Clc10G05877 (gene) Watermelon (cordophanus) v2

Overview


Name	Clc10G05877
Type	gene
Organism	Citrullus lanatus subsp. cordophanus cv. cordophanus (Watermelon (cordophanus) v2)
Description	DNA-directed RNA polymerase subunit beta
Location	ClcChr10: 7320683 .. 7322292 (+)
RNA-Seq Expression	Clc10G05877
Synteny	Clc10G05877

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.

ATGGCTAAATTTGACAAAGTAATTTCTCAAAATTTTGTTTCTGTAATTTTTTTTTTTTCCATTTTCATACGTGTGCCCATATTTCTTTCTCTTTGGTCTCCTTTCACGCATATCTATTCTCTCCCATTGTCTCCTCTCTCTCTCCCTTCATTGTTCATCCTAACTTCCTTTTTCCATTTTAAATTAATTTTCTTCCTTTTTACTTCATTATCCTGTTCTTTTTTTTTTTTTTTTTCTCATTTGTCTTCTATCTTCTTTCAGATTTTTTTTCATTAACAAGTTTTTAGTTATAACGAGATGTTCCGTGATATTGAAAGACAGGTCTTAACTTAGATAAGTTAATAACTTGTGTTTGTGATAATTTGTAAAATAAATATGCTTGCGACAAGTATGATAAGTCCCAAAAGATCTTTCCGTTTTTATTACTAATATTGGAAAGTGACTTTTTGATAGTTGAAATAAAGTGAATTAAACTTTGATTTGTTTTATCAATTCTTTCTTGATTTGCTTCATTATTGGAAATGGATTTAGTAAAATTTTTTTTTATTGTTATTGAATCAATAAAAAGTTGCCCATTAATCCTCGGCATATTAATCATACGTTGAAAGATATCTATGTATATGTTTTCAACGAAAAATTTTAAAAAATGATACGATTTACGAATTAATCGTACATTTCTTTTTTTTAATATCTTTAAAATATTTTTCTGAGATTCAAATATTTTATCATCATAACTTATTTTGTTAGGACTAATATTTATTTCTGTATTTAGAAACTCTTTTTTCGTGTCTTTTCTAATTTTTTCAATTTTTTTTAGTATGGTGTTTGTTCTATCAGTCAGATCTTTCATCTTTTTTTCTCTCAATGAAAAATTTGTCCAATCCATAGACCGAGTTATAATGGAGGAGCCGGGGATCATTCGATTACTTATTATCGAATTTTTTTCGTTTTTAGCTTCATTCAACTCGTATATTTCTTTCAATTCAAATAATCGAATTGGGTTTCGTTGTGAAAGTTCTGTTATTATTTGTTTTATAAAAAAAATGTTTTTGATGACCCAGTTTTTTGTTTCTTTTGAGATATTTATAAACAAGTTTGTTCTTTCTTTTAAAAGTCTTAGAATTGGAAAACGCTTCTTTTTCCATTTTTTAATTTTTTTTTCGAGTTCTTTTATTAACATGGGTTCAAAAAACGAAAGTTGTTTTCGGGGAGAACCAAAAGGCAGTTCAGCTTCCATTCCCCAAACTGTTAAAAAACAAAAATCATTTTTTTGTCCTTTCTTTTTTGTTGAATCTTTATTAGGGGATTGTGAGGCTCATTACTTCAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAAACAGTATATAAGGCATACCCAGTAAAACTTACAAGTAAACCAGATATAGAACAAAGATGTGAATTAGGAAGGATTGGTCGACGAAATCTGAACCAGAGACTTAATCTTGATATACCTGAGAACAATACATTTTTGTTACCGCGAGATATATTGGCAGCTGCAGATCATTTGATTGGACTGAAATTTGGAATGGGTACACTTGACGATATGAATCAATTTCATATTTAA

mRNA sequence

ATGGCTAAATTTGACAAAGGGATTGTGAGGCTCATTACTTCAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAAACAGTATATAAGGCATACCCAGATTGGTCGACGAAATCTGAACCAGAGACTTAATCTTGATATACCTGAGAACAATACATTTTTGTTACCGCGAGATATATTGGCAGCTGCAGATCATTTGATTGGACTGAAATTTGGAATGGGTACACTTGACGATATGAATCAATTTCATATTTAA

Coding sequence (CDS)

ATGGCTAAATTTGACAAAGGGATTGTGAGGCTCATTACTTCAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAAACAGTATATAAGGCATACCCAGATTGGTCGACGAAATCTGAACCAGAGACTTAATCTTGATATACCTGAGAACAATACATTTTTGTTACCGCGAGATATATTGGCAGCTGCAGATCATTTGATTGGACTGAAATTTGGAATGGGTACACTTGACGATATGAATCAATTTCATATTTAA

