Carg07899 (gene) Silver-seed gourd (SMH-JMG-627) v2

Overview


Name	Carg07899
Type	gene
Organism	Cucurbita argyrosperma subsp. argyrosperma cv. SMH-JMG-627 (Silver-seed gourd (SMH-JMG-627) v2)
Description	DNA-directed RNA polymerases IV and V subunit 4-like
Location	Carg_Chr07: 1614334 .. 1615767 (+)
RNA-Seq Expression	Carg07899
Synteny	Carg07899

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.

ATGGATGGAAACAAATTATGTACTACTGTGGAACTATGCTTTTGTACCAATCCAGCACTCCTAGTGTGCTGTATAGTGCTCTTTTTCTTAGTCCATTCAAACTCTGTTGAGTGCTTAACTGAAGATTCTAGAACCCTCAAGAAATATGGTGTAGCGGACAGTGAGGTAGTTATATCTATCTTCTTTTTTGCCTTCTTAAAAATTAATTCCTTAGATTGATGAACTGACCATTATTAATTTTAACGTAGATATGTGTGATTGCTAATGTCTGCCCAGACACTACTGATGAAGTTTTTGCTCTTGTTCCATCTTTGAAGGTACAGTATAAGTTTTTATAATCTCTGTAACTTACATCACCATGCCATATGAACATAGTTAAACACATATTTAGTTTCTATACTTCGATTCTTGTAGTGTTTTAGTCTTGTTGTAATTTCTTTTAGTAAAATGTTAGTCTGCCCTGTTTAGAGGCCATTTTTTAAAGTTGAACTATTCTTAAATGATTCTAAAGTGTGCTTTTAAGGACTTCTGATCATACAATTGAATAGGTAGTTAAACACTGTTACAAAAATGAAAAGCATCCGTCCAAGCCCACCGCTAGCAGAAATTGTCCTCTTTGGGTTTTCTTTTCGGGTTTCCCTTCAAGGTTTTTAAAACCGTCTGCTAGGGTGAGGTTTTCACACCCTTATAAAGAATGTTTCATTCCCCTCTCCAACCGATGTGGGATCTCACAATCCACCTCCCTTCAGGGCCTAGCGTCCTCGCTGCCACTCATTCTCCTCTCCAATCGATGTGTGACCCCCTAATCTACCCCCTTTAGGGCCCAATGTCCTCGTTGGCACACCGCCTAATGTCCATCCCTTTGGGGCTCGGCGTCTTCGCTAGCACACTGCCCAATATCCGGCTCTTATACCATTTTATATCAGTGAGTATCTATGAGTGTTTGAGTCAACTTGCATGCAGCAGCTCGATTGATCTCATGGGACAGTCGTTTGATCCTACTACATTTGAATCAGTCAAAACATTTTAAAGATGCTTCCAGAGACGGGGTTGGAGTGGTTATGCATGTTTGGAATGTTGATCCTATGACACTATGATTTATTAATTTATTTTGCTTCAACATGATTTCATACAAAGCAGAGCAAAAGAAGTAAGCTAACCGAACCTCTGAACAACGTCTTGATTGAGCTAGCCAAGCTAAAATCATCCTGAAGTGAAGTCACAAGGTTGGTTGCTTACCGTTGCTGGTGCTCAGGTCCGGTTGCCTTCATCCTACGAAGATTGCTTTATATGGCGCTTAGAAAGTTAAGACCTTTTTTTCTCTTTCAATGCAATTCAATAGAGATATAACTGTATTTGCTTACTGGAATTGTTGATATATAGTGTAGAAATAGGGGCTACTCTGCTGAGAGAATGCCTCTCCCAGGTGAATGA

mRNA sequence

ATGGATGGAAACAAATTATGTACTACTGTGGAACTATGCTTTTGTACCAATCCAGCACTCCTAGTGTGCTGTATAGTGCTCTTTTTCTTAGTCCATTCAAACTCTGTTGAGTGCTTAACTGAAGATTCTAGAACCCTCAAGAAATATGGTGTAGCGGACAGTGAGATATGTGTGATTGCTAATGTCTGCCCAGACACTACTGATGAAGTTTTTGCTCTTGTTCCATCTTTGAAGTGTAGAAATAGGGGCTACTCTGCTGAGAGAATGCCTCTCCCAGGTGAATGA

