ClCG10G006060 (gene) Watermelon (Charleston Gray)

Overview
NameClCG10G006060
Typegene
OrganismCitrullus lanatus (Watermelon (Charleston Gray))
DescriptionDNA-directed RNA polymerase subunit beta
LocationCG_Chr10 : 8099411 .. 8101018 (+)
Genome Viewer
Sequences
The following sequences are available for this feature:

Gene sequence (with intron)

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

mRNA sequence

ATGGCTAAATTTGACAAAGGGATTGTGAGGCTCATTACTTCAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAAACAGTATATAAGGCATACCCAGATTGGTCGACGAAATCTGAACCAGAGACTTAATCTTGATATACCTGAGAACAATACATTTTTGTTACCGCGAGATATATTGGCAGCTGCAGATCATTTGATTGGACTGAAATTTGGAATGGGTACACTTGACGATATGAATCAATTTCATATTTAA

Coding sequence (CDS)

ATGGCTAAATTTGACAAAGGGATTGTGAGGCTCATTACTTCAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAAACAGTATATAAGGCATACCCAGATTGGTCGACGAAATCTGAACCAGAGACTTAATCTTGATATACCTGAGAACAATACATTTTTGTTACCGCGAGATATATTGGCAGCTGCAGATCATTTGATTGGACTGAAATTTGGAATGGGTACACTTGACGATATGAATCAATTTCATATTTAA

Protein sequence

MAKFDKGIVRLITSTSPRVPRMDLLVVERVAQKQYIRHTQIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLDDMNQFHI
Homology
[Close]
BLAST of ClCG10G006060 vs. Swiss-Prot
Match: RPOB_SPIOL (DNA-directed RNA polymerase subunit beta OS=Spinacia oleracea GN=rpoB PE=3 SV=1)

HSP 1 Score: 95.5 bits (236), Expect = 3.2e-19
Identity = 44/48 (91.67%), Postives = 46/48 (95.83%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. Swiss-Prot
Match: RPOB_CUCSA (DNA-directed RNA polymerase subunit beta OS=Cucumis sativus GN=rpoB PE=3 SV=2)

HSP 1 Score: 95.5 bits (236), Expect = 3.2e-19
Identity = 46/48 (95.83%), Postives = 45/48 (93.75%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. Swiss-Prot
Match: RPOB_LEMMI (DNA-directed RNA polymerase subunit beta OS=Lemna minor GN=rpoB PE=3 SV=1)

HSP 1 Score: 94.7 bits (234), Expect = 5.4e-19
Identity = 43/48 (89.58%), Postives = 45/48 (93.75%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. Swiss-Prot
Match: RPOB_EUCGG (DNA-directed RNA polymerase subunit beta OS=Eucalyptus globulus subsp. globulus GN=rpoB PE=3 SV=1)

HSP 1 Score: 94.4 bits (233), Expect = 7.1e-19
Identity = 43/48 (89.58%), Postives = 46/48 (95.83%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. Swiss-Prot
Match: RPOB_PIPCE (DNA-directed RNA polymerase subunit beta OS=Piper cenocladum GN=rpoB PE=3 SV=1)

HSP 1 Score: 94.4 bits (233), Expect = 7.1e-19
Identity = 45/63 (71.43%), Postives = 52/63 (82.54%), Query Frame = 1 

Query: 29  RVAQKQYIRHT----QIGRRNLNQRLNLDIPENNTFLLPRDILAAADHLIGLKFGMGTLD 88
           R  QK++ +      +IGRRN+N+RLNLDIP+NNTFLLPRD+LAAADHLIG+KFGMGTLD
Sbjct: 245 RELQKKFFQQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLD 304

