ClCG02G000115 (gene) Watermelon (Charleston Gray) v2.5

Overview


Name	ClCG02G000115
Type	gene
Organism	Citrullus lanatus subsp. vulgaris cv. Charleston Gray (Watermelon (Charleston Gray) v2.5)
Description	DNA-directed RNA polymerase subunit beta
Location	CG_Chr02: 168702 .. 168953 (-)
RNA-Seq Expression	ClCG02G000115
Synteny	ClCG02G000115

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.

ATGATAAAGGTAGCGGGAAGACATGGAAATAAAGGTATTGTTTCAAAAATTTTGCCTAGAGAAGATATGCCTTATTTGCAAAATGGAAGACCTATTGATATGGTTTTCAATCCATTAGGAGTCCCCTCACGAATGAATGTAGGACAGATATTTGAGTGCTCACTCGGGTTAGTGGGATATACTTCTATCACAACATATATAAGTATTAGAAGTCTATCACACGTAGCAATGAACGATATGTTTTGTGGTTAA

mRNA sequence

ATGATAAAGGTAGCGGGAAGACATGGAAATAAAGGTATTGTTTCAAAAATTTTGCCTAGAGAAGATATGCCTTATTTGCAAAATGGAAGACCTATTGATATGGTTTTCAATCCATTAGGAGTCCCCTCACGAATGAATGTAGGACAGATATTTGAGTGCTCACTCGGGTTAGTGGGATATACTTCTATCACAACATATATAAGTATTAGAAGTCTATCACACGTAGCAATGAACGATATGTTTTGTGGTTAA

Coding sequence (CDS)

ATGATAAAGGTAGCGGGAAGACATGGAAATAAAGGTATTGTTTCAAAAATTTTGCCTAGAGAAGATATGCCTTATTTGCAAAATGGAAGACCTATTGATATGGTTTTCAATCCATTAGGAGTCCCCTCACGAATGAATGTAGGACAGATATTTGAGTGCTCACTCGGGTTAGTGGGATATACTTCTATCACAACATATATAAGTATTAGAAGTCTATCACACGTAGCAATGAACGATATGTTTTGTGGTTAA

Protein sequence

MIKVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVGYTSITTYISIRSLSHVAMNDMFCG

Homology

[Close]

BLAST of ClCG02G000115 vs. NCBI nr
Match: AHM89856.1 (RNA polymerase beta subunit [Lagenaria siceraria])

HSP 1 Score: 120.2 bits (300), Expect = 8.6e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. NCBI nr
Match: YP_009753166.1 (RNA polymerase subunit beta [Trichosanthes truncata] >QIT06238.1 RNA polymerase subunit beta [Trichosanthes truncata])

HSP 1 Score: 120.2 bits (300), Expect = 8.6e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. NCBI nr
Match: YP_009236272.1 (RNA polymerase beta subunit [Gynostemma pentaphyllum] >YP_009440149.1 RNA polymerase beta subunit [Gynostemma longipes] >AMF83983.1 RNA polymerase beta subunit [Gynostemma pentaphyllum] >ANI25177.1 RNA polymerase beta subunit [Gynostemma pentaphyllum] >ATG86892.1 RNA polymerase beta subunit [Gynostemma longipes])

HSP 1 Score: 120.2 bits (300), Expect = 8.6e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. NCBI nr
Match: YP_009752827.1 (RNA polymerase subunit beta [Baijiania yunnanensis] >QIT05899.1 RNA polymerase subunit beta [Baijiania yunnanensis])

HSP 1 Score: 120.2 bits (300), Expect = 8.6e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. NCBI nr
Match: AHM88854.1 (RNA polymerase beta subunit, partial [Lagenaria siceraria])

HSP 1 Score: 120.2 bits (300), Expect = 8.6e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 807 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 863

[Close]

BLAST of ClCG02G000115 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: 120.2 bits (300), Expect = 1.1e-26
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy Swiss-Prot
Match: Q09MI6 (DNA-directed RNA polymerase subunit beta OS=Citrus sinensis OX=2711 GN=rpoB PE=3 SV=1)

HSP 1 Score: 117.1 bits (292), Expect = 9.6e-26
Identity = 53/57 (92.98%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPR+DMPYLQ+GRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy Swiss-Prot
Match: Q09X25 (DNA-directed RNA polymerase subunit beta OS=Morus indica OX=248361 GN=rpoB PE=3 SV=1)