Coding sequence (CDS)

ATGGATGGAAACAAATTATGTACTACTGTGGAACTATGCTTTTGTACCAATCCAGCACTCCTAGTGTGCTGTATAGTGCTCTTTTTCTTAGTCCATTCAAACTCTGTTGAGTGCTTAACTGAAGATTCTAGAACCCTCAAGAAATATGGTGTAGCGGACAGTGAGATATGTGTGATTGCTAATGTCTGCCCAGACACTACTGATGAAGTTTTTGCTCTTGTTCCATCTTTGAAGTGTAGAAATAGGGGCTACTCTGCTGAGAGAATGCCTCTCCCAGGTGAATGA

Protein sequence

MDGNKLCTTVELCFCTNPALLVCCIVLFFLVHSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCRNRGYSAERMPLPGE

Homology

[Close]

BLAST of Carg07899 vs. NCBI nr
Match: KAG7026686.1 (DNA-directed RNA polymerases IV and V subunit 4, partial [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 198.7 bits (504), Expect = 2.2e-47
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 0


Query: 1  MDGNKLCTTVELCFCTNPALLVCCIVLFFLVHSNSVECLTEDSRTLKKYGVADSEICVIA 60
          MDGNKLCTTVELCFCTNPALLVCCIVLFFLVHSNSVECLTEDSRTLKKYGVADSEICVIA
Sbjct: 1  MDGNKLCTTVELCFCTNPALLVCCIVLFFLVHSNSVECLTEDSRTLKKYGVADSEICVIA 60

Query: 61 NVCPDTTDEVFALVPSLKCRNRGYSAERMPLPGE 95
          NVCPDTTDEVFALVPSLKCRNRGYSAERMPLPGE
Sbjct: 61 NVCPDTTDEVFALVPSLKCRNRGYSAERMPLPGE 94

[Close]

BLAST of Carg07899 vs. NCBI nr
Match: KAG6594716.1 (DNA-directed RNA polymerases IV and V subunit 4, partial [Cucurbita argyrosperma subsp. sororia])

HSP 1 Score: 74.3 bits (181), Expect = 6.2e-10
Identity = 36/49 (73.47%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVFALVPSLK +
Sbjct: 152 HYVNTESVRPVLETLKKYGVADSEICVIANVCPDTTDEVFALVPSLKSK 200

[Close]

BLAST of Carg07899 vs. NCBI nr
Match: XP_023517147.1 (DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 74.3 bits (181), Expect = 6.2e-10
Identity = 36/49 (73.47%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVFALVPSLK +
Sbjct: 148 HYVNTESVRPVLETLKKYGVADSEICVIANVCPDTTDEVFALVPSLKSK 196

[Close]

BLAST of Carg07899 vs. NCBI nr
Match: XP_023517145.1 (DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 [Cucurbita pepo subsp. pepo] >XP_023517146.1 DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 74.3 bits (181), Expect = 6.2e-10
Identity = 36/49 (73.47%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVFALVPSLK +
Sbjct: 152 HYVNTESVRPVLETLKKYGVADSEICVIANVCPDTTDEVFALVPSLKSK 200

[Close]

BLAST of Carg07899 vs. NCBI nr
Match: XP_022926859.1 (DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 [Cucurbita moschata])

HSP 1 Score: 73.2 bits (178), Expect = 1.4e-09
Identity = 35/49 (71.43%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVF+LVPSLK +
Sbjct: 148 HYVNTELVRPVLETLKKYGVADSEICVIANVCPDTTDEVFSLVPSLKSK 196

[Close]

BLAST of Carg07899 vs. ExPASy Swiss-Prot
Match: Q6DBA5 (DNA-directed RNA polymerases IV and V subunit 4 OS=Arabidopsis thaliana OX=3702 GN=NRPD4 PE=1 SV=2)

HSP 1 Score: 49.3 bits (116), Expect = 2.8e-05
Identity = 21/50 (42.00%), Postives = 32/50 (64.00%), Query Frame = 0


