Cp4.1LG03g11520 (gene) Cucurbita pepo (Zucchini)

Overview
NameCp4.1LG03g11520
Typegene
OrganismCucurbita pepo (Cucurbita pepo (Zucchini))
DescriptionRNA polymerase II transcription factor SIII (Elongin) subunit A
LocationCp4.1LG03 : 11019012 .. 11019364 (+)
Genome Viewer
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.
ATGTTGGTCAAACCGATCTAAATTTCCTTGAACATATTTTGCCGCATTGCACCGTCGACCAACTGATGCATATAGAGAACTGTTCGAAAAGAAGAGATCTCACTCCAATAACAAACAAATTATGGAAAACTTTCTACGAAAAAAAGTTCGGTAAGGATGGTGTCAACTGTGTTCTTGATAGGATGAAGCATAAGGAATCGTTCAGATGGAAGCAAATGTACGAGTTGAAGATGAAGGAATTAGAAGAGAAGGCGGTAGAAATTGAAAAACGATATATACAAAACTGCCGAAACGAAAAAGCTCGAAAACAGAGTCGTCAAGTAAAGATATGTGAGATATCGCCATCGAGTAAG

mRNA sequence

ATGTTGAACTGTTCGAAAAGAAGAGATCTCACTCCAATAACAAACAAATTATGGAAAACTTTCTACGAAAAAAAGTTCGGTAAGGATGGTGTCAACTGTGTTCTTGATAGGATGAAGCATAAGGAATCGTTCAGATGGAAGCAAATGTACGAGTTGAAGATGAAGGAATTAGAAGAGAAGGCGGTAGAAATTGAAAAACGATATATACAAAACTGCCGAAACGAAAAAGCTCGAAAACAGAGTCGTCAAGTAAAGATATGTGAGATATCGCCATCGAGTAAG

Coding sequence (CDS)

ATGTTGAACTGTTCGAAAAGAAGAGATCTCACTCCAATAACAAACAAATTATGGAAAACTTTCTACGAAAAAAAGTTCGGTAAGGATGGTGTCAACTGTGTTCTTGATAGGATGAAGCATAAGGAATCGTTCAGATGGAAGCAAATGTACGAGTTGAAGATGAAGGAATTAGAAGAGAAGGCGGTAGAAATTGAAAAACGATATATACAAAACTGCCGAAACGAAAAAGCTCGAAAACAGAGTCGTCAAGTAAAGATATGTGAGATATCGCCATCGAGTAAG

Protein sequence

MLNCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKESFRWKQMYELKMKELEEKAVEIEKRYIQNCRNEKARKQSRQVKICEISPSSK
Homology
[Close]
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match: A0A0A0KJR8_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G511010 PE=4 SV=1)

HSP 1 Score: 101.7 bits (252), Expect = 5.1e-19
Identity = 52/85 (61.18%), Postives = 63/85 (74.12%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKESFRWKQMYELKMKELEEKAV 62
           NCSK RDLTPITNKLWK FYE+KFGKD V+ V+      E+F+W  +Y  KMKELE +A 
Sbjct: 53  NCSKGRDLTPITNKLWKNFYERKFGKDDVDIVVKN----ETFKWMDLYVAKMKELENRAK 112

Query: 63  EIEKRYIQNCRNEKARKQSRQVKIC 88
           +IE R IQ+ + EKARKQSRQ+  C
Sbjct: 113 KIEDRIIQSYQKEKARKQSRQIVFC 133

[Close]
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match: A0A0K9REH1_SPIOL (Uncharacterized protein OS=Spinacia oleracea GN=SOVF_080700 PE=4 SV=1)

HSP 1 Score: 89.4 bits (220), Expect = 2.6e-15
Identity = 45/94 (47.87%), Postives = 67/94 (71.28%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKH-KESFRWKQMYELKMKELEEKA 62
           N +  RDL+P+T+KLWK FYE +FG   V  V++R+K  K +F W+Q+Y+ K+KE+ E  
Sbjct: 65  NATSERDLSPVTDKLWKKFYEAEFGAKSVEVVVERVKKFKVTFNWRQLYQAKLKEINENV 124

Query: 63  VEIEKRYIQNCRNEKARKQSRQVKIC-EISPSSK 95
            E  +R  Q+ +NE ARKQSRQ+++C ++ PSSK
Sbjct: 125 EESLERLTQSYKNESARKQSRQIQLCAKVPPSSK 158

[Close]
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match: A0A068VD51_COFCA (Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00002667001 PE=4 SV=1)

HSP 1 Score: 87.4 bits (215), Expect = 9.9e-15
Identity = 44/93 (47.31%), Postives = 66/93 (70.97%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKA 62
           NC++ RDL+P+TNKLWK F+E++FG +    V+ RMK +   F+W+++Y+ K +ELEEK 
Sbjct: 50  NCTEGRDLSPVTNKLWKKFFERQFGAESAELVVARMKKRRVEFKWRELYKAKSQELEEKE 109

