Cp4.1LG13g07760.1 (mRNA) Cucurbita pepo (Zucchini) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cp4.1LG13g07760.1
Type	mRNA
Organism	Cucurbita pepo (Cucurbita pepo (Zucchini))
Description	DNA-directed RNA polymerase II subunit RPB4
Location	Cp4.1LG13 : 8369649 .. 8374140 (+)
Sequence length	2020

Genome Viewer

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: five_prime_UTRCDSthree_prime_UTR

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

CATATATTTTCCTCACAGTAATGGGCCTTCTCTGAGTAACGTCTGAGTTGAAAACGAAGAACCGCCCTCTCTGTTTTTGCCGTCACGTCTTGCCGCCGGATCTCGCCCCTAACCCTCTCTGTGTTTGTGGTGCGTCCTCTCTCAGGCCGTTCTCTATTTGAAATCTCATCTAGCTGATTATTAATACATGCATTTTTATAATTCCAGATGTTGGTAGAATTTGGTATTCATCTCCGATCTCGAAGATTACGAATCTGTTCTTCTTTGAAAGTTGAAAATTTTTGTTTTTCTGTTCTTTTTTCTAATCAGTGTGTTGGTGTTTAGGCATTTAGTTAGGGCTCAAATGCCCTTCTCTGTTCCCTAATGCTGCTGATTATTATGATTAATGGAAAGTTGATTTGCGCTTCATTTAAATCTGAAATCTATCTGTCATTTACCTCGAAAAGATTCAAGATTAACCTCGAAAAGATTCAAGATTAACCTCGAACAAGTTGGATGGAGCTTTTGCAATTTGAATTGAAGATTTTATGTTCCTAGGCTCGCAAAGTGTATTACTAACCTTTAAACTTTGTTTGATTGATGGGGAACGTTAATAGAATTGTGACCTATATGAGTGTTTTCATGGGGAATGGGAAACGTTAATGACTTTCATTACGAAAACAATTTCTATATGTTATAGACTAAATCCTTCAAAAGTAAATTGAAGAATCTTTAGTGCCATACCTTATTCAGAGTCTTCTTTCATAAGGTTATCAATTTTATATATCGTTAGTTGTTGACTCTGAATTTTCGGTTCTTTTACTATACTTCTGATGCCAGGCTATGTGGTAGGAAGTTTGCTGTGTGGAATGGAGATTTGATTTATTAGTCTAGTTTCGCGACGGGATTTTTTGTAATATCAATTTTGTAGTTTGATCTTGCTCTAATCATTTCCAGATTTTGTAGGTAGTCCAAAACTCCAACTTCAGGCATGTCTGGAGAGGAGGAAGAAAATGCTGCAGAGCTTAAAATTGGGGATGGTACCGATCTTTCTATAAATCTGTGATTTTCTATTAATATTCAATGAGATTTTAAGTCTCTTAAATGACTTTCAACGATGTTTTTCATTCATATATTTGAAAATTTTGAATCTGATGTGCAATTCATGTATTTAATCTTTTATTTTGCTTCAAAAGTGAGAAGCTTAATTTATTACGTTGTTCCCCATGCCTTATTATACGTACCCTTCACATTCTTTGAACCTTCTACTAGCCAATGTGGTGATTGTTCTTTTGTTTTTAACAGTGCGTATGGCTTGGACTGAATATGTGGATTGAATGTAAACACACTGATTAATCCTGAAAGTAGTTTCATGGGTAGAAATGTAAAGAAATTGCTTTTGTTTTTTGGTAAGAAACAGAGCGTTCACTGAGCAAAATAAAGTAATGTTCGAGCACTTACAAAAAAAAAAAAAAAAAGGCCTTCAAAAGGAGACATCAATTATAAGCAAAGAAATCACGAGCTCTTATATGGTTCTAAGGTTTCTGAAATTTTGGATGAAGATATTTGATCTATGCAAAATCTTAAATTTAATCTATAATCATTTTGTCATGAAGATAACTATTATAAGCTTTTCCATGATAATGTAAGGTGCTTTAGAATAGCCAAATCTTTGGTTTATATGGATAAGTAACTATTTGAAATTTAAGCTCTTGCCATCGAAATCGTTTTAGGGAATACTCTTAAGCTTTTTCATTCCCTTGTATTTATTTCGCTCTTTGTTATAAGGTGCATAAAAGGAAAATATAGAACGTGATAATTGACATTTACTTCCGTTGGCCGCCTGCAGAGTTCTTAAAAGCTAAGTGTTTAATGAATTGTGAAGTTTCTTTGATTCTTGAACACAAGTATGAGCAGCTTCAACAAATGTCTGAGGATCCAACCAATCAAGTTTCTCAGTGAGTTTTACGTTTATTCTTTATTGTTTCATAAGTTAATTTAGAGTTTCTCTTCCTTGCTGGAATAGCTGAAATATATAGCTAAATTATGATATCCATTCTAACGTTCCATACAACACGAGGGATTTTTAATTCTGGTCTTCTTCTGCAGAGTGTTTGAAAAGTCTCTGCAATATGTGAAACGGTTCAGCCGCTATAAGAACCCCGATGCTGTTAGACAAGTCCGAGAGTATCCTTTAAACTGTACATGTTAATATTTTACATTTTGTGGGATGGTGGGATGGTGGGAAGGATGGGTTGTGCATATCCACGATATGCTATAACTTACCCCATTTTGAACTAGGACTTTACAACTGCAATTCTCTTGCTAGACCAAGAACTCTCTGGTTAGCTGTTATTTAGGAAATAGTGAATAAATTAGCTAAAGTTCATTATATCTCAGCAGCTATACTATATTATAGGTTTCCTAGGTATCCATCTGAAACGATCCACTACTTTGATATTTCATTCATGACTGTAAGTTACAAACGAAAGTTTGGGTTCATCATTTAAAATCGCATCGAAGATGTTAAATCTTAACTACTACCATATAGAATTCTAAGCAGGTATCAGTTGGCTGAGTTTGAGGTATGTGTACATAATCACATGGTTTAATCAACTTGCTGATTGTTATTCTATGGGAAGGTTTATCTCATCGCTCTTGAAATTTGCAGCTCTGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAGGAAGCTATTTCCATGGTTCCATCTTTGAAGGTATCTCTTGCCACCCTTTTTAGGCCTTCATTAAATGGTTGTATATTTTTTGGTATTTTGCTAATCATAAATAGTTACCAACTTTTAGAAAGTTCCCGTTGGGTTTATCTTTCAACGACGAACATGCATCGAGTTTTACACGATCTCTAAAAGTTTTAAAACTGAAGATAGTAACTTTTTTAACAAAAAGTGAAAAAAAATTGTTTATAGATGGATCAGAGTCGCTTATAAATGCTTTTGTTGCAGACTAAAGGAAGAGCACATGACGATGAAGCAATCGAGAAGATGTTGAACGATCTTTCATTAATCAAAAAGTTCGAGTAGTTAGCTCTCTAAATCTGGTTAAATGTGTTAATCCATTCCTTGGCATTTCTCACCTAAAACAATAGAGAATTGTACCCTTCTAATCAGAGTCTAATAATAAGTTTTTAGGCATGTACCTAAACGTTCAATTTTATTGCTTATAGATCGCTAATACTCTGTTCGATGACTATGCTATTAGACACTTCTTGAAGTTAAGAGACCCGATAAACATATAACCAAAACTATGTGGATTAAACTTCTTTCCATCTCTCATCTCAATATTTNTTAAAAAAAAAAAAAAAAAAAAAAAAAAACCAAAGAAGTTATATAAAGTGGTACGGACATCAGAAGTATCAAGATTTCCTATCAAACCCTCAGTTGTTCATAATTAGACTGTTTTTTTTAGTACATAGATTTGATGCATGGAAGCTTACTACACAGACTGGATAGAACGACACACTCGACAAAAACCAGAACTAGTCGATGTCGTCTTGTCACATAATTTTATCTTAGGAAAGAAGATGATCATCTTAAGAATCTAACAACAGTTAACTATTTTGCTTAATCGTCAGGTTTCCATTGTACCAGAGCTAATGTATGGCGGCCGCCGCAGGCAACAAGTTTGGCAGTCCAACGACCATTCTCAGCCCCACGAGGAGGGGGAATGTCAATGGGAACTTCCTCTGGTTGCCCAGTTGTTACCTTCCTTCCATATCCAAGCCGCCCATGGTCACCTCGCCCGAACTGCCATACACATAAACAAAAATTTTGAATGAAAATTAGGACCTCCAACGGGTGTGGCGATGATCTAGAGTCTCAGCTTTCGTTCCAAATCATCACCACACCATAAAATAAGCTGAAAGTTGATGAATCAAGAAAACGTCCAAACTTAAATAATAAGACAGTAATATAATGATTCTTCATGAAACACATTAGAAAAACAAAAATCCAGAGCCGGTTTCATCATAGGATGATGTCTCAAACAAGGTTGTTGATCAAGACTAACCGAAAACATGCGGCCGTCACTTGTTACTGCAACTGAGTGTGTGCCTCCACATGATACCTGTGCCAACGAATGAGATAGTGGCATATTCAAAGGATTTCTACTTCTGTCAAATAATAACTGCAGCTCAAACTCTTATTCCTAATTCTCAGCATGGTCCTGAGATTAAATTCCAAAATAGAAACATAGCATTCAACTGCTATCTCAAATACTCCCTTTTTAATTAATAAGAAACTATTTGTTCGATGGGTTTATCTAAGATACCGTTATCCTTTTCGAACCAGAACTATATCAGCTTACCGATGAAGGATTACCTTATAGATGGTCGAAGACTCGAATGTATGAAATCAAACGGAAATGTTTGTTTTCCCATTCATGCATCAAACTAAATATCCTGTCATTACACCACTATACCCATACTTCCACTACAACTGTTGTAACAGTCCAAACCCATTGCTAGCAGATAT