Query: 31  VHSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           VH  + + + +    LK YG++D E+CVIAN   ++ DEV A +PSLK +
Sbjct: 134 VHYTNPQSVRKVLEPLKTYGISDGEMCVIANASSESVDEVLAFIPSLKTK 183

[Close]

BLAST of Carg07899 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: 46.6 bits (109), Expect = 1.8e-04
Identity = 17/42 (40.48%), Postives = 29/42 (69.05%), Query Frame = 0


Query: 46  LKKYGVADSEICVIANVCPDTTDEVFALVPSLKCRNRGYSAE 88
           L ++ + + E+CV+ N+CP+T +E  A+VPSLK + R +  E
Sbjct: 81  LSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHDDE 122

[Close]

BLAST of Carg07899 vs. ExPASy TrEMBL
Match: A0A6J1EJD9 (DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 OS=Cucurbita moschata OX=3662 GN=LOC111433844 PE=4 SV=1)

HSP 1 Score: 73.2 bits (178), Expect = 6.6e-10
Identity = 35/49 (71.43%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVF+LVPSLK +
Sbjct: 152 HYVNTELVRPVLETLKKYGVADSEICVIANVCPDTTDEVFSLVPSLKSK 200

[Close]

BLAST of Carg07899 vs. ExPASy TrEMBL
Match: A0A6J1EGC4 (DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 OS=Cucurbita moschata OX=3662 GN=LOC111433844 PE=4 SV=1)

HSP 1 Score: 73.2 bits (178), Expect = 6.6e-10
Identity = 35/49 (71.43%), Postives = 39/49 (79.59%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDTTDEVF+LVPSLK +
Sbjct: 148 HYVNTELVRPVLETLKKYGVADSEICVIANVCPDTTDEVFSLVPSLKSK 196

[Close]

BLAST of Carg07899 vs. ExPASy TrEMBL
Match: A0A6J1KMD1 (DNA-directed RNA polymerases IV and V subunit 4-like OS=Cucurbita maxima OX=3661 GN=LOC111497005 PE=4 SV=1)

HSP 1 Score: 72.0 bits (175), Expect = 1.5e-09
Identity = 35/49 (71.43%), Postives = 38/49 (77.55%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           H  + E +     TLKKYGVADSEICVIANVCPDT DEVFALVPSLK +
Sbjct: 152 HYVNTESVRPVLETLKKYGVADSEICVIANVCPDTIDEVFALVPSLKSK 200

[Close]

BLAST of Carg07899 vs. ExPASy TrEMBL
Match: A0A0A0KH45 (RPOL4c domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_6G510870 PE=4 SV=1)

HSP 1 Score: 71.2 bits (173), Expect = 2.5e-09
Identity = 34/47 (72.34%), Postives = 37/47 (78.72%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLK 79
           H  + E +     TLKKYGV DSEICVIANVCPDTTDEVFAL+PSLK
Sbjct: 151 HYVNAESVRPVLETLKKYGVTDSEICVIANVCPDTTDEVFALLPSLK 197

[Close]

BLAST of Carg07899 vs. ExPASy TrEMBL
Match: A0A1S3B2C2 (DNA-directed RNA polymerases IV and V subunit 4 isoform X1 OS=Cucumis melo OX=3656 GN=LOC103485216 PE=4 SV=1)

HSP 1 Score: 70.9 bits (172), Expect = 3.3e-09
Identity = 33/47 (70.21%), Postives = 37/47 (78.72%), Query Frame = 0


Query: 32  HSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLK 79
           H  + E +     TLKKYG+ DSEICVIANVCPDTTDEVFAL+PSLK
Sbjct: 151 HYVNAESVRPVLETLKKYGITDSEICVIANVCPDTTDEVFALLPSLK 197

[Close]

BLAST of Carg07899 vs. TAIR 10
Match: AT4G15950.1 (RNA polymerase II, Rpb4, core protein )

HSP 1 Score: 49.3 bits (116), Expect = 2.0e-06
Identity = 21/50 (42.00%), Postives = 32/50 (64.00%), Query Frame = 0