HSP 1 Score: 117.1 bits (292), Expect = 9.6e-26
Identity = 53/57 (92.98%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPR+DMPYLQ+GRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy Swiss-Prot
Match: A4QJA7 (DNA-directed RNA polymerase subunit beta OS=Aethionema cordifolium OX=434059 GN=rpoB PE=3 SV=1)

HSP 1 Score: 116.7 bits (291), Expect = 1.3e-25
Identity = 52/57 (91.23%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGI+SKILPR+DMPYLQ+GRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 822 KVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 878

[Close]

BLAST of ClCG02G000115 vs. ExPASy Swiss-Prot
Match: A4QJJ1 (DNA-directed RNA polymerase subunit beta OS=Aethionema grandiflorum OX=72657 GN=rpoB PE=3 SV=1)

HSP 1 Score: 116.7 bits (291), Expect = 1.3e-25
Identity = 52/57 (91.23%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGI+SKILPR+DMPYLQ+GRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 822 KVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 878

[Close]

BLAST of ClCG02G000115 vs. ExPASy TrEMBL
Match: A0A218KG28 (DNA-directed RNA polymerase subunit beta OS=Cucumis sativus var. hardwickii OX=319220 GN=rpoB PE=3 SV=1)

HSP 1 Score: 120.2 bits (300), Expect = 4.2e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 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: 120.2 bits (300), Expect = 4.2e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy TrEMBL
Match: A0A1X9Q1B9 (DNA-directed RNA polymerase subunit beta OS=Cucumis sativus OX=3659 GN=rpoB PE=3 SV=1)

HSP 1 Score: 120.2 bits (300), Expect = 4.2e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy TrEMBL
Match: A0A249RZI0 (DNA-directed RNA polymerase subunit beta OS=Cucumis melo var. cantalupensis OX=3658 GN=rpoB PE=3 SV=1)

HSP 1 Score: 120.2 bits (300), Expect = 4.2e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. ExPASy TrEMBL
Match: A0A1S4ETZ9 (DNA-directed RNA polymerase subunit beta OS=Cucumis melo OX=3656 GN=rpoB PE=3 SV=1)

HSP 1 Score: 120.2 bits (300), Expect = 4.2e-24
Identity = 55/57 (96.49%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGIVSKILPREDMPYLQNGRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 819 KVAGRHGNKGIVSKILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 875

[Close]

BLAST of ClCG02G000115 vs. TAIR 10
Match: ATCG00190.1 (RNA polymerase subunit beta )

HSP 1 Score: 116.7 bits (291), Expect = 8.9e-27
Identity = 52/57 (91.23%), Postives = 56/57 (98.25%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLVG 60
           KVAGRHGNKGI+SKILPR+DMPYLQ+GRP+DMVFNPLGVPSRMNVGQIFECSLGL G
Sbjct: 821 KVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 877

[Close]

BLAST of ClCG02G000115 vs. TAIR 10
Match: AT4G21710.1 (DNA-directed RNA polymerase family protein )

HSP 1 Score: 58.5 bits (140), Expect = 2.9e-09
Identity = 25/56 (44.64%), Postives = 34/56 (60.71%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSLGLV 59
           K + RHG KG V     +EDMP+   G   D++ NP  +PSRM +GQ+ EC +G V
Sbjct: 940 KFSSRHGQKGTVGMTYTQEDMPWTIEGVTPDIIVNPHAIPSRMTIGQLIECIMGKV 995

[Close]

BLAST of ClCG02G000115 vs. TAIR 10
Match: AT5G45140.1 (nuclear RNA polymerase C2 )

HSP 1 Score: 52.4 bits (124), Expect = 2.1e-07
Identity = 22/50 (44.00%), Postives = 32/50 (64.00%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFE 53
           K + RHG KG+   I+ +ED P+ + G   D++ NP G PSRM VG++ E
Sbjct: 915 KFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIE 964

[Close]

BLAST of ClCG02G000115 vs. TAIR 10
Match: AT1G29940.1 (nuclear RNA polymerase A2 )

HSP 1 Score: 45.1 bits (105), Expect = 3.3e-05
Identity = 21/52 (40.38%), Postives = 31/52 (59.62%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPY--LQNGRPIDMVFNPLGVPSRMNVGQIFE 53
           K + RHG KG+ S++ P  DMP+  +   RP D++ NP   PSRM +  + E
Sbjct: 898 KFSSRHGQKGVCSQLWPDIDMPFNGVTGMRP-DLIINPHAFPSRMTIAMLLE 948

[Close]

BLAST of ClCG02G000115 vs. TAIR 10
Match: AT3G18090.1 (nuclear RNA polymerase D2B )

