Carg01525 (gene) Silver-seed gourd

NameCarg01525
Typegene
OrganismCucurbita argyrosperma (Silver-seed gourd)
DescriptionLOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4
LocationCucurbita_argyrosperma_scaffold_004 : 1451612 .. 1452237 (-)
The following sequences are available for this feature:

Gene sequence (with intron)

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

mRNA sequence

ATGGCCTCTGCTCCTTCGAAGCTCTATGCAGGTTCTTCTTCAATTCCTCTCTCCTTTCATATGGATTCTCAGGTACTTGCTTTTCTGAACTCCATTTTAGTTCTGAATCAACTTAATGAGGTTGTGGTCATTGGTACCGGATATGCTTCATGCAAGTATCTATACAACTCGTCTTCTTACTCAAATCGTAGCCTTGAAGATGGCAGAATGCCTGCACTTTGCACTCGTTTATTGAATAATTTGGAGGAATTCATGATTGGGGATGAGCAGTCAATCAAGGAAGATCCCAGAGGAGGGACCATGTCTTCACTTCTTTCTGGATCGCTCTCCATGGCTTTGTGTTGTATCCTTGTTGATGATTTTTGGTGCTGA

Coding sequence (CDS)

ATGGCCTCTGCTCCTTCGAAGCTCTATGCAGGTTCTTCTTCAATTCCTCTCTCCTTTCATATGGATTCTCAGGTACTTGCTTTTCTGAACTCCATTTTAGTTCTGAATCAACTTAATGAGGTTGTGGTCATTGGTACCGGATATGCTTCATGCAAGTATCTATACAACTCGTCTTCTTACTCAAATCGTAGCCTTGAAGATGGCAGAATGCCTGCACTTTGCACTCGTTTATTGAATAATTTGGAGGAATTCATGATTGGGGATGAGCAGTCAATCAAGGAAGATCCCAGAGGAGGGACCATGTCTTCACTTCTTTCTGGATCGCTCTCCATGGCTTTGTGTTGTATCCTTGTTGATGATTTTTGGTGCTGA

Protein sequence

MASAPSKLYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSLLSGSLSMALCCILVDDFWC
BLAST of Carg01525 vs. NCBI nr
Match: XP_023550583.1 (RNA polymerase II transcription factor B subunit 4 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 186.4 bits (472), Expect = 5.7e-44
Identity = 105/133 (78.95%), Postives = 108/133 (81.20%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  + S+P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTYSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 120

BLAST of Carg01525 vs. NCBI nr
Match: XP_022938728.1 (RNA polymerase II transcription factor B subunit 4 [Cucurbita moschata])

HSP 1 Score: 184.9 bits (468), Expect = 1.7e-43
Identity = 104/133 (78.20%), Postives = 108/133 (81.20%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  + S+P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTYSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSI+EDPRGGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIEEDPRGGTMSS 120

BLAST of Carg01525 vs. NCBI nr
Match: XP_022993825.1 (RNA polymerase II transcription factor B subunit 4 [Cucurbita maxima])

HSP 1 Score: 183.0 bits (463), Expect = 6.3e-43
Identity = 103/131 (78.63%), Postives = 106/131 (80.92%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  + S+P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTYSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 115
           IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPR GTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPREGTMSS 120

BLAST of Carg01525 vs. NCBI nr
Match: XP_008441918.2 (PREDICTED: LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4 [Cucumis melo])

HSP 1 Score: 180.3 bits (456), Expect = 4.1e-42
Identity = 101/133 (75.94%), Postives = 106/133 (79.70%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  +SS+P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTSSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSN  LEDGRMPALCTRLL NLEEF+IGDEQSIKEDP+GGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNHGLEDGRMPALCTRLLKNLEEFVIGDEQSIKEDPKGGTMSS 120