Query: 63  VEIEKRYIQNCRNEKARKQSRQVKIC-EISPSS 94
            +I +R  Q   NE A KQ R+V+IC ++ PSS
Sbjct: 110 KKISERLKQRYANEAAEKQKRRVQICTKVPPSS 142

[Close]
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match: A0A061DLI5_THECC (Nucleus, subunit A, putative isoform 3 OS=Theobroma cacao GN=TCM_001808 PE=4 SV=1)

HSP 1 Score: 87.4 bits (215), Expect = 9.9e-15
Identity = 47/92 (51.09%), Postives = 68/92 (73.91%), Query Frame = 1 

Query: 5   SKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKAVE 64
           +K RDL+P+T+KLWK FYE +FG+   N V++RMK K+ SFRW+Q+YE K+K+++E   +
Sbjct: 11  TKGRDLSPVTDKLWKNFYELQFGRASTNLVIERMKLKKVSFRWRQLYEAKLKDVQEAENK 70

Query: 65  IEKRYIQNCRNEKARKQSRQVKIC-EISPSSK 95
              R  Q  + E ARKQSRQV++C ++ PSSK
Sbjct: 71  AIDRLKQLYKKEDARKQSRQVQLCTKVPPSSK 102

[Close]
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match: A0A061DJY1_THECC (Nucleus, subunit A, putative isoform 2 OS=Theobroma cacao GN=TCM_001808 PE=4 SV=1)

HSP 1 Score: 87.4 bits (215), Expect = 9.9e-15
Identity = 47/92 (51.09%), Postives = 68/92 (73.91%), Query Frame = 1 

Query: 5   SKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKAVE 64
           +K RDL+P+T+KLWK FYE +FG+   N V++RMK K+ SFRW+Q+YE K+K+++E   +
Sbjct: 67  TKGRDLSPVTDKLWKNFYELQFGRASTNLVIERMKLKKVSFRWRQLYEAKLKDVQEAENK 126

Query: 65  IEKRYIQNCRNEKARKQSRQVKIC-EISPSSK 95
              R  Q  + E ARKQSRQV++C ++ PSSK
Sbjct: 127 AIDRLKQLYKKEDARKQSRQVQLCTKVPPSSK 158

[Close]
BLAST of Cp4.1LG03g11520 vs. TAIR10
Match: AT2G42780.1 (AT2G42780.1 FUNCTIONS IN: molecular_function unknown)

HSP 1 Score: 68.2 bits (165), Expect = 3.2e-12
Identity = 33/88 (37.50%), Postives = 59/88 (67.05%), Query Frame = 1 

Query: 9   DLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE--SFRWKQMYELKMKELEEKAVEIEK 68
           DL+PIT+K WK FY+K +G++ +  +++ ++  +   F+W+ +YELK+  +++K  E+  
Sbjct: 62  DLSPITDKFWKGFYKKHYGEEDMKDLIEDLEWNKVNDFKWRNLYELKVIAVQQKEKELGG 121

Query: 69  RYIQNCRNEKARKQSRQVKICEISPSSK 95
           R  +  ++E  RKQSRQ K+C  +P SK
Sbjct: 122 RLKERYKDENERKQSRQTKVCSKAPPSK 149

[Close]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match: gi|700193830|gb|KGN49034.1| (hypothetical protein Csa_6G511010 [Cucumis sativus])

HSP 1 Score: 101.7 bits (252), Expect = 7.3e-19
Identity = 52/85 (61.18%), Postives = 63/85 (74.12%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKESFRWKQMYELKMKELEEKAV 62
           NCSK RDLTPITNKLWK FYE+KFGKD V+ V+      E+F+W  +Y  KMKELE +A 
Sbjct: 53  NCSKGRDLTPITNKLWKNFYERKFGKDDVDIVVKN----ETFKWMDLYVAKMKELENRAK 112

Query: 63  EIEKRYIQNCRNEKARKQSRQVKIC 88
           +IE R IQ+ + EKARKQSRQ+  C
Sbjct: 113 KIEDRIIQSYQKEKARKQSRQIVFC 133

[Close]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match: gi|902213886|gb|KNA17359.1| (hypothetical protein SOVF_080700 [Spinacia oleracea])

HSP 1 Score: 89.4 bits (220), Expect = 3.7e-15
Identity = 45/94 (47.87%), Postives = 67/94 (71.28%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKH-KESFRWKQMYELKMKELEEKA 62
           N +  RDL+P+T+KLWK FYE +FG   V  V++R+K  K +F W+Q+Y+ K+KE+ E  
Sbjct: 65  NATSERDLSPVTDKLWKKFYEAEFGAKSVEVVVERVKKFKVTFNWRQLYQAKLKEINENV 124