Query: 31  VHSNSVECLTEDSRTLKKYGVADSEICVIANVCPDTTDEVFALVPSLKCR 81
           VH  + + + +    LK YG++D E+CVIAN   ++ DEV A +PSLK +
Sbjct: 134 VHYTNPQSVRKVLEPLKTYGISDGEMCVIANASSESVDEVLAFIPSLKTK 183

[Close]

BLAST of Carg07899 vs. TAIR 10
Match: AT5G09920.1 (RNA polymerase II, Rpb4, core protein )

HSP 1 Score: 46.6 bits (109), Expect = 1.3e-05
Identity = 17/42 (40.48%), Postives = 29/42 (69.05%), Query Frame = 0


Query: 46  LKKYGVADSEICVIANVCPDTTDEVFALVPSLKCRNRGYSAE 88
           L ++ + + E+CV+ N+CP+T +E  A+VPSLK + R +  E
Sbjct: 81  LSRHQLTEFELCVLGNLCPETVEEAVAMVPSLKTKGRAHDDE 122

The following BLAST results are available for this feature:

BLAST of Carg07899 vs. NCBI nr


Match Name	E-value	Identity	Description
KAG7026686.1	2.2e-47	100.00	DNA-directed RNA polymerases IV and V subunit 4, partial [Cucurbita argyrosperma...	[more]
KAG6594716.1	6.2e-10	73.47	DNA-directed RNA polymerases IV and V subunit 4, partial [Cucurbita argyrosperma...	[more]
XP_023517147.1	6.2e-10	73.47	DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 [Cucurbita pepo ...	[more]
XP_023517145.1	6.2e-10	73.47	DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 [Cucurbita pepo ...	[more]
XP_022926859.1	1.4e-09	71.43	DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 [Cucurbita mosch...	[more]

BLAST of Carg07899 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q6DBA5	2.8e-05	42.00	DNA-directed RNA polymerases IV and V subunit 4 OS=Arabidopsis thaliana OX=3702 ...	[more]
O48890	1.8e-04	40.48	DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana OX=3702 GN=NRPB...	[more]

BLAST of Carg07899 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1EJD9	6.6e-10	71.43	DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 OS=Cucurbita mos...	[more]
A0A6J1EGC4	6.6e-10	71.43	DNA-directed RNA polymerases IV and V subunit 4-like isoform X2 OS=Cucurbita mos...	[more]
A0A6J1KMD1	1.5e-09	71.43	DNA-directed RNA polymerases IV and V subunit 4-like OS=Cucurbita maxima OX=3661...	[more]
A0A0A0KH45	2.5e-09	72.34	RPOL4c domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_6G510870 PE=4...	[more]
A0A1S3B2C2	3.3e-09	70.21	DNA-directed RNA polymerases IV and V subunit 4 isoform X1 OS=Cucumis melo OX=36...	[more]

BLAST of Carg07899 vs. TAIR 10


Match Name	E-value	Identity	Description
AT4G15950.1	2.0e-06	42.00	RNA polymerase II, Rpb4, core protein	[more]
AT5G09920.1	1.3e-05	40.48	RNA polymerase II, Rpb4, core protein	[more]

InterPro

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

Position :

Zoom :

x 1


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR038324	Rpb4/RPC9 superfamily	GENE3D	1.20.1250.40		coord: 31..89 e-value: 3.1E-9 score: 38.8
None	No IPR available	PANTHER	PTHR21297:SF2	DNA-DIRECTED RNA POLYMERASES IV AND V SUBUNIT 4	coord: 45..80
None	No IPR available	PANTHER	PTHR21297	DNA-DIRECTED RNA POLYMERASE II	coord: 45..80
IPR010997	HRDC-like superfamily	SUPERFAMILY	47819	HRDC-like	coord: 44..80

Relationships

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


Feature Name	Unique Name	Type
Carg07899-RA	Carg07899-RA	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006352	DNA-templated transcription, initiation
biological_process	GO:0044237	cellular metabolic process
cellular_component	GO:0005634	nucleus
cellular_component	GO:0030880	RNA polymerase complex
molecular_function	GO:0003899	DNA-directed 5'-3' RNA polymerase activity
molecular_function	GO:0000166	nucleotide binding