ClCG07G004170.1 (mRNA) Watermelon (Charleston Gray)

Overview
NameClCG07G004170.1
TypemRNA
OrganismCitrullus lanatus (Watermelon (Charleston Gray))
DescriptionDNA-directed RNA polymerase subunit beta
LocationCG_Chr07 : 4875532 .. 4875941 (-)
Sequence length228
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.
ATGAATTCCCTAGAAACTTCTATAGTAAATGAACTATATAGAATTGTGATCAGTCAAATATTGCAAAGCCTCGGTATCTATTACCGGTCAGAATTGGACCATAACGAAATTTTGGTCTATACCGGCACCATAATATCTGATTGGGGAGGAAGATTAGAATTAGAGATTGACCGAAAAGCAAGGATATGGGCTCGTGTGAGTAGGAAACAGAAAATATCTATTCTAGTTCTATCATAGCTATGAGTTCGAATCTAAAAGAAATTCTTGAGAATGTTTGCTACCTTGAAATTTTTTTGTCTTACCTAAATGATAAGGAGAAAAACAAAATTGGATCAAAAGAAAATGTTATTTTGGAGTTTTATCAACAATTTTTTTGTGTAGGTAGAGATCCGGTATTTTCAGAATCCTTA

mRNA sequence

ATGAATTCCCTAGAAACTTCTATAGTAAATGAACTATATAGAATTGTGATCAGTCAAATATTGCAAAGCCTCGGTATCTATTACCGGTCAGAATTGGACCATAACGAAATTTTGGTCTATACCGGCACCATAATATCTGATTGGGGAGGAAGATTAGAATTAGAGATTGACCGAAAAGCAAGGATATGGGCTCGTGTGAGTAGAGATCCGGTATTTTCAGAATCCTTA

Coding sequence (CDS)

ATGAATTCCCTAGAAACTTCTATAGTAAATGAACTATATAGAATTGTGATCAGTCAAATATTGCAAAGCCTCGGTATCTATTACCGGTCAGAATTGGACCATAACGAAATTTTGGTCTATACCGGCACCATAATATCTGATTGGGGAGGAAGATTAGAATTAGAGATTGACCGAAAAGCAAGGATATGGGCTCGTGTGAGTAGAGATCCGGTATTTTCAGAATCCTTA

Protein sequence

MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKARIWARVSRDPVFSESL
Homology
[Close]
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match: RPOB_CUCSA (DNA-directed RNA polymerase subunit beta OS=Cucumis sativus GN=rpoB PE=3 SV=2)

HSP 1 Score: 123.2 bits (308), Expect = 1.2e-27
Identity = 63/68 (92.65%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match: RPOB_VITVI (DNA-directed RNA polymerase subunit beta OS=Vitis vinifera GN=rpoB PE=3 SV=1)

HSP 1 Score: 121.7 bits (304), Expect = 3.4e-27
Identity = 61/68 (89.71%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVI+QILQS GIYYRSELDHN I VYTGTI+SDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVINQILQSPGIYYRSELDHNGISVYTGTIVSDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match: RPOB_OENEH (DNA-directed RNA polymerase subunit beta OS=Oenothera elata subsp. hookeri GN=rpoB PE=3 SV=2)

HSP 1 Score: 121.3 bits (303), Expect = 4.5e-27
Identity = 61/68 (89.71%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 108 MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 167

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 168 RIWARVSR 175

[Close]
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match: RPOB_GOSBA (DNA-directed RNA polymerase subunit beta OS=Gossypium barbadense GN=rpoB PE=3 SV=1)

HSP 1 Score: 121.3 bits (303), Expect = 4.5e-27
Identity = 61/68 (89.71%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match: RPOB_GOSHI (DNA-directed RNA polymerase subunit beta OS=Gossypium hirsutum GN=rpoB PE=3 SV=1)

HSP 1 Score: 121.3 bits (303), Expect = 4.5e-27
Identity = 61/68 (89.71%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match: A0A0E3N260_HIBSY (DNA-directed RNA polymerase subunit beta OS=Hibiscus syriacus GN=rpoB PE=3 SV=1)