mRNA sequence

CATATATTTTCCTCACAGTAATGGGCCTTCTCTGAGTAACGTCTGAGTTGAAAACGAAGAACCGCCCTCTCTGTTTTTGCCGTCACGTCTTGCCGCCGGATCTCGCCCCTAACCCTCTCTGTGTTTGTGGTAGTCCAAAACTCCAACTTCAGGCATGTCTGGAGAGGAGGAAGAAAATGCTGCAGAGCTTAAAATTGGGGATGAGTTCTTAAAAGCTAAGTGTTTAATGAATTGTGAAGTTTCTTTGATTCTTGAACACAAGTATGAGCAGCTTCAACAAATGTCTGAGGATCCAACCAATCAAGTTTCTCAAGTGTTTGAAAAGTCTCTGCAATATGTGAAACGGTTCAGCCGCTATAAGAACCCCGATGCTGTTAGACAAGTCCGAGAAATTCTAAGCAGGTATCAGTTGGCTGAGTTTGAGCTCTGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAGGAAGCTATTTCCATGGTTCCATCTTTGAAGACTAAAGGAAGAGCACATGACGATGAAGCAATCGAGAAGATGTTGAACGATCTTTCATTAATCAAAAAGTTCGAGTAGTTAGCTCTCTAAATCTGGTTAAATGTGTTAATCCATTCCTTGGCATTTCTCACCTAAAACAATAGAGAATTGTACCCTTCTAATCAGAGTCTAATAATAAGTTTTTAGGCATGTACCTAAACGTTCAATTTTATTGCTTATAGATCGCTAATACTCTGTTCGATGACTATGCTATTAGACACTTCTTGAAGTTAAGAGACCCGATAAACATATAACCAAAACTATGTGGATTAAACTTCTTTCCATCTCTCATCTCAATATTTNTTAAAAAAAAAAAAAAAAAAAAAAAAAAACCAAAGAAGTTATATAAAGTGGTACGGACATCAGAAGTATCAAGATTTCCTATCAAACCCTCAGTTGTTCATAATTAGACTGTTTTTTTTAGTACATAGATTTGATGCATGGAAGCTTACTACACAGACTGGATAGAACGACACACTCGACAAAAACCAGAACTAGTCGATGTCGTCTTGTCACATAATTTTATCTTAGGAAAGAAGATGATCATCTTAAGAATCTAACAACAGTTAACTATTTTGCTTAATCGTCAGGTTTCCATTGTACCAGAGCTAATGTATGGCGGCCGCCGCAGGCAACAAGTTTGGCAGTCCAACGACCATTCTCAGCCCCACGAGGAGGGGGAATGTCAATGGGAACTTCCTCTGGTTGCCCAGTTGTTACCTTCCTTCCATATCCAAGCCGCCCATGGTCACCTCGCCCGAACTGCCATACACATAAACAAAAATTTTGAATGAAAATTAGGACCTCCAACGGGTGTGGCGATGATCTAGAGTCTCAGCTTTCGTTCCAAATCATCACCACACCATAAAATAAGCTGAAAGTTGATGAATCAAGAAAACGTCCAAACTTAAATAATAAGACAGTAATATAATGATTCTTCATGAAACACATTAGAAAAACAAAAATCCAGAGCCGGTTTCATCATAGGATGATGTCTCAAACAAGGTTGTTGATCAAGACTAACCGAAAACATGCGGCCGTCACTTGTTACTGCAACTGAGTGTGTGCCTCCACATGATACCTGTGCCAACGAATGAGATAGTGGCATATTCAAAGGATTTCTACTTCTGTCAAATAATAACTGCAGCTCAAACTCTTATTCCTAATTCTCAGCATGGTCCTGAGATTAAATTCCAAAATAGAAACATAGCATTCAACTGCTATCTCAAATACTCCCTTTTTAATTAATAAGAAACTATTTGTTCGATGGGTTTATCTAAGATACCGTTATCCTTTTCGAACCAGAACTATATCAGCTTACCGATGAAGGATTACCTTATAGATGGTCGAAGACTCGAATGTATGAAATCAAACGGAAATGTTTGTTTTCCCATTCATGCATCAAACTAAATATCCTGTCATTACACCACTATACCCATACTTCCACTACAACTGTTGTAACAGTCCAAACCCATTGCTAGCAGATAT

