Carg01525-RA (mRNA) Silver-seed gourd (SMH-JMG-627) v2

Overview


Name	Carg01525-RA
Type	mRNA
Organism	Cucurbita argyrosperma subsp. argyrosperma cv. SMH-JMG-627 (Silver-seed gourd (SMH-JMG-627) v2)
Description	RNA polymerase II transcription factor B subunit 4
Location	Carg_Chr15: 3501602 .. 3502227 (+)
Sequence length	372
RNA-Seq Expression	Carg01525-RA
Synteny	Carg01525-RA

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide

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

Homology

[Close]

BLAST of Carg01525-RA vs. NCBI nr
Match: KAG7016494.1 (RNA polymerase II transcription factor B subunit 4, partial [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 244.2 bits (622), Expect = 5.9e-61
Identity = 123/123 (100.00%), Postives = 123/123 (100.00%), Query Frame = 0


Query: 1   MASAPSKLYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSY 60
           MASAPSKLYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSY
Sbjct: 1   MASAPSKLYAGSSSIPLSFHMDSQVLAFLNSILVLNQLNEVVVIGTGYASCKYLYNSSSY 60

Query: 61  SNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSLLSGSLSMALCCILVDD 120
           SNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSLLSGSLSMALCCILVDD
Sbjct: 61  SNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSSLLSGSLSMALCCILVDD 120

Query: 121 FWC 124
           FWC
Sbjct: 121 FWC 123

[Close]

BLAST of Carg01525-RA vs. NCBI nr
Match: KAG6578972.1 (LysM domain-containing GPI-anchored protein 1, partial [Cucurbita argyrosperma subsp. sororia])

HSP 1 Score: 186.4 bits (472), Expect = 1.5e-43
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: 552 MASAPSKLYADDVSLLVVLLDTNPFFWSTYSLPFSKFL-SHVLAFLNSILVLNQLNEVVV 611

Query: 61  IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 117
           IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS
Sbjct: 612 IGTGYASCKYLYNSSSYSNRSLEDGRMPALCTRLLNNLEEFMIGDEQSIKEDPRGGTMSS 671

[Close]

BLAST of Carg01525-RA 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 = 1.5e-43
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

[Close]

BLAST of Carg01525-RA 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 = 4.2e-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

[Close]

BLAST of Carg01525-RA 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 = 1.6e-42
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

[Close]

BLAST of Carg01525-RA vs. ExPASy Swiss-Prot
Match: Q8LF41 (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 = 3.2e-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

[Close]

BLAST of Carg01525-RA vs. ExPASy TrEMBL
Match: A0A6J1FJQ6 (RNA polymerase II transcription factor B subunit 4 OS=Cucurbita moschata OX=3662 GN=LOC111444867 PE=3 SV=1)

HSP 1 Score: 184.9 bits (468), Expect = 2.0e-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

[Close]

BLAST of Carg01525-RA vs. ExPASy TrEMBL
Match: A0A6J1JZK7 (RNA polymerase II transcription factor B subunit 4 OS=Cucurbita maxima OX=3661 GN=LOC111489720 PE=3 SV=1)

HSP 1 Score: 183.0 bits (463), Expect = 7.8e-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

[Close]

BLAST of Carg01525-RA vs. ExPASy TrEMBL
Match: A0A5A7U2L2 (RNA polymerase II transcription factor B subunit 4 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold648G001190 PE=3 SV=1)

HSP 1 Score: 180.3 bits (456), Expect = 5.0e-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

[Close]

BLAST of Carg01525-RA vs. ExPASy TrEMBL
Match: A0A1S3B4H7 (LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4 OS=Cucumis melo OX=3656 GN=LOC103485913 PE=3 SV=1)

HSP 1 Score: 180.3 bits (456), Expect = 5.0e-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

[Close]

BLAST of Carg01525-RA vs. ExPASy TrEMBL
Match: A0A0A0LMM2 (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_2G072450 PE=3 SV=1)

