MS004298 (gene) Bitter gourd (TR) v1

Overview


Name	MS004298
Type	gene
Organism	Momordica charantia cv. TR (Bitter gourd (TR) v1)
Description	DNA-directed RNA polymerase
Location	scaffold92: 1607530 .. 1607929 (+)
RNA-Seq Expression	MS004298
Synteny	MS004298

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSpolypeptide

Hold the cursor over a type above to highlight its positions in the sequence below.

CCTGACAAATTTTGCAGGATTGGGAAGCAAGTCGACGGTCCTCATCCGATCGATTCGGACATTGACAAGCAGTTTCTTGGCCTTCCTATCAAGTCAGCCGTCGACAAGTTCCAACTTCTTCCTGAATTTTTGAAGGTGTGAATCATCACGTTGCGTTTGCTTGTTGTGATTATCAGTTTAATATGCAGAAGGCACCACGACAATACCTCTACTATACTGCTTTTGTTTGAATTTCAGATGATGATTAGTAATACACCCAGTGTTAATCATCTGGTTGCAGGTAAGAGGTCTGGTTCGACAACACTTGGATTCCTTTAACTACTTCGTGAATACAGAGATAAAGAAGATAGTCAAAGCAAACGATCGCATTGAATCCAGCACTGATCCGAGTATTTATCTT

mRNA sequence

CCTGACAAATTTTGCAGGATTGGGAAGCAAGTCGACGGTCCTCATCCGATCGATTCGGACATTGACAAGCAGTTTCTTGGCCTTCCTATCAAGTCAGCCGTCGACAAGTTCCAACTTCTTCCTGAATTTTTGAAGGTAAGAGGTCTGGTTCGACAACACTTGGATTCCTTTAACTACTTCGTGAATACAGAGATAAAGAAGATAGTCAAAGCAAACGATCGCATTGAATCCAGCACTGATCCGAGTATTTATCTT

Coding sequence (CDS)

CCTGACAAATTTTGCAGGATTGGGAAGCAAGTCGACGGTCCTCATCCGATCGATTCGGACATTGACAAGCAGTTTCTTGGCCTTCCTATCAAGTCAGCCGTCGACAAGTTCCAACTTCTTCCTGAATTTTTGAAGGTAAGAGGTCTGGTTCGACAACACTTGGATTCCTTTAACTACTTCGTGAATACAGAGATAAAGAAGATAGTCAAAGCAAACGATCGCATTGAATCCAGCACTGATCCGAGTATTTATCTT

Protein sequence

PDKFCRIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIESSTDPSIYL

Homology

[Close]

BLAST of MS004298 vs. NCBI nr
Match: XP_022138958.1 (DNA-directed RNA polymerase III subunit 2 [Momordica charantia])

HSP 1 Score: 163.3 bits (412), Expect = 9.1e-37
Identity = 79/80 (98.75%), Postives = 80/80 (100.00%), Query Frame = 0


Query: 6  RIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI 65
          +IGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI
Sbjct: 11 KIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI 70

Query: 66 KKIVKANDRIESSTDPSIYL 86
          KKIVKANDRIESSTDPSIYL
Sbjct: 71 KKIVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. NCBI nr
Match: XP_023541760.1 (DNA-directed RNA polymerase III subunit 2 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 149.4 bits (376), Expect = 1.4e-32
Identity = 74/78 (94.87%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRIESSTDPSIYL
Sbjct: 73 IVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. NCBI nr
Match: KAG6573766.1 (DNA-directed RNA polymerase III subunit 2, partial [Cucurbita argyrosperma subsp. sororia])

HSP 1 Score: 149.4 bits (376), Expect = 1.4e-32
Identity = 74/78 (94.87%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRIESSTDPSIYL
Sbjct: 73 IVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. NCBI nr
Match: XP_022945802.1 (DNA-directed RNA polymerase III subunit 2 isoform X1 [Cucurbita moschata])