Coding sequence (CDS)

ATGTCTGGAGAGGAGGAAGAAAATGCTGCAGAGCTTAAAATTGGGGATGAGTTCTTAAAAGCTAAGTGTTTAATGAATTGTGAAGTTTCTTTGATTCTTGAACACAAGTATGAGCAGCTTCAACAAATGTCTGAGGATCCAACCAATCAAGTTTCTCAAGTGTTTGAAAAGTCTCTGCAATATGTGAAACGGTTCAGCCGCTATAAGAACCCCGATGCTGTTAGACAAGTCCGAGAAATTCTAAGCAGGTATCAGTTGGCTGAGTTTGAGCTCTGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAGGAAGCTATTTCCATGGTTCCATCTTTGAAGACTAAAGGAAGAGCACATGACGATGAAGCAATCGAGAAGATGTTGAACGATCTTTCATTAATCAAAAAGTTCGAGTAG

Protein sequence

MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHDDEAIEKMLNDLSLIKKFE

Homology

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BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot
Match: NRPB4_ARATH (DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana GN=NRPB4 PE=1 SV=1)

HSP 1 Score: 259.2 bits (661), Expect = 2.5e-68
Identity = 129/138 (93.48%), Postives = 136/138 (98.55%), Query Frame = 1


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

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA++MVPSLKTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSL+K+FE
Sbjct: 121 DEAIEKMLNDLSLVKRFE 138

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BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot
Match: RPB4_HUMAN (DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1)

HSP 1 Score: 101.3 bits (251), Expect = 8.8e-21
Identity = 54/137 (39.42%), Postives = 93/137 (67.88%), Query Frame = 1


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

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ +++PSL  +GR  +D
Sbjct: 70  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSL--EGR-FED 129

Query: 122 EAIEKMLNDLSLIKKFE 139
           E ++++L+D+   + F+
Sbjct: 130 EELQQILDDIQTKRSFQ 141

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BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot
Match: RPB4_MOUSE (DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=1 SV=2)

HSP 1 Score: 101.3 bits (251), Expect = 8.8e-21
Identity = 54/137 (39.42%), Postives = 93/137 (67.88%), Query Frame = 1


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

Query: 62  VKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHDD 121
             RFSR+KN + +  VR +L + +L +FEL  L NLCPET EE+ +++PSL  +GR  +D
Sbjct: 70  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSL--EGR-FED 129

Query: 122 EAIEKMLNDLSLIKKFE 139
           E ++++L+D+   + F+
Sbjct: 130 EELQQILDDIQTKRSFQ 141

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BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot
Match: RPB4_DICDI (DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum GN=polr2d PE=3 SV=1)

HSP 1 Score: 94.7 bits (234), Expect = 8.2e-19
Identity = 55/147 (37.41%), Postives = 88/147 (59.86%), Query Frame = 1