[Close]
BLAST of ClCG10G006060 vs. TrEMBL
Match: A0A0S2IF22_9ROSI (DNA-directed RNA polymerase subunit beta OS=Cucurbita ficifolia GN=rpoB PE=3 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 4.2e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. TrEMBL
Match: A0A0S2IFV9_9ROSI (DNA-directed RNA polymerase subunit beta OS=Cucurbita okeechobeensis GN=rpoB PE=3 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 4.2e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. TrEMBL
Match: A0A0S2IGH2_CUCPE (DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo subsp. fraterna GN=rpoB PE=3 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 4.2e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. TrEMBL
Match: A0A0S2IHF1_CUCPE (DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo var. texana GN=rpoB PE=3 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 4.2e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. TrEMBL
Match: A0A0S2IF40_9ROSI (DNA-directed RNA polymerase subunit beta OS=Cucurbita lundelliana GN=rpoB PE=3 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 4.2e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. TAIR10
Match: ATCG00190.1 (ATCG00190.1 RNA polymerase subunit beta)

HSP 1 Score: 88.6 bits (218), Expect = 2.2e-18
Identity = 40/48 (83.33%), Postives = 44/48 (91.67%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. NCBI nr
Match: gi|952954786|gb|ALO22144.1| (RpoB (plastid) [Cucurbita ficifolia])

HSP 1 Score: 98.6 bits (244), Expect = 6.0e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. NCBI nr
Match: gi|595647253|gb|AHM90682.1| (RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria])

HSP 1 Score: 98.6 bits (244), Expect = 6.0e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. NCBI nr
Match: gi|952954810|gb|ALO22167.1| (RpoB (plastid) [Cucurbita foetidissima])

HSP 1 Score: 98.6 bits (244), Expect = 6.0e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. NCBI nr
Match: gi|595647373|gb|AHM90800.1| (RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria])

HSP 1 Score: 98.6 bits (244), Expect = 6.0e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

[Close]
BLAST of ClCG10G006060 vs. NCBI nr
Match: gi|952954367|gb|ALO21731.1| (RpoB (plastid) [Cucurbita argyrosperma])

HSP 1 Score: 98.6 bits (244), Expect = 6.0e-18
Identity = 47/48 (97.92%), Postives = 48/48 (100.00%), Query Frame = 1 

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

The following BLAST results are available for this feature:
BLAST of ClCG10G006060 vs. Swiss-Prot
Match NameE-valueIdentityDescription
RPOB_SPIOL3.2e-1991.67DNA-directed RNA polymerase subunit beta OS=Spinacia oleracea GN=rpoB PE=3 SV=1[more]
RPOB_CUCSA3.2e-1995.83DNA-directed RNA polymerase subunit beta OS=Cucumis sativus GN=rpoB PE=3 SV=2[more]
RPOB_LEMMI5.4e-1989.58DNA-directed RNA polymerase subunit beta OS=Lemna minor GN=rpoB PE=3 SV=1[more]
RPOB_EUCGG7.1e-1989.58DNA-directed RNA polymerase subunit beta OS=Eucalyptus globulus subsp. globulus ... [more]
RPOB_PIPCE7.1e-1971.43DNA-directed RNA polymerase subunit beta OS=Piper cenocladum GN=rpoB PE=3 SV=1[more]
BLAST of ClCG10G006060 vs. TrEMBL
Match NameE-valueIdentityDescription
A0A0S2IF22_9ROSI4.2e-1897.92DNA-directed RNA polymerase subunit beta OS=Cucurbita ficifolia GN=rpoB PE=3 SV=... [more]
A0A0S2IFV9_9ROSI4.2e-1897.92DNA-directed RNA polymerase subunit beta OS=Cucurbita okeechobeensis GN=rpoB PE=... [more]
A0A0S2IGH2_CUCPE4.2e-1897.92DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo subsp. fraterna GN=rp... [more]
A0A0S2IHF1_CUCPE4.2e-1897.92DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo var. texana GN=rpoB P... [more]
A0A0S2IF40_9ROSI4.2e-1897.92DNA-directed RNA polymerase subunit beta OS=Cucurbita lundelliana GN=rpoB PE=3 S... [more]
BLAST of ClCG10G006060 vs. TAIR10
Match NameE-valueIdentityDescription
ATCG00190.12.2e-1883.33ATCG00190.1 RNA polymerase subunit beta[more]
BLAST of ClCG10G006060 vs. NCBI nr
Match NameE-valueIdentityDescription
gi|952954786|gb|ALO22144.1|6.0e-1897.92RpoB (plastid) [Cucurbita ficifolia][more]
gi|595647253|gb|AHM90682.1|6.0e-1897.92RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria][more]
gi|952954810|gb|ALO22167.1|6.0e-1897.92RpoB (plastid) [Cucurbita foetidissima][more]
gi|595647373|gb|AHM90800.1|6.0e-1897.92RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria][more]
gi|952954367|gb|ALO21731.1|6.0e-1897.92RpoB (plastid) [Cucurbita argyrosperma][more]
Annotated Terms
The following terms have been associated with this gene:
Vocabulary: INTERPRO
TermDefinition
IPR007642RNA_pol_Rpb2_2
Vocabulary: Biological Process
TermDefinition
GO:0006351transcription, DNA-templated
Vocabulary: Molecular Function
TermDefinition
GO:0003677DNA binding
GO:0003899DNA-directed RNA polymerase activity
GO Annotation
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006144 purine nucleobase metabolic process
biological_process GO:0006206 pyrimidine nucleobase metabolic process
biological_process GO:0006351 transcription, DNA-templated
cellular_component GO:0009507 chloroplast
cellular_component GO:0005730 nucleolus
molecular_function GO:0003677 DNA binding
molecular_function GO:0003899 DNA-directed RNA polymerase activity
molecular_function GO:0032549 ribonucleoside binding
Relationships

