMMDCEAFQILDGIKGQLVGLSEDPSIKIPVSYDRALAYVESCVHYTNPQSVRKVLEP 148

Query: 81  LSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE 139
           L  Y +++ E+CV+ N   E+V+E +A +PSLKTK  V  ++ ++  L +LS +K+ E
Sbjct: 149 LKTYGISDGEMCVIANASSESVDEVLAFIPSLKTKKEV-INQPLQDALEELSKLKKSE 205

The following BLAST results are available for this feature:
BLAST of Clc11G06040 vs. NCBI nr
Match NameE-valueIdentityDescription
XP_038884885.15.0e-69100.00DNA-directed RNA polymerase II subunit 4 [Benincasa hispida][more]
XP_004138390.16.6e-6999.28DNA-directed RNA polymerase II subunit 4 [Cucumis sativus] >XP_008456795.1 PREDI... [more]
XP_022939401.17.3e-6897.83DNA-directed RNA polymerase II subunit 4-like [Cucurbita moschata] >XP_022939402... [more]
XP_022133507.11.6e-6797.83DNA-directed RNA polymerase II subunit 4 [Momordica charantia][more]
XP_022954766.12.1e-6797.83DNA-directed RNA polymerase II subunit 4 [Cucurbita moschata] >XP_022954773.1 DN... [more]
BLAST of Clc11G06040 vs. ExPASy Swiss-Prot
Match NameE-valueIdentityDescription
O488901.5e-6894.20DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana OX=3702 GN=NRPB... [more]
O155142.4e-2140.88DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens OX=9606 GN=POLR2D PE... [more]
Q9D7M82.4e-2140.88DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus OX=10090 GN=Polr2d P... [more]
Q54S042.5e-1837.41DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum OX=44689... [more]
Q9VEA57.9e-1738.89DNA-directed RNA polymerase II subunit Rpb4 OS=Drosophila melanogaster OX=7227 G... [more]
BLAST of Clc11G06040 vs. ExPASy TrEMBL
Match NameE-valueIdentityDescription
A0A5D3C0193.2e-6999.28DNA-directed RNA polymerase II subunit 4 OS=Cucumis melo var. makuwa OX=1194695 ... [more]
A0A0A0K7V53.2e-6999.28RPOL4c domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_6G014650 PE=4... [more]
A0A1S3C4R93.2e-6999.28DNA-directed RNA polymerase II subunit 4 OS=Cucumis melo OX=3656 GN=LOC103496636... [more]
A0A6J1JVN33.5e-6897.83DNA-directed RNA polymerase II subunit 4-like OS=Cucurbita maxima OX=3661 GN=LOC... [more]
A0A6J1FFS73.5e-6897.83DNA-directed RNA polymerase II subunit 4-like OS=Cucurbita moschata OX=3662 GN=L... [more]
BLAST of Clc11G06040 vs. TAIR 10
Match NameE-valueIdentityDescription
AT5G09920.11.1e-6994.20RNA polymerase II, Rpb4, core protein [more]
AT4G15950.12.8e-1738.14RNA polymerase II, Rpb4, core protein [more]
InterPro
Analysis Name: InterPro Annotations of Watermelon (cordophanus) v2
Date Performed: 2022-01-31
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006590RNA polymerase Rpb4/RPC9, coreSMARTSM00657rpol4neu2coord: 16..138
e-value: 4.9E-59
score: 212.1
IPR005574RNA polymerase subunit RPB4/RPC9PFAMPF03874RNA_pol_Rpb4coord: 23..132
e-value: 7.9E-24
score: 84.3
IPR038324Rpb4/RPC9 superfamilyGENE3D1.20.1250.40coord: 2..138
e-value: 1.2E-51
score: 176.0
NoneNo IPR availablePANTHERPTHR21297:SF3DNA-DIRECTED RNA POLYMERASE II SUBUNIT 4-LIKEcoord: 1..138
NoneNo IPR availablePANTHERPTHR21297DNA-DIRECTED RNA POLYMERASE IIcoord: 1..138
IPR010997HRDC-like superfamilySUPERFAMILY47819HRDC-likecoord: 3..135

Relationships

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

Feature NameUnique NameType
Clc11G06040.1Clc11G06040.1mRNA


GO Annotation
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0031990 mRNA export from nucleus in response to heat stress
biological_process GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
biological_process GO:0045948 positive regulation of translational initiation
biological_process GO:0034402 recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
biological_process GO:0006367 transcription initiation from RNA polymerase II promoter
biological_process GO:0044237 cellular metabolic process
biological_process GO:0006352 DNA-templated transcription, initiation
cellular_component GO:0000932 P-body
cellular_component GO:0005665 RNA polymerase II, core complex
cellular_component GO:0030880 RNA polymerase complex
molecular_function GO:0003899 DNA-directed 5'-3' RNA polymerase activity
molecular_function GO:0000166 nucleotide binding
molecular_function GO:0031369 translation initiation factor binding