Cla97C01G013780 (gene) Watermelon (97103) v2

NameCla97C01G013780
Typegene
OrganismCitrullus lanatus (Watermelon (97103) v2)
DescriptionDNA-directed RNA polymerases II, IV and V subunit 12
LocationCla97Chr01 : 27600060 .. 27600739 (+)
The following sequences are available for this feature:

Gene sequence (with intron)

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

mRNA sequence

ATGGATCCTCAACCTGAACCAGTCAGCTACATCTGTGGAGATTGTGGAATGGAGAACACTCTGAAGCAGGGTGATGTTATACAGTGCCGAGAGTGTGGTTATCGTATTCTCTACAAGAAGCGCACCCGTCGCAAGTACAAAAGAGCCAGTGGGGTGAGCGAGCTTCCTAGTTCAGCAAATGAAAATAAGTTCCAACCATGGATACAACGATTTTCCATCATTGAGCTCAAAAGAAAAGAATGA

Coding sequence (CDS)

ATGGATCCTCAACCTGAACCAGTCAGCTACATCTGTGGAGATTGTGGAATGGAGAACACTCTGAAGCAGGGTGATGTTATACAGTGCCGAGAGTGTGGTTATCGTATTCTCTACAAGAAGCGCACCCGTCGCAAGTACAAAAGAGCCAGTGGGGTGAGCGAGCTTCCTAGTTCAGCAAATGAAAATAAGTTCCAACCATGGATACAACGATTTTCCATCATTGAGCTCAAAAGAAAAGAATGA

Protein sequence

MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVSELPSSANENKFQPWIQRFSIIELKRKE
BLAST of Cla97C01G013780 vs. NCBI nr
Match: PON74893.1 (RNA polymerase archaeal subunit P/eukaryotic subunit RPABC [Parasponia andersonii])

HSP 1 Score: 101.3 bits (251), Expect = 1.6e-18
Identity = 45/53 (84.91%), Postives = 47/53 (88.68%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVS 54
          MDPQPEPV+YICGDCGMENTLK GDVIQCRECGYRILYKKRTRRK  + S  S
Sbjct: 1  MDPQPEPVTYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRKIDQCSATS 53

BLAST of Cla97C01G013780 vs. NCBI nr
Match: POO03436.1 (RNA polymerase archaeal subunit P/eukaryotic subunit RPABC [Trema orientalis])

HSP 1 Score: 101.3 bits (251), Expect = 1.6e-18
Identity = 45/53 (84.91%), Postives = 47/53 (88.68%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVS 54
          MDPQPEPV+YICGDCGMENTLK GDVIQCRECGYRILYKKRTRRK  + S  S
Sbjct: 1  MDPQPEPVTYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRKIDQCSAAS 53

BLAST of Cla97C01G013780 vs. NCBI nr
Match: XP_015579873.1 (DNA-directed RNA polymerases II, IV and V subunit 12 [Ricinus communis] >XP_016903136.1 PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 12 [Cucumis melo] >XP_016899390.1 PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 12 [Cucumis melo] >XP_016899391.1 PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 12 [Cucumis melo] >XP_022136997.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Momordica charantia] >XP_022954995.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita moschata] >XP_022923649.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita moschata] >XP_022994261.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita maxima] >XP_023001815.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita maxima] >XP_023001816.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita maxima] >XP_023542174.1 DNA-directed RNA polymerases II, IV and V subunit 12 [Cucurbita pepo subsp. pepo] >KGN64215.1 hypothetical protein Csa_1G043180 [Cucumis sativus])

HSP 1 Score: 100.1 bits (248), Expect = 3.5e-18
Identity = 44/44 (100.00%), Postives = 44/44 (100.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. NCBI nr
Match: EEF34914.1 (DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide, putative [Ricinus communis])

HSP 1 Score: 100.1 bits (248), Expect = 3.5e-18
Identity = 44/44 (100.00%), Postives = 44/44 (100.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. NCBI nr
Match: XP_021624767.1 (DNA-directed RNA polymerases II, IV and V subunit 12-like [Manihot esculenta])

HSP 1 Score: 99.8 bits (247), Expect = 4.6e-18
Identity = 48/60 (80.00%), Postives = 51/60 (85.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVSELPSSAN 60
          MDPQPEPVSYICGDCGMENTLK GDVIQCRECGYRILYKKRTRR  ++ S +    SSAN
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRILEKLSNLG--ISSAN 58

BLAST of Cla97C01G013780 vs. TrEMBL
Match: tr|A0A2P5G071|A0A2P5G071_9ROSA (RNA polymerase archaeal subunit P/eukaryotic subunit RPABC OS=Trema orientalis OX=63057 GN=TorRG33x02_006410 PE=4 SV=1)

HSP 1 Score: 101.3 bits (251), Expect = 1.0e-18
Identity = 45/53 (84.91%), Postives = 47/53 (88.68%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVS 54
          MDPQPEPV+YICGDCGMENTLK GDVIQCRECGYRILYKKRTRRK  + S  S
Sbjct: 1  MDPQPEPVTYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRKIDQCSAAS 53