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

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

Query: 124 SLKTKGRAHDDEAIEKMLNDLSLIKKF 138
           SLK      +D+ ++ +L++LS ++KF
Sbjct: 132 SLKKM----EDDELQAILDELSNLRKF 154

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BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot
Match: RPB4_DROME (DNA-directed RNA polymerase II 16 kDa polypeptide OS=Drosophila melanogaster GN=Rpb4 PE=2 SV=5)

HSP 1 Score: 87.0 bits (214), Expect = 1.7e-16
Identity = 48/126 (38.10%), Postives = 80/126 (63.49%), Query Frame = 1


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

Query: 66  SRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHDDEAIE 125
            ++KN + +   R +L + +L +FEL  LGNLCPE  EEA +++PSL  +GR  +DE + 
Sbjct: 71  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSL--EGR-FEDEELR 130

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

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BLAST of Cp4.1LG13g07760.1 vs. TrEMBL
Match: A0A0A0K7V5_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G014650 PE=4 SV=1)

HSP 1 Score: 266.9 bits (681), Expect = 1.3e-68
Identity = 134/138 (97.10%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAI+MVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

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

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TrEMBL
Match: B9H5K4_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0005s08690g PE=4 SV=1)

HSP 1 Score: 263.5 bits (672), Expect = 1.5e-67
Identity = 132/138 (95.65%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGD+FLKAKCLMNCEV+LILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDDFLKAKCLMNCEVALILEHKYEQLQQMSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TrEMBL
Match: A5APH2_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VIT_12s0028g01400 PE=4 SV=1)

HSP 1 Score: 263.5 bits (672), Expect = 1.5e-67
Identity = 132/138 (95.65%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++ILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAVILEHKYEQLQQMSDDPLNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TrEMBL
Match: A0A061DJ22_THECC (RNA polymerase II, Rpb4, core protein isoform 1 OS=Theobroma cacao GN=TCM_001258 PE=4 SV=1)

HSP 1 Score: 261.9 bits (668), Expect = 4.3e-67
Identity = 131/138 (94.93%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIG+EFLKAKCLMNCEV+LILEHKYEQLQQMSEDP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGEEFLKAKCLMNCEVALILEHKYEQLQQMSEDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           D+AIE+MLNDLSLIKKFE
Sbjct: 121 DDAIERMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TrEMBL
Match: A0A0D2T6G2_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_006G238100 PE=4 SV=1)

HSP 1 Score: 260.8 bits (665), Expect = 9.6e-67
Identity = 130/138 (94.20%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIG+EFLKAKCLMNCEV+LILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGEEFLKAKCLMNCEVALILEHKYEQLQQMSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           D+AIE+MLNDLSLIKKFE
Sbjct: 121 DDAIERMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TAIR10
Match: AT5G09920.1 (AT5G09920.1 RNA polymerase II, Rpb4, core protein)

HSP 1 Score: 259.2 bits (661), Expect = 1.4e-69
Identity = 129/138 (93.48%), Postives = 136/138 (98.55%), Query Frame = 1


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

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPETVEEA++MVPSLKTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSL+K+FE
Sbjct: 121 DEAIEKMLNDLSLVKRFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. TAIR10
Match: AT4G15950.1 (AT4G15950.1 RNA polymerase II, Rpb4, core protein)

HSP 1 Score: 84.3 bits (207), Expect = 6.2e-17
Identity = 44/118 (37.29%), Postives = 76/118 (64.41%), Query Frame = 1


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

Query: 81  LSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHDDEAIEKMLNDLSLIKKFE 139
           L  Y +++ E+CV+ N   E+V+E ++ +PSLKTK +   ++ ++  L +LS +KK E
Sbjct: 149 LKTYGISDGEMCVIANASSESVDEVLAFIPSLKTK-KEVINQPLQDALEELSKLKKSE 205

[Close]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr
Match: gi|449441240|ref|XP_004138390.1| (PREDICTED: DNA-directed RNA polymerase II subunit 4 [Cucumis sativus])

HSP 1 Score: 266.9 bits (681), Expect = 1.9e-68
Identity = 134/138 (97.10%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPETVEEAI+MVPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD 120

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

[Close]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr
Match: gi|225446712|ref|XP_002282413.1| (PREDICTED: DNA-directed RNA polymerase II subunit 4 [Vitis vinifera])