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

Feature NameUnique NameType
ClCG10G006060.1ClCG10G006060.1mRNA


InterPro
Analysis Name: InterPro Annotations of watermelon (Charleston Gray)
Date Performed: 2016-09-28
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007642RNA polymerase Rpb2, domain 2GENE3DG3DSA:3.90.1110.10coord: 38..86
score: 8.
IPR007642RNA polymerase Rpb2, domain 2PFAMPF04561RNA_pol_Rpb2_2coord: 32..89
score: 7.8

Synteny
The following gene(s) are orthologous to this gene:

None

The following gene(s) are paralogous to this gene:

None

The following block(s) are covering this gene:
GeneOrganismBlock
ClCG10G006060Silver-seed gourdcarwcgB0641
ClCG10G006060Silver-seed gourdcarwcgB0766
ClCG10G006060Cucumber (Chinese Long) v3cucwcgB194
ClCG10G006060Watermelon (97103) v2wcgwmbB038
ClCG10G006060Wax gourdwcgwgoB080
ClCG10G006060Cucumber (Gy14) v1cgywcgB049
ClCG10G006060Cucumber (Gy14) v1cgywcgB074
ClCG10G006060Cucurbita maxima (Rimu)cmawcgB283
ClCG10G006060Cucurbita maxima (Rimu)cmawcgB614
ClCG10G006060Cucurbita moschata (Rifu)cmowcgB274
ClCG10G006060Cucurbita moschata (Rifu)cmowcgB615
ClCG10G006060Wild cucumber (PI 183967)cpiwcgB190
ClCG10G006060Cucumber (Chinese Long) v2cuwcgB189
ClCG10G006060Melon (DHL92) v3.5.1mewcgB416
ClCG10G006060Watermelon (97103) v1wcgwmB052
ClCG10G006060Cucurbita pepo (Zucchini)cpewcgB001
ClCG10G006060Cucurbita pepo (Zucchini)cpewcgB349
ClCG10G006060Bottle gourd (USVL1VR-Ls)lsiwcgB318
ClCG10G006060Cucumber (Gy14) v2cgybwcgB174
ClCG10G006060Melon (DHL92) v3.6.1medwcgB402