HSP 1 Score: 149.4 bits (376), Expect = 1.4e-32
Identity = 74/78 (94.87%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRIESSTDPSIYL
Sbjct: 73 IVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. NCBI nr
Match: KAG7012839.1 (DNA-directed RNA polymerase III subunit 2 [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 149.4 bits (376), Expect = 1.4e-32
Identity = 74/78 (94.87%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRIESSTDPSIYL
Sbjct: 73 IVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. ExPASy Swiss-Prot
Match: F4KD38 (DNA-directed RNA polymerase III subunit 2 OS=Arabidopsis thaliana OX=3702 GN=NRPC2 PE=2 SV=1)

HSP 1 Score: 103.2 bits (256), Expect = 1.5e-21
Identity = 50/68 (73.53%), Postives = 55/68 (80.88%), Query Frame = 0


Query: 18 DSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIES 77
          D  IDK+ L  PIKS  DKFQL+PEFLKVRGLV+QHLDSFNYF+N  I KIVKAN RI S
Sbjct: 14 DHFIDKEKLSAPIKSTADKFQLVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRITS 73

Query: 78 STDPSIYL 86
          + DPSIYL
Sbjct: 74 TVDPSIYL 81

[Close]

BLAST of MS004298 vs. ExPASy Swiss-Prot
Match: Q9NW08 (DNA-directed RNA polymerase III subunit RPC2 OS=Homo sapiens OX=9606 GN=POLR3B PE=1 SV=2)

HSP 1 Score: 82.8 bits (203), Expect = 2.1e-15
Identity = 36/60 (60.00%), Postives = 48/60 (80.00%), Query Frame = 0


Query: 26 LGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIESSTDPSIYL 85
          L  PI +  +K++LLP FLKV+GLV+QH+DSFNYF+N EIKKI+KAN+++ S  DP  YL
Sbjct: 16 LAAPIPTVEEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKVTSDADPMWYL 75

[Close]

BLAST of MS004298 vs. ExPASy Swiss-Prot
Match: P59470 (DNA-directed RNA polymerase III subunit RPC2 OS=Mus musculus OX=10090 GN=Polr3b PE=1 SV=2)

HSP 1 Score: 82.0 bits (201), Expect = 3.5e-15
Identity = 36/60 (60.00%), Postives = 48/60 (80.00%), Query Frame = 0


Query: 26 LGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIESSTDPSIYL 85
          L  PI +  +K++LLP FLKV+GLV+QH+DSFNYF+N EIKKI+KAN+++ S  DP  YL
Sbjct: 16 LTAPIPTVEEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKVTSDADPMWYL 75

[Close]

BLAST of MS004298 vs. ExPASy Swiss-Prot
Match: P22276 (DNA-directed RNA polymerase III subunit RPC2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RET1 PE=1 SV=2)

HSP 1 Score: 80.5 bits (197), Expect = 1.0e-14
Identity = 37/56 (66.07%), Postives = 45/56 (80.36%), Query Frame = 0


Query: 30 IKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIESSTDPSIYL 86
          I +A DK+ LLP FLKV+GLV+QHLDSFNYFV+T++KKI+KAN  I S  DP  YL
Sbjct: 38 INTAQDKWHLLPAFLKVKGLVKQHLDSFNYFVDTDLKKIIKANQLILSDVDPEFYL 93

[Close]

BLAST of MS004298 vs. ExPASy Swiss-Prot
Match: P25167 (DNA-directed RNA polymerase III subunit RPC2 OS=Drosophila melanogaster OX=7227 GN=RpIII128 PE=2 SV=2)

HSP 1 Score: 79.3 bits (194), Expect = 2.3e-14
Identity = 34/64 (53.12%), Postives = 49/64 (76.56%), Query Frame = 0


Query: 22 DKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIESSTDP 81
          D +   +PIK   +K++L+P FL+V+GLV+QH+DSFN+F+N +IKKIVKAN+ + S  DP
Sbjct: 20 DSKDWSVPIKPLTEKWKLVPAFLQVKGLVKQHIDSFNHFINVDIKKIVKANELVTSGADP 79

Query: 82 SIYL 86
            YL
Sbjct: 80 LFYL 83

[Close]