Query: 63  VEIEKRYIQNCRNEKARKQSRQVKIC-EISPSSK 95
            E  +R  Q+ +NE ARKQSRQ+++C ++ PSSK
Sbjct: 125 EESLERLTQSYKNESARKQSRQIQLCAKVPPSSK 158

[Close]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match: gi|449450878|ref|XP_004143189.1| (PREDICTED: transcription elongation factor B polypeptide 3 [Cucumis sativus])

HSP 1 Score: 87.4 bits (215), Expect = 1.4e-14
Identity = 45/91 (49.45%), Postives = 66/91 (72.53%), Query Frame = 1 

Query: 5   SKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKAVE 64
           S+ RDLTP+T+KLWK FYE++FGK+    V++RM+ K  +FRW Q+YE KM+++E+   +
Sbjct: 55  SEGRDLTPVTDKLWKKFYERQFGKESTTTVIERMRQKRVAFRWIQLYEAKMEDIEKNESK 114

Query: 65  IEKRYIQNCRNEKARKQSRQVKIC-EISPSS 94
              R  Q+   E ARKQSRQ++IC ++ PSS
Sbjct: 115 AADRIKQSYLKENARKQSRQIQICSKVPPSS 145

[Close]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match: gi|590710292|ref|XP_007048788.1| (Nucleus, subunit A, putative isoform 2 [Theobroma cacao])

HSP 1 Score: 87.4 bits (215), Expect = 1.4e-14
Identity = 47/92 (51.09%), Postives = 68/92 (73.91%), Query Frame = 1 

Query: 5   SKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKAVE 64
           +K RDL+P+T+KLWK FYE +FG+   N V++RMK K+ SFRW+Q+YE K+K+++E   +
Sbjct: 67  TKGRDLSPVTDKLWKNFYELQFGRASTNLVIERMKLKKVSFRWRQLYEAKLKDVQEAENK 126

Query: 65  IEKRYIQNCRNEKARKQSRQVKIC-EISPSSK 95
              R  Q  + E ARKQSRQV++C ++ PSSK
Sbjct: 127 AIDRLKQLYKKEDARKQSRQVQLCTKVPPSSK 158

[Close]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match: gi|661877430|emb|CDP18735.1| (unnamed protein product [Coffea canephora])

HSP 1 Score: 87.4 bits (215), Expect = 1.4e-14
Identity = 44/93 (47.31%), Postives = 66/93 (70.97%), Query Frame = 1 

Query: 3   NCSKRRDLTPITNKLWKTFYEKKFGKDGVNCVLDRMKHKE-SFRWKQMYELKMKELEEKA 62
           NC++ RDL+P+TNKLWK F+E++FG +    V+ RMK +   F+W+++Y+ K +ELEEK 
Sbjct: 50  NCTEGRDLSPVTNKLWKKFFERQFGAESAELVVARMKKRRVEFKWRELYKAKSQELEEKE 109

Query: 63  VEIEKRYIQNCRNEKARKQSRQVKIC-EISPSS 94
            +I +R  Q   NE A KQ R+V+IC ++ PSS
Sbjct: 110 KKISERLKQRYANEAAEKQKRRVQICTKVPPSS 142

The following BLAST results are available for this feature:
BLAST of Cp4.1LG03g11520 vs. Swiss-Prot
Match NameE-valueIdentityDescription
BLAST of Cp4.1LG03g11520 vs. TrEMBL
Match NameE-valueIdentityDescription
A0A0A0KJR8_CUCSA5.1e-1961.18Uncharacterized protein OS=Cucumis sativus GN=Csa_6G511010 PE=4 SV=1[more]
A0A0K9REH1_SPIOL2.6e-1547.87Uncharacterized protein OS=Spinacia oleracea GN=SOVF_080700 PE=4 SV=1[more]
A0A068VD51_COFCA9.9e-1547.31Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00002667001 PE=4 SV=1[more]
A0A061DLI5_THECC9.9e-1551.09Nucleus, subunit A, putative isoform 3 OS=Theobroma cacao GN=TCM_001808 PE=4 SV=... [more]
A0A061DJY1_THECC9.9e-1551.09Nucleus, subunit A, putative isoform 2 OS=Theobroma cacao GN=TCM_001808 PE=4 SV=... [more]
BLAST of Cp4.1LG03g11520 vs. TAIR10
Match NameE-valueIdentityDescription
AT2G42780.13.2e-1237.50 FUNCTIONS IN: molecular_function unknown[more]
BLAST of Cp4.1LG03g11520 vs. NCBI nr
Match NameE-valueIdentityDescription
gi|700193830|gb|KGN49034.1|7.3e-1961.18hypothetical protein Csa_6G511010 [Cucumis sativus][more]
gi|902213886|gb|KNA17359.1|3.7e-1547.87hypothetical protein SOVF_080700 [Spinacia oleracea][more]
gi|449450878|ref|XP_004143189.1|1.4e-1449.45PREDICTED: transcription elongation factor B polypeptide 3 [Cucumis sativus][more]
gi|590710292|ref|XP_007048788.1|1.4e-1451.09Nucleus, subunit A, putative isoform 2 [Theobroma cacao][more]
gi|661877430|emb|CDP18735.1|1.4e-1447.31unnamed protein product [Coffea canephora][more]
Annotated Terms
The following terms have been associated with this gene:
Vocabulary: Cellular Component
TermDefinition
GO:0016021integral component of membrane
GO:0005634nucleus
Vocabulary: Biological Process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
Vocabulary: INTERPRO
TermDefinition
IPR010684RNA_pol_II_trans_fac_SIII_A
GO Annotation
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006355 regulation of transcription, DNA-templated
cellular_component GO:0016021 integral component of membrane
cellular_component GO:0005634 nucleus
molecular_function GO:0003674 molecular_function
Relationships