HSP 1 Score: 124.0 bits (310), Expect = 7.7e-26
Identity = 62/68 (91.18%), Postives = 64/68 (94.12%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHNEI VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNEISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match: A0A162J352_HIBSY (RNA polymerase beta subunit OS=Hibiscus syriacus GN=rpoB PE=4 SV=1)

HSP 1 Score: 124.0 bits (310), Expect = 7.7e-26
Identity = 62/68 (91.18%), Postives = 64/68 (94.12%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHNEI VYTGTIISDWGGRLELEIDRKA
Sbjct: 99  MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNEISVYTGTIISDWGGRLELEIDRKA 158

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 159 RIWARVSR 166

[Close]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match: A0A0S2IFV9_9ROSI (DNA-directed RNA polymerase subunit beta OS=Cucurbita okeechobeensis GN=rpoB PE=3 SV=1)

HSP 1 Score: 123.2 bits (308), Expect = 1.3e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match: A0A0S2IFB7_9ROSI (DNA-directed RNA polymerase subunit beta OS=Cucurbita andreana GN=rpoB PE=3 SV=1)

HSP 1 Score: 123.2 bits (308), Expect = 1.3e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match: A0A0S2IG32_CUCPE (DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo subsp. ovifera GN=rpoB PE=3 SV=1)

HSP 1 Score: 123.2 bits (308), Expect = 1.3e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. TAIR10
Match: ATCG00190.1 (ATCG00190.1 RNA polymerase subunit beta)

HSP 1 Score: 118.6 bits (296), Expect = 1.6e-27
Identity = 59/68 (86.76%), Postives = 61/68 (89.71%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYY+SELDHN I VYTGTIISDWGGRLELEID+KA
Sbjct: 107 MNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLELEIDKKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match: gi|813427779|ref|YP_009132931.1| (RNA polymerase beta subunit (chloroplast) [Hibiscus syriacus])

HSP 1 Score: 124.0 bits (310), Expect = 1.1e-25
Identity = 62/68 (91.18%), Postives = 64/68 (94.12%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN +YRIVI+QILQS GIYYRSELDHNEI VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNEISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match: gi|590000407|ref|YP_009004036.1| (RNA polymerase beta subunit [Cucumis hystrix])

HSP 1 Score: 123.2 bits (308), Expect = 1.9e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match: gi|952954367|gb|ALO21731.1| (RpoB (plastid) [Cucurbita argyrosperma])

HSP 1 Score: 123.2 bits (308), Expect = 1.9e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match: gi|68164795|ref|YP_247591.1| (RNA polymerase beta subunit [Cucumis sativus])

HSP 1 Score: 123.2 bits (308), Expect = 1.9e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

[Close]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match: gi|595645751|gb|AHM89205.1| (RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria])

HSP 1 Score: 123.2 bits (308), Expect = 1.9e-25
Identity = 63/68 (92.65%), Postives = 63/68 (92.65%), Query Frame = 1 

Query: 1   MNSLETSIVNELYRIVISQILQSLGIYYRSELDHNEILVYTGTIISDWGGRLELEIDRKA 60
           MNSL TSIVN LYRIVISQILQS GIYYRSELDHN I VYTGTIISDWGGRLELEIDRKA
Sbjct: 107 MNSLGTSIVNGLYRIVISQILQSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

