MS000901 (gene) Bitter gourd (TR) v1

Overview


Name	MS000901
Type	gene
Organism	Momordica charantia cv. TR (Bitter gourd (TR) v1)
Description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
Location	scaffold36: 162099 .. 162694 (+)
RNA-Seq Expression	MS000901
Synteny	MS000901

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.

AGGCAGCGTCGGAACCCCGGGCTAGGGCAGAAAGCGAAGATGATCATCCCAGTACGTTGCTTCACTTGCGGAAAGGTAAGCCATGGAGAAATAAATTCTATTTTTAGTTTAACTACCTTCTACTTATACTCCTATGTGGGAGCCTCTTCTGCAAATTTGCGTTTTTTCTGTTTTCTTGTGTGCAACTATCTTTATCTTTGGTTTGCTGCTTACGAGCACGATAAATTTTTGAATTTGTAATTTTTCAGGTGATTGGAAACAAATGGGATCATTACCTTGATCTTCTACAGGCAGACTATTCTGAAGGGTAAGGATGTAGCCTCCCCTTTTCTTGTCATTTTAAGTTCCCACTCTAAAATTTCTCTCTCAAATTCCTTCTGGACTTTGAAGATTGCCTGGTCAATGTACGATATCTAACCTTTAACCTTGCTATGTAAAGATGATGCTGATGCGTTTTTTCTTGTATTAGAGATGCTCTCGATGCACTGGGCTTGGTTCGCTACTGCTGTAGGCGAATGCTCATGACTCATGTAGACCTTATCGAAAAGCTTCTTAATTACAACAGTAATTTCTCTCTCTTTCTCTACATTCATGCA

mRNA sequence

AGGCAGCGTCGGAACCCCGGGCTAGGGCAGAAAGCGAAGATGATCATCCCAGTACGTTGCTTCACTTGCGGAAAGGTGATTGGAAACAAATGGGATCATTACCTTGATCTTCTACAGGCAGACTATTCTGAAGGAGATGCTCTCGATGCACTGGGCTTGGTTCGCTACTGCTGTAGGCGAATGCTCATGACTCATGTAGACCTTATCGAAAAGCTTCTTAATTACAACAGTAATTTCTCTCTCTTTCTCTACATTCATGCA

Coding sequence (CDS)

AGGCAGCGTCGGAACCCCGGGCTAGGGCAGAAAGCGAAGATGATCATCCCAGTACGTTGCTTCACTTGCGGAAAGGTGATTGGAAACAAATGGGATCATTACCTTGATCTTCTACAGGCAGACTATTCTGAAGGAGATGCTCTCGATGCACTGGGCTTGGTTCGCTACTGCTGTAGGCGAATGCTCATGACTCATGTAGACCTTATCGAAAAGCTTCTTAATTACAACAGTAATTTCTCTCTCTTTCTCTACATTCATGCA

Protein sequence

RQRRNPGLGQKAKMIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNSNFSLFLYIHA

Homology

[Close]

BLAST of MS000901 vs. NCBI nr
Match: KAG6782578.1 (hypothetical protein POTOM_011988 [Populus tomentosa])

HSP 1 Score: 146.4 bits (368), Expect = 1.2e-31
Identity = 67/69 (97.10%), Postives = 68/69 (98.55%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLF 83
          NYNSNFSLF
Sbjct: 61 NYNSNFSLF 69

[Close]

BLAST of MS000901 vs. NCBI nr
Match: KAA0057130.1 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Cucumis melo var. makuwa] >TYJ97111.1 DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Cucumis melo var. makuwa])

HSP 1 Score: 146.4 bits (368), Expect = 1.2e-31
Identity = 68/71 (95.77%), Postives = 69/71 (97.18%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLFLY 85
          NYNSN SL L+
Sbjct: 61 NYNSNPSLSLF 71

[Close]

BLAST of MS000901 vs. NCBI nr
Match: KAF9825663.1 (hypothetical protein H0E87_032116, partial [Populus deltoides])