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

Feature NameUnique NameType
Cp4.1LG03g11520.1Cp4.1LG03g11520.1mRNA


InterPro
Analysis Name: InterPro Annotations of Cucurbita pepo
Date Performed: 2017-12-02
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR010684RNA polymerase II transcription factor SIII, subunit APFAMPF06881Elongin_Acoord: 9..83
score: 1.
NoneNo IPR availableunknownCoilCoilcoord: 47..74
scor

Synteny
The following gene(s) are orthologous to this gene:
GeneOrthologueOrganismBlock
Cp4.1LG03g11520Bhi01G000715Wax gourdcpewgoB0783
The following gene(s) are paralogous to this gene:

None

The following block(s) are covering this gene:
GeneOrganismBlock
Cp4.1LG03g11520Wax gourdcpewgoB0762
Cp4.1LG03g11520Cucurbita pepo (Zucchini)cpecpeB184
Cp4.1LG03g11520Cucurbita pepo (Zucchini)cpecpeB337
Cp4.1LG03g11520Cucurbita pepo (Zucchini)cpecpeB482
Cp4.1LG03g11520Cucumber (Gy14) v1cgycpeB0682
Cp4.1LG03g11520Cucurbita maxima (Rimu)cmacpeB003
Cp4.1LG03g11520Cucurbita maxima (Rimu)cmacpeB283
Cp4.1LG03g11520Cucurbita maxima (Rimu)cmacpeB403
Cp4.1LG03g11520Cucurbita maxima (Rimu)cmacpeB837
Cp4.1LG03g11520Cucurbita maxima (Rimu)cmacpeB928
Cp4.1LG03g11520Cucurbita moschata (Rifu)cmocpeB245
Cp4.1LG03g11520Cucurbita moschata (Rifu)cmocpeB365
Cp4.1LG03g11520Cucurbita moschata (Rifu)cmocpeB787
Cp4.1LG03g11520Cucurbita moschata (Rifu)cmocpeB862
Cp4.1LG03g11520Wild cucumber (PI 183967)cpecpiB611
Cp4.1LG03g11520Cucumber (Chinese Long) v2cpecuB609
Cp4.1LG03g11520Bottle gourd (USVL1VR-Ls)cpelsiB484
Cp4.1LG03g11520Bottle gourd (USVL1VR-Ls)cpelsiB512
Cp4.1LG03g11520Watermelon (Charleston Gray)cpewcgB559
Cp4.1LG03g11520Watermelon (Charleston Gray)cpewcgB562
Cp4.1LG03g11520Watermelon (97103) v1cpewmB613
Cp4.1LG03g11520Watermelon (97103) v1cpewmB623
Cp4.1LG03g11520Melon (DHL92) v3.5.1cpemeB555
Cp4.1LG03g11520Melon (DHL92) v3.5.1cpemeB585
Cp4.1LG03g11520Cucumber (Gy14) v2cgybcpeB406
Cp4.1LG03g11520Melon (DHL92) v3.6.1cpemedB659
Cp4.1LG03g11520Melon (DHL92) v3.6.1cpemedB693
Cp4.1LG03g11520Silver-seed gourdcarcpeB0106
Cp4.1LG03g11520Silver-seed gourdcarcpeB0860
Cp4.1LG03g11520Silver-seed gourdcarcpeB0986
Cp4.1LG03g11520Silver-seed gourdcarcpeB1164
Cp4.1LG03g11520Cucumber (Chinese Long) v3cpecucB0759