BLAST of Carg01525 vs. NCBI nr
Match: XP_004152842.1 (PREDICTED: general transcription factor IIH subunit 3 [Cucumis sativus] >XP_011648981.1 PREDICTED: general transcription factor IIH subunit 3 [Cucumis sativus] >KGN61231.1 hypothetical protein Csa_2G072450 [Cucumis sativus])

HSP 1 Score: 179.1 bits (453), Expect = 9.1e-42
Identity = 100/133 (75.19%), Postives = 106/133 (79.70%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  +S++P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTSALPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSN  LEDGRMPALCTRLL NLEEF+IGDEQSIKEDP+GGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNHGLEDGRMPALCTRLLKNLEEFVIGDEQSIKEDPKGGTMSS 120

BLAST of Carg01525 vs. TAIR10
Match: AT1G18340.1 (basal transcription factor complex subunit-related)

HSP 1 Score: 89.4 bits (220), Expect = 1.7e-18
Identity = 58/113 (51.33%), Postives = 74/113 (65.49%), Query Frame = 0

Query: 8   LYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSYSNRSLED 67
           L+  ++SI  S  + S VLAFLN++L LNQLN+VVVI TGY+SC Y+Y+SS  SN    +
Sbjct: 25  LFWSTTSITFSQFL-SHVLAFLNAVLGLNQLNQVVVIATGYSSCDYIYDSSLTSNHGNFE 84

Query: 68  GR---MPALCTRLLNNLEEFMIGDEQSIKEDPRGGTM-SSLLSGSLSMALCCI 117
                MPA+   LL  LEEF+  DE+  KE+     + S LLSGSLSMALC I
Sbjct: 85  SNGTGMPAIFGSLLKKLEEFVTKDEELSKEEVSEDRIPSCLLSGSLSMALCYI 136

BLAST of Carg01525 vs. Swiss-Prot
Match: sp|Q8LF41|TFB4_ARATH (General transcription and DNA repair factor IIH subunit TFB4 OS=Arabidopsis thaliana OX=3702 GN=TFB4 PE=2 SV=1)

HSP 1 Score: 89.4 bits (220), Expect = 3.1e-17
Identity = 58/113 (51.33%), Postives = 74/113 (65.49%), Query Frame = 0

Query: 8   LYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSYSNRSLED 67
           L+  ++SI  S  + S VLAFLN++L LNQLN+VVVI TGY+SC Y+Y+SS  SN    +
Sbjct: 25  LFWSTTSITFSQFL-SHVLAFLNAVLGLNQLNQVVVIATGYSSCDYIYDSSLTSNHGNFE 84

Query: 68  GR---MPALCTRLLNNLEEFMIGDEQSIKEDPRGGTM-SSLLSGSLSMALCCI 117
                MPA+   LL  LEEF+  DE+  KE+     + S LLSGSLSMALC I
Sbjct: 85  SNGTGMPAIFGSLLKKLEEFVTKDEELSKEEVSEDRIPSCLLSGSLSMALCYI 136

BLAST of Carg01525 vs. TrEMBL
Match: tr|A0A1S3B4H7|A0A1S3B4H7_CUCME (LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4 OS=Cucumis melo OX=3656 GN=LOC103485913 PE=4 SV=1)

HSP 1 Score: 180.3 bits (456), Expect = 2.7e-42
Identity = 101/133 (75.94%), Postives = 106/133 (79.70%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  +SS+P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTSSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSN  LEDGRMPALCTRLL NLEEF+IGDEQSIKEDP+GGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNHGLEDGRMPALCTRLLKNLEEFVIGDEQSIKEDPKGGTMSS 120

BLAST of Carg01525 vs. TrEMBL
Match: tr|A0A0A0LMM2|A0A0A0LMM2_CUCSA (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_2G072450 PE=4 SV=1)

HSP 1 Score: 179.1 bits (453), Expect = 6.1e-42
Identity = 100/133 (75.19%), Postives = 106/133 (79.70%), Query Frame = 0