BLAST of Cla97C01G013780 vs. TrEMBL
Match: tr|A0A2P5DNN3|A0A2P5DNN3_PARAD (RNA polymerase archaeal subunit P/eukaryotic subunit RPABC OS=Parasponia andersonii OX=3476 GN=PanWU01x14_046100 PE=4 SV=1)

HSP 1 Score: 101.3 bits (251), Expect = 1.0e-18
Identity = 45/53 (84.91%), Postives = 47/53 (88.68%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGVS 54
          MDPQPEPV+YICGDCGMENTLK GDVIQCRECGYRILYKKRTRRK  + S  S
Sbjct: 1  MDPQPEPVTYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRKIDQCSATS 53

BLAST of Cla97C01G013780 vs. TrEMBL
Match: tr|A0A1S4E4H5|A0A1S4E4H5_CUCME (DNA-directed RNA polymerases II, IV and V subunit 12 OS=Cucumis melo OX=3656 GN=LOC103482567 PE=4 SV=1)

HSP 1 Score: 100.1 bits (248), Expect = 2.3e-18
Identity = 44/44 (100.00%), Postives = 44/44 (100.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. TrEMBL
Match: tr|B9SNE7|B9SNE7_RICCO (DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide, putative OS=Ricinus communis OX=3988 GN=RCOM_0175610 PE=4 SV=1)

HSP 1 Score: 100.1 bits (248), Expect = 2.3e-18
Identity = 44/44 (100.00%), Postives = 44/44 (100.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. TrEMBL
Match: tr|A0A0A0LQM4|A0A0A0LQM4_CUCSA (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_1G043180 PE=4 SV=1)

HSP 1 Score: 100.1 bits (248), Expect = 2.3e-18
Identity = 44/44 (100.00%), Postives = 44/44 (100.00%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. Swiss-Prot
Match: sp|Q9FLM8|NRPBC_ARATH (DNA-directed RNA polymerases II, IV and V subunit 12 OS=Arabidopsis thaliana OX=3702 GN=NRPB12 PE=1 SV=1)

HSP 1 Score: 92.4 bits (228), Expect = 2.4e-18
Identity = 39/44 (88.64%), Postives = 41/44 (93.18%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDP PEPV+Y+CGDCG ENTLK GDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPAPEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. Swiss-Prot
Match: sp|Q9C8M4|RPBCL_ARATH (DNA-directed RNA polymerase subunit 12-like protein OS=Arabidopsis thaliana OX=3702 GN=NRPB12L PE=3 SV=1)

HSP 1 Score: 70.5 bits (171), Expect = 9.7e-12
Identity = 33/52 (63.46%), Postives = 38/52 (73.08%), Query Frame = 0

Query: 2  DPQPEP-VSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGV 53
          D QPE  V Y+CGDCG EN LK+GDV QCR+CG+RILYKKR   K +   GV
Sbjct: 10 DKQPEQLVIYVCGDCGQENILKRGDVFQCRDCGFRILYKKRILDKKETRIGV 61

BLAST of Cla97C01G013780 vs. Swiss-Prot
Match: sp|Q3ZBC0|RPAB4_BOVIN (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus OX=9913 GN=POLR2K PE=1 SV=1)

HSP 1 Score: 65.9 bits (159), Expect = 2.4e-10
Identity = 26/42 (61.90%), Postives = 34/42 (80.95%), Query Frame = 0

Query: 3  PQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKR 51

BLAST of Cla97C01G013780 vs. Swiss-Prot
Match: sp|P53803|RPAB4_HUMAN (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens OX=9606 GN=POLR2K PE=1 SV=1)

HSP 1 Score: 65.9 bits (159), Expect = 2.4e-10
Identity = 26/42 (61.90%), Postives = 34/42 (80.95%), Query Frame = 0

Query: 3  PQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKR 51

BLAST of Cla97C01G013780 vs. Swiss-Prot
Match: sp|Q63871|RPAB4_MOUSE (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus OX=10090 GN=Polr2k PE=3 SV=2)

HSP 1 Score: 65.9 bits (159), Expect = 2.4e-10
Identity = 26/42 (61.90%), Postives = 34/42 (80.95%), Query Frame = 0

Query: 3  PQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKR 51

BLAST of Cla97C01G013780 vs. TAIR10
Match: AT5G41010.1 (DNA directed RNA polymerase, 7 kDa subunit)

HSP 1 Score: 92.4 bits (228), Expect = 1.3e-19
Identity = 39/44 (88.64%), Postives = 41/44 (93.18%), Query Frame = 0

Query: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRR 45
          MDP PEPV+Y+CGDCG ENTLK GDVIQCRECGYRILYKKRTRR
Sbjct: 1  MDPAPEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRR 44

BLAST of Cla97C01G013780 vs. TAIR10
Match: AT1G53690.1 (DNA directed RNA polymerase, 7 kDa subunit)

HSP 1 Score: 70.5 bits (171), Expect = 5.4e-13
Identity = 33/52 (63.46%), Postives = 38/52 (73.08%), Query Frame = 0