HSP 1 Score: 42.7 bits (99), Expect = 1.6e-04
Identity = 18/53 (33.96%), Postives = 29/53 (54.72%), Query Frame = 0


Query: 3   KVAGRHGNKGIVSKILPREDMPYLQNGRPIDMVFNPLGVPSRMNVGQIFECSL 56
           K +  HG KG++  +  +++ P+   G   D+V NP   PSR   GQ+ E +L
Sbjct: 795 KFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAAL 847

The following BLAST results are available for this feature:

BLAST of ClCG02G000115 vs. NCBI nr


Match Name	E-value	Identity	Description
AHM89856.1	8.6e-24	96.49	RNA polymerase beta subunit [Lagenaria siceraria]	[more]
YP_009753166.1	8.6e-24	96.49	RNA polymerase subunit beta [Trichosanthes truncata] >QIT06238.1 RNA polymerase ...	[more]
YP_009236272.1	8.6e-24	96.49	RNA polymerase beta subunit [Gynostemma pentaphyllum] >YP_009440149.1 RNA polyme...	[more]
YP_009752827.1	8.6e-24	96.49	RNA polymerase subunit beta [Baijiania yunnanensis] >QIT05899.1 RNA polymerase s...	[more]
AHM88854.1	8.6e-24	96.49	RNA polymerase beta subunit, partial [Lagenaria siceraria]	[more]

BLAST of ClCG02G000115 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q4VZP1	1.1e-26	96.49	DNA-directed RNA polymerase subunit beta OS=Cucumis sativus OX=3659 GN=rpoB PE=3...	[more]
Q09MI6	9.6e-26	92.98	DNA-directed RNA polymerase subunit beta OS=Citrus sinensis OX=2711 GN=rpoB PE=3...	[more]
Q09X25	9.6e-26	92.98	DNA-directed RNA polymerase subunit beta OS=Morus indica OX=248361 GN=rpoB PE=3 ...	[more]
A4QJA7	1.3e-25	91.23	DNA-directed RNA polymerase subunit beta OS=Aethionema cordifolium OX=434059 GN=...	[more]
A4QJJ1	1.3e-25	91.23	DNA-directed RNA polymerase subunit beta OS=Aethionema grandiflorum OX=72657 GN=...	[more]

BLAST of ClCG02G000115 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A218KG28	4.2e-24	96.49	DNA-directed RNA polymerase subunit beta OS=Cucumis sativus var. hardwickii OX=3...	[more]
A0A6H0ETN6	4.2e-24	96.49	DNA-directed RNA polymerase subunit beta OS=Trichosanthes kirilowii OX=3677 GN=r...	[more]
A0A1X9Q1B9	4.2e-24	96.49	DNA-directed RNA polymerase subunit beta OS=Cucumis sativus OX=3659 GN=rpoB PE=3...	[more]
A0A249RZI0	4.2e-24	96.49	DNA-directed RNA polymerase subunit beta OS=Cucumis melo var. cantalupensis OX=3...	[more]
A0A1S4ETZ9	4.2e-24	96.49	DNA-directed RNA polymerase subunit beta OS=Cucumis melo OX=3656 GN=rpoB PE=3 SV...	[more]

BLAST of ClCG02G000115 vs. TAIR 10


Match Name	E-value	Identity	Description
ATCG00190.1	8.9e-27	91.23	RNA polymerase subunit beta	[more]
AT4G21710.1	2.9e-09	44.64	DNA-directed RNA polymerase family protein	[more]
AT5G45140.1	2.1e-07	44.00	nuclear RNA polymerase C2	[more]
AT1G29940.1	3.3e-05	40.38	nuclear RNA polymerase A2	[more]
AT3G18090.1	1.6e-04	33.96	nuclear RNA polymerase D2B	[more]

InterPro

Analysis Name: InterPro Annotations of Watermelon (Charleston Gray) v2.5
Date Performed: 2022-01-31


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	PFAM	PF00562	RNA_pol_Rpb2_6	coord: 3..61 e-value: 3.4E-30 score: 105.4
IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	GENE3D	2.40.270.10		coord: 2..76 e-value: 1.7E-32 score: 114.9
IPR015712	DNA-directed RNA polymerase, subunit 2	PANTHER	PTHR20856	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	coord: 3..59
None	No IPR available	PANTHER	PTHR20856:SF30	DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA	coord: 3..59
None	No IPR available	SUPERFAMILY	64484	beta and beta-prime subunits of DNA dependent RNA-polymerase	coord: 3..67

Relationships

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


Feature Name	Unique Name	Type
ClCG02G000115.1	ClCG02G000115.1	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