CuGenDBv2

Gene ID	MS015772
Organism	Momordica charantia cv. TR (Bitter gourd (TR) v1)
Description	DNA-directed RNA polymerase subunit
Genome location	scaffold1230:105524..110738
RNA-Seq Expression	MS015772
Synteny	MS015772
Gene Ontology terms	GO:0001193 - maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (biological process) GO:0006283 - transcription-coupled nucleotide-excision repair (biological process) GO:0006367 - transcription initiation from RNA polymerase II promoter (biological process) GO:0006379 - mRNA cleavage (biological process) GO:0005665 - RNA polymerase II, core complex (cellular component) GO:0005730 - nucleolus (cellular component) GO:0003676 - nucleic acid binding (molecular function) GO:0003899 - DNA-directed 5'-3' RNA polymerase activity (molecular function) GO:0008270 - zinc ion binding (molecular function)
InterPro domains	IPR001222 - Zinc finger, TFIIS-type IPR001529 - DNA-directed RNA polymerase, M/15kDa subunit IPR012164 - DNA-directed RNA polymerase subunit/transcription factor S IPR034012 - Pol II subunit B9, C-terminal zinc ribbon

Homology

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GenBank top hits

e value

%identity

Alignment

EXB55730.1 DNA-directed RNA polymerase II subunit [Morus notabilis]

8.1e-57

97.14

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Query:  SNNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCG
        SNNILYPKEDRD+KILLYACRNCDHQEVADNNCVYRNEIHH+VGERTQVLQDVAADPTLPRTK+VRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCG
Subjt:  SNNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCG

Query:  HRWRD
        HRWRD
Subjt:  HRWRD

XP_008438942.1 PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 9A [Cucumis melo]

2.8e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

XP_024019992.1 DNA-directed RNA polymerases II, IV and V subunit 9A [Morus notabilis]

3.1e-56

97.12

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRD+KILLYACRNCDHQEVADNNCVYRNEIHH+VGERTQVLQDVAADPTLPRTK+VRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

XP_024963039.1 DNA-directed RNA polymerases II, IV and V subunit 9A [Cynara cardunculus var. scolymus]

6.9e-56

97.12

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKED+D+KILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQC HGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

XP_030503042.1 DNA-directed RNA polymerases II, IV and V subunit 9A [Cannabis sativa]

6.2e-57

99.04

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHH+VGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

TrEMBL top hits

e value

%identity

Alignment

A0A0A0L816 DNA-directed RNA polymerase subunit

1.4e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

A0A5A7U5C7 DNA-directed RNA polymerase subunit

1.4e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

A0A6J1CBU6 DNA-directed RNA polymerase subunit

1.4e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

A0A6J1FM50 DNA-directed RNA polymerase subunit

1.4e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

A0A6J1I879 DNA-directed RNA polymerase subunit

1.4e-57

100

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWRD
Subjt:  RWRD

SwissProt top hits

e value

%identity

Alignment

P36954 DNA-directed RNA polymerase II subunit RPB9

2.6e-34

59.05

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG
        NN+LYPKED++ +ILLYACRNCD+Q+ ADN+C+Y N+I H V E TQ++ DV+ DPTLPRT+   C +C H EAVFFQ+ +AR E+ M L++VC  P+CG
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG

Query:  HRWRD
        HRW +
Subjt:  HRWRD

P60898 DNA-directed RNA polymerase II subunit RPB9

2.6e-34

59.05

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG
        NN+LYPKED++ +ILLYACRNCD+Q+ ADN+C+Y N+I H V E TQ++ DV+ DPTLPRT+   C +C H EAVFFQ+ +AR E+ M L++VC  P+CG
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG

Query:  HRWRD
        HRW +
Subjt:  HRWRD

Q32P73 DNA-directed RNA polymerase II subunit RPB9

2.6e-34

59.05

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG
        NN+LYPKED++ +ILLYACRNCD+Q+ ADN+C+Y N+I H V E TQ++ DV+ DPTLPRT+   C +C H EAVFFQ+ +AR E+ M L++VC  P+CG
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQA-TARGEEGMTLFFVCCNPNCG

Query:  HRWRD
        HRW +
Subjt:  HRWRD

Q6NLH0 DNA-directed RNA polymerases II, IV and V subunit 9A

3.3e-53

85.58

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKED+++KILLYACRNCDHQEVADN+CVYRNE+HH+V ERTQ+L DVA+DPTLPRTKAVRC++C H EAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWR+
Subjt:  RWRD

Q8L5V0 DNA-directed RNA polymerases II, IV and V subunit 9B

5.7e-53

84.62

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKED+++ ILLYACRNCDHQE ADNNCVYRNE+HH+V E+TQ+L DVA+DPTLPRTKAVRCA+C HGEAVFFQATARGEEGMTLFFVCCNPNC H
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWR+
Subjt:  RWRD

Arabidopsis top hits

e value

%identity

Alignment

AT3G16980.1 RNA polymerases M/15 Kd subunit

2.4e-54

85.58

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKED+++KILLYACRNCDHQEVADN+CVYRNE+HH+V ERTQ+L DVA+DPTLPRTKAVRC++C H EAVFFQATARGEEGMTLFFVCCNPNCGH
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWR+
Subjt:  RWRD

AT4G16265.1 RNA polymerases M/15 Kd subunit

4.0e-54

84.62

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Query:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
        NNILYPKED+++ ILLYACRNCDHQE ADNNCVYRNE+HH+V E+TQ+L DVA+DPTLPRTKAVRCA+C HGEAVFFQATARGEEGMTLFFVCCNPNC H
Subjt:  NNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH

Query:  RWRD
        RWR+
Subjt:  RWRD

Sequences

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CDS sequence

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TTGAAAATTTGGAAATTGTTATGTTTCAGTAACAACATTCTCTACCCGAAGGAGGACAGAGATGAGAAGATTCTTCTCTATGCGTGTCGCAACTGCGATCACCAGGAAGT
TGCTGATAATAACTGTGTCTATAGAAATGAGATCCATCATGCTGTAGGGGAACGGACTCAAGTTCTGCAAGATGTTGCTGCAGATCCAACTCTTCCTCGCACTAAAGCTG
TTCGATGTGCTCAATGCAACCATGGAGAAGCTGTCTTCTTCCAGGCCACTGCCAGAGGGGAGGAAGGTATGACATTGTTCTTCGTTTGCTGCAATCCAAATTGTGGCCAC
AGATGGAGAGAT

mRNA sequence

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Protein sequence

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LKIWKLLCFSNNILYPKEDRDEKILLYACRNCDHQEVADNNCVYRNEIHHAVGERTQVLQDVAADPTLPRTKAVRCAQCNHGEAVFFQATARGEEGMTLFFVCCNPNCGH
RWRD

MS015772 (gene) of Bitter gourd (TR) v1 genome