Query: 1   MASAPSKLYA-----------------GSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVV 60
           MASAPSKLYA                  +S++P S  + S VLAFLNSILVLNQLNEVVV
Sbjct: 1   MASAPSKLYADDVSLLVVLLDTNPFFWSTSALPFSKFL-SHVLAFLNSILVLNQLNEVVV 60

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSN  LEDGRMPALCTRLL NLEEF+IGDEQSIKEDP+GGTMSS
Sbjct: 61  IGTGYASCKYLYNSSSYSNHGLEDGRMPALCTRLLKNLEEFVIGDEQSIKEDPKGGTMSS 120

BLAST of Carg01525 vs. TrEMBL
Match: tr|A0A0B0PXZ5|A0A0B0PXZ5_GOSAR (General transcription factor IIH subunit 3 OS=Gossypium arboreum OX=29729 GN=F383_14476 PE=4 SV=1)

HSP 1 Score: 135.6 bits (340), Expect = 7.7e-29
Identity = 80/133 (60.15%), Postives = 90/133 (67.67%), Query Frame = 0

Query: 1   MASAPSKLYAGS---------------SSIPLSF-HMDSQVLAFLNSILVLNQLNEVVVI 60
           MASAPSKLYA                 SS  LSF    S VLAFLN+IL LNQLN+VVVI
Sbjct: 1   MASAPSKLYADDVSLVVVLLDTNPFFWSSSSLSFSQFLSHVLAFLNAILTLNQLNQVVVI 60

Query: 61  GTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSL 118
            TGY SC Y+++SSS  NRS E+GRMP +C+ LL  LEEF+I DEQ  KE+P G   SSL
Sbjct: 61  ATGYNSCDYVFDSSSDLNRSFENGRMPVMCSSLLQKLEEFLIKDEQLSKEEPEGKIKSSL 120

BLAST of Carg01525 vs. TrEMBL
Match: tr|A0A2P5VN08|A0A2P5VN08_GOSBA (Uncharacterized protein OS=Gossypium barbadense OX=3634 GN=GOBAR_AA40491 PE=4 SV=1)

HSP 1 Score: 135.6 bits (340), Expect = 7.7e-29
Identity = 80/133 (60.15%), Postives = 90/133 (67.67%), Query Frame = 0

Query: 1   MASAPSKLYAGS---------------SSIPLSF-HMDSQVLAFLNSILVLNQLNEVVVI 60
           MASAPSKLYA                 SS  LSF    S VLAFLN+IL LNQLN+VVVI
Sbjct: 1   MASAPSKLYADDVSLVVVLLDTNPFFWSSSSLSFSQFLSHVLAFLNAILTLNQLNQVVVI 60

Query: 61  GTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSL 118
            TGY SC Y+++SSS  NRS E+GRMP +C+ LL  LEEF+I DEQ  KE+P G   SSL
Sbjct: 61  ATGYNSCDYVFDSSSDLNRSFENGRMPVMCSSLLQKLEEFLIKDEQLSKEEPEGKIKSSL 120

BLAST of Carg01525 vs. TrEMBL
Match: tr|A0A2P5Q8A4|A0A2P5Q8A4_GOSBA (Uncharacterized protein OS=Gossypium barbadense OX=3634 GN=GOBAR_DD32338 PE=4 SV=1)

HSP 1 Score: 133.7 bits (335), Expect = 2.9e-28
Identity = 79/133 (59.40%), Postives = 89/133 (66.92%), Query Frame = 0

Query: 1   MASAPSKLYAGS---------------SSIPLSF-HMDSQVLAFLNSILVLNQLNEVVVI 60
           MASAPSKLYA                 SS  LSF    S VLAFLN+IL LNQLN+VVVI
Sbjct: 1   MASAPSKLYADDVSLVVVLLDTNPFFWSSSSLSFSQFLSHVLAFLNAILTLNQLNQVVVI 60