Query: 2  DPQPEP-VSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRKYKRASGV 53
          D QPE  V Y+CGDCG EN LK+GDV QCR+CG+RILYKKR   K +   GV
Sbjct: 10 DKQPEQLVIYVCGDCGQENILKRGDVFQCRDCGFRILYKKRILDKKETRIGV 61

The following BLAST results are available for this feature:
Match NameE-valueIdentityDescription
PON74893.11.6e-1884.91RNA polymerase archaeal subunit P/eukaryotic subunit RPABC [Parasponia andersoni... [more]
POO03436.11.6e-1884.91RNA polymerase archaeal subunit P/eukaryotic subunit RPABC [Trema orientalis][more]
XP_015579873.13.5e-18100.00DNA-directed RNA polymerases II, IV and V subunit 12 [Ricinus communis] >XP_0169... [more]
EEF34914.13.5e-18100.00DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide, putative [Ricin... [more]
XP_021624767.14.6e-1880.00DNA-directed RNA polymerases II, IV and V subunit 12-like [Manihot esculenta][more]
Match NameE-valueIdentityDescription
tr|A0A2P5G071|A0A2P5G071_9ROSA1.0e-1884.91RNA polymerase archaeal subunit P/eukaryotic subunit RPABC OS=Trema orientalis O... [more]
tr|A0A2P5DNN3|A0A2P5DNN3_PARAD1.0e-1884.91RNA polymerase archaeal subunit P/eukaryotic subunit RPABC OS=Parasponia anderso... [more]
tr|A0A1S4E4H5|A0A1S4E4H5_CUCME2.3e-18100.00DNA-directed RNA polymerases II, IV and V subunit 12 OS=Cucumis melo OX=3656 GN=... [more]
tr|B9SNE7|B9SNE7_RICCO2.3e-18100.00DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide, putative OS=Ric... [more]
tr|A0A0A0LQM4|A0A0A0LQM4_CUCSA2.3e-18100.00Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_1G043180 PE=4 SV=1[more]
Match NameE-valueIdentityDescription
sp|Q9FLM8|NRPBC_ARATH2.4e-1888.64DNA-directed RNA polymerases II, IV and V subunit 12 OS=Arabidopsis thaliana OX=... [more]
sp|Q9C8M4|RPBCL_ARATH9.7e-1263.46DNA-directed RNA polymerase subunit 12-like protein OS=Arabidopsis thaliana OX=3... [more]
sp|Q3ZBC0|RPAB4_BOVIN2.4e-1061.90DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus OX=9913... [more]
sp|P53803|RPAB4_HUMAN2.4e-1061.90DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens OX=96... [more]
sp|Q63871|RPAB4_MOUSE2.4e-1061.90DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus OX=10... [more]
Match NameE-valueIdentityDescription
AT5G41010.11.3e-1988.64DNA directed RNA polymerase, 7 kDa subunit[more]
AT1G53690.15.4e-1363.46DNA directed RNA polymerase, 7 kDa subunit[more]
The following terms have been associated with this gene:
Vocabulary: Molecular Function
TermDefinition
GO:0003677DNA binding
GO:0003899DNA-directed RNA polymerase activity
Vocabulary: Biological Process
TermDefinition
GO:0006351transcription, DNA-templated
Vocabulary: INTERPRO
TermDefinition
IPR029040RPABC4/Spt4
IPR006591RNAP_P/RPABC4
GO Assignments
This gene 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
biological_process GO:0000394 RNA splicing, via endonucleolytic cleavage and ligation
biological_process GO:0006366 transcription from RNA polymerase II promoter
biological_process GO:0008150 biological_process
cellular_component GO:0005730 nucleolus
cellular_component GO:0005665 DNA-directed RNA polymerase II, core complex
cellular_component GO:0000418 DNA-directed RNA polymerase IV complex
cellular_component GO:0000419 DNA-directed RNA polymerase V complex
cellular_component GO:0005575 cellular_component
molecular_function GO:0003677 DNA binding
molecular_function GO:0003899 DNA-directed RNA polymerase activity
molecular_function GO:0003674 molecular_function

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

Feature NameUnique NameType
Cla97C01G013780.1Cla97C01G013780.1mRNA


Analysis Name: InterPro Annotations of watermelon 97103 v2
Date Performed: 2019-05-12
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4SMARTSM00659rpolcxc3coord: 8..51
e-value: 5.3E-17
score: 72.5
IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4PFAMPF03604DNA_RNApol_7kDcoord: 10..41
e-value: 9.7E-17
score: 60.3
NoneNo IPR availableGENE3DG3DSA:2.20.28.30coord: 1..49
e-value: 3.5E-22
score: 79.5
NoneNo IPR availablePANTHERPTHR12056DNA-DIRECTED RNA POLYMERASES I, II, AND IIIcoord: 3..46
NoneNo IPR availablePRODOMPD012151coord: 14..37
e-value: 8.0E-7
score: 120.0
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4SUPERFAMILYSSF63393RNA polymerase subunitscoord: 7..46