Protein sequence

MAKFDKGIVRLITSTSPRVPRMDLLVVERVAQKQYIRHTQIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMNQFHI

Homology

[Close]

BLAST of Clc10G05877 vs. NCBI nr
Match: AHM89856.1 (RNA polymerase beta subunit [Lagenaria siceraria])

HSP 1 Score: 99.0 bits (245), Expect = 2.3e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. NCBI nr
Match: YP_009753166.1 (RNA polymerase subunit beta [Trichosanthes truncata] >QIT06238.1 RNA polymerase subunit beta [Trichosanthes truncata])

HSP 1 Score: 99.0 bits (245), Expect = 2.3e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. NCBI nr
Match: AHM88854.1 (RNA polymerase beta subunit, partial [Lagenaria siceraria])

HSP 1 Score: 99.0 bits (245), Expect = 2.3e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 248 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 295

[Close]

BLAST of Clc10G05877 vs. NCBI nr
Match: YP_009753697.1 (RNA polymerase subunit beta [Trichosanthes nervifolia] >QIT05308.1 RNA polymerase subunit beta [Trichosanthes nervifolia])

HSP 1 Score: 99.0 bits (245), Expect = 2.3e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. NCBI nr
Match: AHM90682.1 (RNA polymerase beta subunit [Lagenaria siceraria])

HSP 1 Score: 99.0 bits (245), Expect = 2.3e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot
Match: Q4VZP1 (DNA-directed RNA polymerase subunit beta OS=Cucumis sativus OX=3659 GN=rpoB PE=3 SV=2)

HSP 1 Score: 95.9 bits (237), Expect = 2.5e-19
Identity = 46/48 (95.83%), Postives = 47/48 (97.92%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLL RDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLQRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot
Match: P11703 (DNA-directed RNA polymerase subunit beta OS=Spinacia oleracea OX=3562 GN=rpoB PE=3 SV=1)

HSP 1 Score: 95.9 bits (237), Expect = 2.5e-19
Identity = 44/48 (91.67%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRN+N+RLNLDIPENNTFLLPRDILAAADHLIG+KFGMGTLDDMN
Sbjct: 260 RIGRRNMNRRLNLDIPENNTFLLPRDILAAADHLIGMKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot
Match: A9L988 (DNA-directed RNA polymerase subunit beta OS=Lemna minor OX=4472 GN=rpoB PE=3 SV=1)

HSP 1 Score: 95.1 bits (235), Expect = 4.3e-19
Identity = 43/48 (89.58%), Postives = 47/48 (97.92%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRN+NQRLNLDIP NNTFLLPRD+LAAADHLIG+KFGMGTLDDMN
Sbjct: 260 RIGRRNINQRLNLDIPHNNTFLLPRDVLAAADHLIGMKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot
Match: Q49L06 (DNA-directed RNA polymerase subunit beta OS=Eucalyptus globulus subsp. globulus OX=71271 GN=rpoB PE=3 SV=1)

HSP 1 Score: 94.7 bits (234), Expect = 5.6e-19
Identity = 43/48 (89.58%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRN+N+RLNLDIP+NNTFLLPRDILAAADHLIG+KFGMGTLDDMN
Sbjct: 260 RIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot
Match: A7Y3B9 (DNA-directed RNA polymerase subunit beta OS=Ipomoea purpurea OX=4121 GN=rpoB PE=3 SV=1)

HSP 1 Score: 94.7 bits (234), Expect = 5.6e-19
Identity = 43/48 (89.58%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRN+N+RLNLDIP+NNTFLLPRD+LAAADHLIGLKFGMGTLDDMN
Sbjct: 257 RIGRRNMNRRLNLDIPQNNTFLLPRDLLAAADHLIGLKFGMGTLDDMN 304

[Close]

BLAST of Clc10G05877 vs. ExPASy TrEMBL
Match: A0A6H0ETN6 (DNA-directed RNA polymerase subunit beta OS=Trichosanthes kirilowii OX=3677 GN=rpoB PE=3 SV=1)

HSP 1 Score: 99.0 bits (245), Expect = 1.1e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy TrEMBL
Match: A0A1P8LDX8 (DNA-directed RNA polymerase subunit beta OS=Citrullus mucosospermus OX=519315 GN=rpoB PE=3 SV=1)

HSP 1 Score: 99.0 bits (245), Expect = 1.1e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy TrEMBL
Match: A0A6M3RVI4 (DNA-directed RNA polymerase subunit beta OS=Trichosanthes kirilowii var. japonica OX=61011 GN=rpoB PE=3 SV=1)

HSP 1 Score: 99.0 bits (245), Expect = 1.1e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy TrEMBL
Match: A0A2Z2CGF9 (DNA-directed RNA polymerase subunit beta OS=Coccinia grandis OX=387127 GN=rpoB PE=3 SV=1)