HSP 1 Score: 263.5 bits (672), Expect = 2.1e-67
Identity = 132/138 (95.65%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEV++ILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVAVILEHKYEQLQQMSDDPLNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr
Match: gi|224083811|ref|XP_002307132.1| (hypothetical protein POPTR_0005s08690g [Populus trichocarpa])

HSP 1 Score: 263.5 bits (672), Expect = 2.1e-67
Identity = 132/138 (95.65%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGD+FLKAKCLMNCEV+LILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDDFLKAKCLMNCEVALILEHKYEQLQQMSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr
Match: gi|802759611|ref|XP_012089384.1| (PREDICTED: DNA-directed RNA polymerase II subunit 4 [Jatropha curcas])

HSP 1 Score: 263.5 bits (672), Expect = 2.1e-67
Identity = 132/138 (95.65%), Postives = 137/138 (99.28%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENA+ELKIGDEFLKAKCLMNCEV+LILEHKYEQLQQMS+DP NQVSQVFEKSLQ
Sbjct: 1   MSGEEEENASELKIGDEFLKAKCLMNCEVALILEHKYEQLQQMSDDPMNQVSQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAI+MVPS+KTKGRAHD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTKGRAHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

[Close]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr
Match: gi|659119066|ref|XP_008459458.1| (PREDICTED: DNA-directed RNA polymerase II subunit 4-like [Cucumis melo])

HSP 1 Score: 262.3 bits (669), Expect = 4.7e-67
Identity = 132/138 (95.65%), Postives = 135/138 (97.83%), Query Frame = 1


Query: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQ 60
           MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQ +EDPTNQ+SQVFEKSLQ
Sbjct: 1   MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQISQVFEKSLQ 60

Query: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEAISMVPSLKTKGRAHD 120
           YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEA S+VPSLKTKGR HD
Sbjct: 61  YVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEATSIVPSLKTKGRVHD 120

Query: 121 DEAIEKMLNDLSLIKKFE 139
           DEAIEKMLNDLSLIKKFE
Sbjct: 121 DEAIEKMLNDLSLIKKFE 138

The following BLAST results are available for this feature:

BLAST of Cp4.1LG13g07760.1 vs. Swiss-Prot


Match Name	E-value	Identity	Description
NRPB4_ARATH	2.5e-68	93.48	DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana GN=NRPB4 PE=1 S...	[more]
RPB4_HUMAN	8.8e-21	39.42	DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1	[more]
RPB4_MOUSE	8.8e-21	39.42	DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=1 SV=2	[more]
RPB4_DICDI	8.2e-19	37.41	DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum GN=polr2...	[more]
RPB4_DROME	1.7e-16	38.10	DNA-directed RNA polymerase II 16 kDa polypeptide OS=Drosophila melanogaster GN=...	[more]

BLAST of Cp4.1LG13g07760.1 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0K7V5_CUCSA	1.3e-68	97.10	Uncharacterized protein OS=Cucumis sativus GN=Csa_6G014650 PE=4 SV=1	[more]
B9H5K4_POPTR	1.5e-67	95.65	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0005s08690g PE=4 SV=1	[more]
A5APH2_VITVI	1.5e-67	95.65	Putative uncharacterized protein OS=Vitis vinifera GN=VIT_12s0028g01400 PE=4 SV=...	[more]
A0A061DJ22_THECC	4.3e-67	94.93	RNA polymerase II, Rpb4, core protein isoform 1 OS=Theobroma cacao GN=TCM_001258...	[more]
A0A0D2T6G2_GOSRA	9.6e-67	94.20	Uncharacterized protein OS=Gossypium raimondii GN=B456_006G238100 PE=4 SV=1	[more]

BLAST of Cp4.1LG13g07760.1 vs. TAIR10


Match Name	E-value	Identity	Description
AT5G09920.1	1.4e-69	93.48	RNA polymerase II, Rpb4, core protein	[more]
AT4G15950.1	6.2e-17	37.29	RNA polymerase II, Rpb4, core protein	[more]