BLAST of MS004298 vs. ExPASy TrEMBL
Match: A0A6J1CEJ1 (DNA-directed RNA polymerase subunit beta OS=Momordica charantia OX=3673 GN=LOC111010008 PE=3 SV=1)

HSP 1 Score: 163.3 bits (412), Expect = 4.4e-37
Identity = 79/80 (98.75%), Postives = 80/80 (100.00%), Query Frame = 0


Query: 6  RIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI 65
          +IGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI
Sbjct: 11 KIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEI 70

Query: 66 KKIVKANDRIESSTDPSIYL 86
          KKIVKANDRIESSTDPSIYL
Sbjct: 71 KKIVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. ExPASy TrEMBL
Match: A0A6J1G1X8 (DNA-directed RNA polymerase subunit beta OS=Cucurbita moschata OX=3662 GN=LOC111449942 PE=3 SV=1)

HSP 1 Score: 149.4 bits (376), Expect = 6.6e-33
Identity = 74/78 (94.87%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRIESSTDPSIYL
Sbjct: 73 IVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. ExPASy TrEMBL
Match: A0A6J1HQP0 (DNA-directed RNA polymerase subunit beta OS=Cucurbita maxima OX=3661 GN=LOC111466504 PE=3 SV=1)

HSP 1 Score: 148.3 bits (373), Expect = 1.5e-32
Identity = 73/78 (93.59%), Postives = 75/78 (96.15%), Query Frame = 0


Query: 8  GKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 67
          GKQVD P+ I SDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK
Sbjct: 13 GKQVDDPNAIGSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKK 72

Query: 68 IVKANDRIESSTDPSIYL 86
          IVKANDRI+SSTDPSIYL
Sbjct: 73 IVKANDRIQSSTDPSIYL 90

[Close]

BLAST of MS004298 vs. ExPASy TrEMBL
Match: A0A5D3C055 (DNA-directed RNA polymerase OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold347G00180 PE=3 SV=1)

HSP 1 Score: 146.4 bits (368), Expect = 5.6e-32
Identity = 72/85 (84.71%), Postives = 77/85 (90.59%), Query Frame = 0


Query: 1  PDKFCRIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYF 60
          P+   +  KQ D  +PIDSDIDKQF+GLPIKSAVDKFQLLPEFLKVRGLV+QHLDSFNYF
Sbjct: 6  PEDASKNEKQGDDSNPIDSDIDKQFIGLPIKSAVDKFQLLPEFLKVRGLVKQHLDSFNYF 65

Query: 61 VNTEIKKIVKANDRIESSTDPSIYL 86
          VNTEIKKIVKANDRIESSTDPSIYL
Sbjct: 66 VNTEIKKIVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. ExPASy TrEMBL
Match: A0A5A7UBS2 (DNA-directed RNA polymerase subunit beta OS=Cucumis melo var. makuwa OX=1194695 GN=E6C27_scaffold481G00090 PE=3 SV=1)

HSP 1 Score: 146.4 bits (368), Expect = 5.6e-32
Identity = 72/85 (84.71%), Postives = 77/85 (90.59%), Query Frame = 0


Query: 1  PDKFCRIGKQVDGPHPIDSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYF 60
          P+   +  KQ D  +PIDSDIDKQF+GLPIKSAVDKFQLLPEFLKVRGLV+QHLDSFNYF
Sbjct: 6  PEDASKNEKQGDDSNPIDSDIDKQFIGLPIKSAVDKFQLLPEFLKVRGLVKQHLDSFNYF 65

Query: 61 VNTEIKKIVKANDRIESSTDPSIYL 86
          VNTEIKKIVKANDRIESSTDPSIYL
Sbjct: 66 VNTEIKKIVKANDRIESSTDPSIYL 90

[Close]

BLAST of MS004298 vs. TAIR 10
Match: AT5G45140.1 (nuclear RNA polymerase C2 )

HSP 1 Score: 103.2 bits (256), Expect = 1.0e-22
Identity = 50/68 (73.53%), Postives = 55/68 (80.88%), Query Frame = 0