Query: 61  RIWARVSR 69
           RIWARVSR
Sbjct: 167 RIWARVSR 174

The following BLAST results are available for this feature:
BLAST of ClCG07G004170.1 vs. Swiss-Prot
Match NameE-valueIdentityDescription
RPOB_CUCSA1.2e-2792.65DNA-directed RNA polymerase subunit beta OS=Cucumis sativus GN=rpoB PE=3 SV=2[more]
RPOB_VITVI3.4e-2789.71DNA-directed RNA polymerase subunit beta OS=Vitis vinifera GN=rpoB PE=3 SV=1[more]
RPOB_OENEH4.5e-2789.71DNA-directed RNA polymerase subunit beta OS=Oenothera elata subsp. hookeri GN=rp... [more]
RPOB_GOSBA4.5e-2789.71DNA-directed RNA polymerase subunit beta OS=Gossypium barbadense GN=rpoB PE=3 SV... [more]
RPOB_GOSHI4.5e-2789.71DNA-directed RNA polymerase subunit beta OS=Gossypium hirsutum GN=rpoB PE=3 SV=1[more]
BLAST of ClCG07G004170.1 vs. TrEMBL
Match NameE-valueIdentityDescription
A0A0E3N260_HIBSY7.7e-2691.18DNA-directed RNA polymerase subunit beta OS=Hibiscus syriacus GN=rpoB PE=3 SV=1[more]
A0A162J352_HIBSY7.7e-2691.18RNA polymerase beta subunit OS=Hibiscus syriacus GN=rpoB PE=4 SV=1[more]
A0A0S2IFV9_9ROSI1.3e-2592.65DNA-directed RNA polymerase subunit beta OS=Cucurbita okeechobeensis GN=rpoB PE=... [more]
A0A0S2IFB7_9ROSI1.3e-2592.65DNA-directed RNA polymerase subunit beta OS=Cucurbita andreana GN=rpoB PE=3 SV=1[more]
A0A0S2IG32_CUCPE1.3e-2592.65DNA-directed RNA polymerase subunit beta OS=Cucurbita pepo subsp. ovifera GN=rpo... [more]
BLAST of ClCG07G004170.1 vs. TAIR10
Match NameE-valueIdentityDescription
ATCG00190.11.6e-2786.76ATCG00190.1 RNA polymerase subunit beta[more]
BLAST of ClCG07G004170.1 vs. NCBI nr
Match NameE-valueIdentityDescription
gi|813427779|ref|YP_009132931.1|1.1e-2591.18RNA polymerase beta subunit (chloroplast) [Hibiscus syriacus][more]
gi|590000407|ref|YP_009004036.1|1.9e-2592.65RNA polymerase beta subunit [Cucumis hystrix][more]
gi|952954367|gb|ALO21731.1|1.9e-2592.65RpoB (plastid) [Cucurbita argyrosperma][more]
gi|68164795|ref|YP_247591.1|1.9e-2592.65RNA polymerase beta subunit [Cucumis sativus][more]
gi|595645751|gb|AHM89205.1|1.9e-2592.65RNA polymerase beta subunit (chloroplast) [Lagenaria siceraria][more]
Annotated Terms
The following terms have been associated with this mRNA:
Vocabulary: INTERPRO
TermDefinition
IPR007642RNA_pol_Rpb2_2
IPR015712DNA-dir_RNA_pol_su2
Vocabulary: Biological Process
TermDefinition
GO:0006351transcription, DNA-templated
Vocabulary: Molecular Function
TermDefinition
GO:0003677DNA binding
GO:0003899DNA-directed RNA polymerase activity
GO:0032549ribonucleoside binding
GO Annotation
GO Assignments
This mRNA is annotated with the following GO terms.
Category Term Accession Term Name
biological_process GO:0006351 transcription, DNA-templated
biological_process GO:0006144 purine nucleobase metabolic process
biological_process GO:0006206 pyrimidine nucleobase metabolic process
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

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

Feature NameUnique NameType
ClCG07G004170ClCG07G004170gene


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

Feature NameUnique NameType
ClCG07G004170.1ClCG07G004170.1-proteinpolypeptide


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

Feature NameUnique NameType
ClCG07G004170.1.cds2ClCG07G004170.1.cds2CDS
ClCG07G004170.1.cds1ClCG07G004170.1.cds1CDS


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: 25..70
score: 1.
IPR007642RNA polymerase Rpb2, domain 2PFAMPF04561RNA_pol_Rpb2_2coord: 25..68
score: 3.
IPR015712DNA-directed RNA polymerase, subunit 2PANTHERPTHR20856DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2coord: 6..68
score: 1.0
NoneNo IPR availablePANTHERPTHR20856:SF20DNA-DIRECTED RNA POLYMERASE SUBUNIT BETAcoord: 6..68
score: 1.0
NoneNo IPR availableunknownSSF64484beta and beta-prime subunits of DNA dependent RNA-polymerasecoord: 8..68
score: 3.3