HSP 1 Score: 179.1 bits (453), Expect = 1.1e-41
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

[Close]

BLAST of Carg01525-RA vs. TAIR 10
Match: AT1G18340.1 (basal transcription factor complex subunit-related )

HSP 1 Score: 89.4 bits (220), Expect = 2.3e-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

The following BLAST results are available for this feature:

BLAST of Carg01525-RA vs. NCBI nr


Match Name	E-value	Identity	Description
KAG7016494.1	5.9e-61	100.00	RNA polymerase II transcription factor B subunit 4, partial [Cucurbita argyrospe...	[more]
KAG6578972.1	1.5e-43	78.95	LysM domain-containing GPI-anchored protein 1, partial [Cucurbita argyrosperma s...	[more]
XP_023550583.1	1.5e-43	78.95	RNA polymerase II transcription factor B subunit 4 [Cucurbita pepo subsp. pepo]	[more]
XP_022938728.1	4.2e-43	78.20	RNA polymerase II transcription factor B subunit 4 [Cucurbita moschata]	[more]
XP_022993825.1	1.6e-42	78.63	RNA polymerase II transcription factor B subunit 4 [Cucurbita maxima]	[more]

BLAST of Carg01525-RA vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q8LF41	3.2e-17	51.33	General transcription and DNA repair factor IIH subunit TFB4 OS=Arabidopsis thal...	[more]

BLAST of Carg01525-RA vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1FJQ6	2.0e-43	78.20	RNA polymerase II transcription factor B subunit 4 OS=Cucurbita moschata OX=3662...	[more]
A0A6J1JZK7	7.8e-43	78.63	RNA polymerase II transcription factor B subunit 4 OS=Cucurbita maxima OX=3661 G...	[more]
A0A5A7U2L2	5.0e-42	75.94	RNA polymerase II transcription factor B subunit 4 OS=Cucumis melo var. makuwa O...	[more]
A0A1S3B4H7	5.0e-42	75.94	LOW QUALITY PROTEIN: RNA polymerase II transcription factor B subunit 4 OS=Cucum...	[more]
A0A0A0LMM2	1.1e-41	75.19	Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_2G072450 PE=3 SV=1	[more]

BLAST of Carg01525-RA vs. TAIR 10


Match Name	E-value	Identity	Description
AT1G18340.1	2.3e-18	51.33	basal transcription factor complex subunit-related	[more]

InterPro

Analysis Name: InterPro Annotations of Silver-seed gourd (SMH-JMG-627) v2
Date Performed: 2021-10-25


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR036465	von Willebrand factor A-like domain superfamily	GENE3D	3.40.50.410	von Willebrand factor, type A domain	coord: 3..118 e-value: 3.5E-13 score: 51.7
IPR004600	TFIIH subunit Tfb4/GTF2H3	PFAM	PF03850	Tfb4	coord: 12..116 e-value: 6.1E-12 score: 45.6
IPR004600	TFIIH subunit Tfb4/GTF2H3	PANTHER	PTHR12831	TRANSCRIPTION INITIATION FACTOR IIH TFIIH , POLYPEPTIDE 3-RELATED	coord: 23..116

Relationships

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


Feature Name	Unique Name	Type
Carg01525	Carg01525	gene

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


Feature Name	Unique Name	Type
Carg01525-RA:1	Carg01525-RA:1	exon
Carg01525-RA:2	Carg01525-RA:2	exon

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


Feature Name	Unique Name	Type
Carg01525-RA:cds	Carg01525-RA:cds	CDS
Carg01525-RA:cds	Carg01525-RA:cds_2	CDS

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


Feature Name	Unique Name	Type
Carg01525-RA	Carg01525-RA-protein	polypeptide

GO Annotation

GO Assignments

This mRNA 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
biological_process	GO:0070816	phosphorylation of RNA polymerase II C-terminal domain
cellular_component	GO:0000439	transcription factor TFIIH core complex
cellular_component	GO:0005675	transcription factor TFIIH holo complex
molecular_function	GO:0046872	metal ion binding