Query: 18 DSDIDKQFLGLPIKSAVDKFQLLPEFLKVRGLVRQHLDSFNYFVNTEIKKIVKANDRIES 77
          D  IDK+ L  PIKS  DKFQL+PEFLKVRGLV+QHLDSFNYF+N  I KIVKAN RI S
Sbjct: 14 DHFIDKEKLSAPIKSTADKFQLVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRITS 73

Query: 78 STDPSIYL 86
          + DPSIYL
Sbjct: 74 TVDPSIYL 81

The following BLAST results are available for this feature:

BLAST of MS004298 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_022138958.1	9.1e-37	98.75	DNA-directed RNA polymerase III subunit 2 [Momordica charantia]	[more]
XP_023541760.1	1.4e-32	94.87	DNA-directed RNA polymerase III subunit 2 [Cucurbita pepo subsp. pepo]	[more]
KAG6573766.1	1.4e-32	94.87	DNA-directed RNA polymerase III subunit 2, partial [Cucurbita argyrosperma subsp...	[more]
XP_022945802.1	1.4e-32	94.87	DNA-directed RNA polymerase III subunit 2 isoform X1 [Cucurbita moschata]	[more]
KAG7012839.1	1.4e-32	94.87	DNA-directed RNA polymerase III subunit 2 [Cucurbita argyrosperma subsp. argyros...	[more]

BLAST of MS004298 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
F4KD38	1.5e-21	73.53	DNA-directed RNA polymerase III subunit 2 OS=Arabidopsis thaliana OX=3702 GN=NRP...	[more]
Q9NW08	2.1e-15	60.00	DNA-directed RNA polymerase III subunit RPC2 OS=Homo sapiens OX=9606 GN=POLR3B P...	[more]
P59470	3.5e-15	60.00	DNA-directed RNA polymerase III subunit RPC2 OS=Mus musculus OX=10090 GN=Polr3b ...	[more]
P22276	1.0e-14	66.07	DNA-directed RNA polymerase III subunit RPC2 OS=Saccharomyces cerevisiae (strain...	[more]
P25167	2.3e-14	53.13	DNA-directed RNA polymerase III subunit RPC2 OS=Drosophila melanogaster OX=7227 ...	[more]

BLAST of MS004298 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1CEJ1	4.4e-37	98.75	DNA-directed RNA polymerase subunit beta OS=Momordica charantia OX=3673 GN=LOC11...	[more]
A0A6J1G1X8	6.6e-33	94.87	DNA-directed RNA polymerase subunit beta OS=Cucurbita moschata OX=3662 GN=LOC111...	[more]
A0A6J1HQP0	1.5e-32	93.59	DNA-directed RNA polymerase subunit beta OS=Cucurbita maxima OX=3661 GN=LOC11146...	[more]
A0A5D3C055	5.6e-32	84.71	DNA-directed RNA polymerase OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaf...	[more]
A0A5A7UBS2	5.6e-32	84.71	DNA-directed RNA polymerase subunit beta OS=Cucumis melo var. makuwa OX=1194695 ...	[more]

BLAST of MS004298 vs. TAIR 10


Match Name	E-value	Identity	Description
AT5G45140.1	1.0e-22	73.53	nuclear RNA polymerase C2	[more]

InterPro

Analysis Name: InterPro Annotations of Bitter gourd (TR) v1
Date Performed: 2021-10-25


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	GENE3D	3.90.1100.10		coord: 40..84 e-value: 6.1E-7 score: 30.6
None	No IPR available	PANTHER	PTHR20856:SF8	DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC2	coord: 30..85
None	No IPR available	SUPERFAMILY	64484	beta and beta-prime subunits of DNA dependent RNA-polymerase	coord: 30..78
IPR015712	DNA-directed RNA polymerase, subunit 2	PANTHER	PTHR20856	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	coord: 30..85

Relationships

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


Feature Name	Unique Name	Type
MS004298.1	MS004298.1	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
molecular_function	GO:0003899	DNA-directed 5'-3' RNA polymerase activity
molecular_function	GO:0032549	ribonucleoside binding