HSP 1 Score: 99.0 bits (245), Expect = 1.1e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. ExPASy TrEMBL
Match: X2F5U4 (DNA-directed RNA polymerase subunit beta OS=Lagenaria siceraria OX=3668 GN=rpoB PE=3 SV=1)

HSP 1 Score: 99.0 bits (245), Expect = 1.1e-17
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN
Sbjct: 260 RIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 307

[Close]

BLAST of Clc10G05877 vs. TAIR 10
Match: ATCG00190.1 (RNA polymerase subunit beta )

HSP 1 Score: 89.0 bits (219), Expect = 2.2e-18
Identity = 40/48 (83.33%), Postives = 46/48 (95.83%), Query Frame = 0


Query: 40  QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMN 88
           +IGRRN+N RLNL+IP+NN FLLPRD+LAAADHLIG+KFGMGTLDDMN
Sbjct: 260 RIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMN 307

The following BLAST results are available for this feature:

BLAST of Clc10G05877 vs. NCBI nr


Match Name	E-value	Identity	Description
AHM89856.1	2.3e-17	97.92	RNA polymerase beta subunit [Lagenaria siceraria]	[more]
YP_009753166.1	2.3e-17	97.92	RNA polymerase subunit beta [Trichosanthes truncata] >QIT06238.1 RNA polymerase ...	[more]
AHM88854.1	2.3e-17	97.92	RNA polymerase beta subunit, partial [Lagenaria siceraria]	[more]
YP_009753697.1	2.3e-17	97.92	RNA polymerase subunit beta [Trichosanthes nervifolia] >QIT05308.1 RNA polymeras...	[more]
AHM90682.1	2.3e-17	97.92	RNA polymerase beta subunit [Lagenaria siceraria]	[more]

BLAST of Clc10G05877 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q4VZP1	2.5e-19	95.83	DNA-directed RNA polymerase subunit beta OS=Cucumis sativus OX=3659 GN=rpoB PE=3...	[more]
P11703	2.5e-19	91.67	DNA-directed RNA polymerase subunit beta OS=Spinacia oleracea OX=3562 GN=rpoB PE...	[more]
A9L988	4.3e-19	89.58	DNA-directed RNA polymerase subunit beta OS=Lemna minor OX=4472 GN=rpoB PE=3 SV=...	[more]
Q49L06	5.6e-19	89.58	DNA-directed RNA polymerase subunit beta OS=Eucalyptus globulus subsp. globulus ...	[more]
A7Y3B9	5.6e-19	89.58	DNA-directed RNA polymerase subunit beta OS=Ipomoea purpurea OX=4121 GN=rpoB PE=...	[more]

BLAST of Clc10G05877 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6H0ETN6	1.1e-17	97.92	DNA-directed RNA polymerase subunit beta OS=Trichosanthes kirilowii OX=3677 GN=r...	[more]
A0A1P8LDX8	1.1e-17	97.92	DNA-directed RNA polymerase subunit beta OS=Citrullus mucosospermus OX=519315 GN...	[more]
A0A6M3RVI4	1.1e-17	97.92	DNA-directed RNA polymerase subunit beta OS=Trichosanthes kirilowii var. japonic...	[more]
A0A2Z2CGF9	1.1e-17	97.92	DNA-directed RNA polymerase subunit beta OS=Coccinia grandis OX=387127 GN=rpoB P...	[more]
X2F5U4	1.1e-17	97.92	DNA-directed RNA polymerase subunit beta OS=Lagenaria siceraria OX=3668 GN=rpoB ...	[more]

BLAST of Clc10G05877 vs. TAIR 10


Match Name	E-value	Identity	Description
ATCG00190.1	2.2e-18	83.33	RNA polymerase subunit beta	[more]

InterPro

Analysis Name: InterPro Annotations of Watermelon (cordophanus) v2
Date Performed: 2022-01-31

Position :

Zoom :

x 1


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR007642	RNA polymerase Rpb2, domain 2	PFAM	PF04561	RNA_pol_Rpb2_2	coord: 32..89 e-value: 8.5E-14 score: 51.6
IPR037034	RNA polymerase Rpb2, domain 2 superfamily	GENE3D	3.90.1110.10	RNA polymerase Rpb2, domain 2	coord: 8..85 e-value: 8.3E-11 score: 44.2
None	No IPR available	PANTHER	PTHR20856:SF30	DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA	coord: 25..89
IPR015712	DNA-directed RNA polymerase, subunit 2	PANTHER	PTHR20856	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	coord: 25..89

Relationships

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


Feature Name	Unique Name	Type
Clc10G05877.1	Clc10G05877.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006351	transcription, DNA-templated
cellular_component	GO:0009507	chloroplast
molecular_function	GO:0003677	DNA binding
molecular_function	GO:0003899	DNA-directed 5'-3' RNA polymerase activity
molecular_function	GO:0032549	ribonucleoside binding