BLAST of Cp4.1LG13g07760.1 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|449441240\|ref\|XP_004138390.1\|	1.9e-68	97.10	PREDICTED: DNA-directed RNA polymerase II subunit 4 [Cucumis sativus]	[more]
gi\|225446712\|ref\|XP_002282413.1\|	2.1e-67	95.65	PREDICTED: DNA-directed RNA polymerase II subunit 4 [Vitis vinifera]	[more]
gi\|224083811\|ref\|XP_002307132.1\|	2.1e-67	95.65	hypothetical protein POPTR_0005s08690g [Populus trichocarpa]	[more]
gi\|802759611\|ref\|XP_012089384.1\|	2.1e-67	95.65	PREDICTED: DNA-directed RNA polymerase II subunit 4 [Jatropha curcas]	[more]
gi\|659119066\|ref\|XP_008459458.1\|	4.7e-67	95.65	PREDICTED: DNA-directed RNA polymerase II subunit 4-like [Cucumis melo]	[more]

Annotated Terms

The following terms have been associated with this mRNA:

Vocabulary: **Biological Process**
Term	Definition
GO:0044237	cellular metabolic process
GO:0006351	transcription, DNA-templated

Vocabulary: **Molecular Function**
Term	Definition
GO:0003824	catalytic activity
GO:0000166	nucleotide binding
GO:0003899	DNA-directed RNA polymerase activity

Vocabulary: **INTERPRO**
Term	Definition
IPR010997	HRDC-like_sf
IPR006590	RNA_pol_Rpb4/RPC9_core
IPR005574	RPB4/RPC9

GO Annotation

GO Assignments

This mRNA is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0044237	cellular metabolic process
biological_process	GO:0006351	transcription, DNA-templated
biological_process	GO:0006144	purine nucleobase metabolic process
biological_process	GO:0006206	pyrimidine nucleobase metabolic process
biological_process	GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation
biological_process	GO:0006366	transcription from RNA polymerase II promoter
cellular_component	GO:0005665	DNA-directed RNA polymerase II, core complex
cellular_component	GO:0005730	nucleolus
molecular_function	GO:0003824	catalytic activity
molecular_function	GO:0003899	DNA-directed RNA polymerase activity
molecular_function	GO:0000166	nucleotide binding

Relationships

This mRNA is a part of the following gene feature(s):


Feature Name	Unique Name	Type
Cp4.1LG13g07760	Cp4.1LG13g07760	gene

The following polypeptide feature(s) derives from this mRNA:


Feature Name	Unique Name	Type
Cp4.1LG13g07760.1	Cp4.1LG13g07760.1-protein	polypeptide

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


Feature Name	Unique Name	Type
Cp4.1LG13g07760.1:five_prime_utr:002	Cp4.1LG13g07760.1:five_prime_utr:002	five_prime_UTR
Cp4.1LG13g07760.1:five_prime_utr:001	Cp4.1LG13g07760.1:five_prime_utr:001	five_prime_UTR

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


Feature Name	Unique Name	Type
Cp4.1LG13g07760.1:cds:006	Cp4.1LG13g07760.1:cds:006	CDS
Cp4.1LG13g07760.1:cds:005	Cp4.1LG13g07760.1:cds:005	CDS
Cp4.1LG13g07760.1:cds:004	Cp4.1LG13g07760.1:cds:004	CDS
Cp4.1LG13g07760.1:cds:003	Cp4.1LG13g07760.1:cds:003	CDS
Cp4.1LG13g07760.1:cds:002	Cp4.1LG13g07760.1:cds:002	CDS
Cp4.1LG13g07760.1:cds:001	Cp4.1LG13g07760.1:cds:001	CDS

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


Feature Name	Unique Name	Type
Cp4.1LG13g07760.1:three_prime_utr:001	Cp4.1LG13g07760.1:three_prime_utr:001	three_prime_UTR

InterPro

Analysis Name: InterPro Annotations of Cucurbita pepo
Date Performed: 2017-12-02


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR005574	RNA polymerase II, Rpb4	PFAM	PF03874	RNA_pol_Rpb4	coord: 23..132 score: 1.0
IPR006590	RNA polymerase II, Rpb4, core	SMART	SM00657	rpol4neu2	coord: 16..138 score: 1.4
IPR010997	HRDC-like	unknown	SSF47819	HRDC-like	coord: 3..136 score: 1.35
None	No IPR available	PANTHER	PTHR21297	DNA-DIRECTED RNA POLYMERASE II	coord: 1..138 score: 3.6