Query: 61  GTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSL 118
            TGY SC Y+++SSS  NRS E+GRMP +C+ LL  LEEF+I DEQ  KE+P G    SL
Sbjct: 61  ATGYNSCDYVFDSSSDLNRSFENGRMPVMCSSLLQKLEEFLITDEQLSKEEPEGKIKPSL 120

The following BLAST results are available for this feature:
Match NameE-valueIdentityDescription
XP_023550583.15.7e-4478.95RNA polymerase II transcription factor B subunit 4 [Cucurbita pepo subsp. pepo][more]
XP_022938728.11.7e-4378.20RNA polymerase II transcription factor B subunit 4 [Cucurbita moschata][more]
XP_022993825.16.3e-4378.63RNA polymerase II transcription factor B subunit 4 [Cucurbita maxima][more]
XP_008441918.24.1e-4275.94PREDICTED: LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit... [more]
XP_004152842.19.1e-4275.19PREDICTED: general transcription factor IIH subunit 3 [Cucumis sativus] >XP_0116... [more]
Match NameE-valueIdentityDescription
AT1G18340.11.7e-1851.33basal transcription factor complex subunit-related[more]
Match NameE-valueIdentityDescription
sp|Q8LF41|TFB4_ARATH3.1e-1751.33General transcription and DNA repair factor IIH subunit TFB4 OS=Arabidopsis thal... [more]
Match NameE-valueIdentityDescription
tr|A0A1S3B4H7|A0A1S3B4H7_CUCME2.7e-4275.94LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4 OS=Cucum... [more]
tr|A0A0A0LMM2|A0A0A0LMM2_CUCSA6.1e-4275.19Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_2G072450 PE=4 SV=1[more]
tr|A0A0B0PXZ5|A0A0B0PXZ5_GOSAR7.7e-2960.15General transcription factor IIH subunit 3 OS=Gossypium arboreum OX=29729 GN=F38... [more]
tr|A0A2P5VN08|A0A2P5VN08_GOSBA7.7e-2960.15Uncharacterized protein OS=Gossypium barbadense OX=3634 GN=GOBAR_AA40491 PE=4 SV... [more]
tr|A0A2P5Q8A4|A0A2P5Q8A4_GOSBA2.9e-2859.40Uncharacterized protein OS=Gossypium barbadense OX=3634 GN=GOBAR_DD32338 PE=4 SV... [more]
The following terms have been associated with this gene:
Vocabulary: Biological Process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
GO:0006289nucleotide-excision repair
Vocabulary: Cellular Component
TermDefinition
GO:0000439core TFIIH complex
Vocabulary: INTERPRO
TermDefinition
IPR004600TFIIH_Tfb4/GTF2H3
IPR036465vWFA_dom_sf
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006289 nucleotide-excision repair
biological_process GO:0006355 regulation of transcription, DNA-templated
cellular_component GO:0000439 core TFIIH complex
molecular_function GO:0003674 molecular_function

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

Feature NameUnique NameType
Carg01525-RACarg01525-RAmRNA


Analysis Name: InterPro Annotations of silver-seed gourd
Date Performed: 2019-03-07
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036465von Willebrand factor A-like domain superfamilyGENE3DG3DSA:3.40.50.410coord: 3..118
e-value: 1.1E-11
score: 46.7
IPR004600TFIIH subunit Tfb4/GTF2H3PFAMPF03850Tfb4coord: 12..116
e-value: 1.3E-11
score: 44.4
IPR004600TFIIH subunit Tfb4/GTF2H3PANTHERPTHR12831TRANSCRIPTION INITIATION FACTOR IIH TFIIH , POLYPEPTIDE 3-RELATEDcoord: 16..116

The following gene(s) are orthologous to this gene:
GeneOrthologueOrganismBlock
Carg01525CmaCh15G006840Cucurbita maxima (Rimu)carcmaB1148
Carg01525CmoCh15G006990Cucurbita moschata (Rifu)carcmoB1118
The following gene(s) are paralogous to this gene:

None