HSP 1 Score: 146.4 bits (368), Expect = 1.2e-31
Identity = 67/69 (97.10%), Postives = 68/69 (98.55%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLF 83
          NYNSNFSLF
Sbjct: 61 NYNSNFSLF 69

[Close]

BLAST of MS000901 vs. NCBI nr
Match: KAB5564305.1 (hypothetical protein DKX38_004359 [Salix brachista])

HSP 1 Score: 146.0 bits (367), Expect = 1.5e-31
Identity = 67/70 (95.71%), Postives = 68/70 (97.14%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLFL 84
          NYNSNFS FL
Sbjct: 61 NYNSNFSFFL 70

[Close]

BLAST of MS000901 vs. NCBI nr
Match: KAF9685616.1 (hypothetical protein SADUNF_Sadunf03G0073100 [Salix dunnii])

HSP 1 Score: 144.4 bits (363), Expect = 4.5e-31
Identity = 66/68 (97.06%), Postives = 67/68 (98.53%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSL 82
          NYNSNFSL
Sbjct: 61 NYNSNFSL 68

[Close]

BLAST of MS000901 vs. ExPASy Swiss-Prot
Match: Q9SYA6 (DNA-directed RNA polymerase subunit 10-like protein OS=Arabidopsis thaliana OX=3702 GN=NRPB10L PE=1 SV=1)

HSP 1 Score: 134.0 bits (336), Expect = 7.9e-31
Identity = 59/64 (92.19%), Postives = 63/64 (98.44%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MI+PVRCFTCGKVIGNKWD YL+LLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIVPVRCFTCGKVIGNKWDTYLELLQADYAEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNS 78
          NYN+
Sbjct: 61 NYNT 64

[Close]

BLAST of MS000901 vs. ExPASy Swiss-Prot
Match: Q8LFJ6 (DNA-directed RNA polymerases II, IV and V subunit 10 OS=Arabidopsis thaliana OX=3702 GN=NRPB10 PE=1 SV=1)

HSP 1 Score: 131.7 bits (330), Expect = 3.9e-30
Identity = 59/64 (92.19%), Postives = 61/64 (95.31%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQ DY+EGDALDAL LVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDQYLDLLQLDYTEGDALDALQLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNS 78
          NYN+
Sbjct: 61 NYNT 64

[Close]

BLAST of MS000901 vs. ExPASy Swiss-Prot
Match: Q39290 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Brassica napus OX=3708 PE=3 SV=1)

HSP 1 Score: 131.7 bits (330), Expect = 3.9e-30
Identity = 59/64 (92.19%), Postives = 61/64 (95.31%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQ DY+EGDALDAL LVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDAYLDLLQLDYTEGDALDALNLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNS 78
          NYN+
Sbjct: 61 NYNT 64

[Close]

BLAST of MS000901 vs. ExPASy Swiss-Prot
Match: Q55AB6 (DNA-directed RNA polymerases I, II, and III subunit rpabc5 OS=Dictyostelium discoideum OX=44689 GN=polr2l PE=3 SV=1)

HSP 1 Score: 121.7 bits (304), Expect = 4.1e-27
Identity = 55/62 (88.71%), Postives = 57/62 (91.94%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YL LLQ DY+EGDALDAL L RYCCRRML+THVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDAYLSLLQIDYTEGDALDALCLKRYCCRRMLLTHVDLIEKLL 60

Query: 74 NY 76
          NY
Sbjct: 61 NY 62

[Close]

BLAST of MS000901 vs. ExPASy Swiss-Prot
Match: Q32P78 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus OX=9913 GN=POLR2L PE=1 SV=1)

HSP 1 Score: 120.9 bits (302), Expect = 7.0e-27
Identity = 52/62 (83.87%), Postives = 58/62 (93.55%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGK++GNKW+ YL LLQA+Y+EGDALDALGL RYCCRRML+ HVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL 60

Query: 74 NY 76
          NY
Sbjct: 61 NY 62

[Close]

BLAST of MS000901 vs. ExPASy TrEMBL
Match: A0A5A7UPU3 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold371G00170 PE=3 SV=1)

HSP 1 Score: 146.4 bits (368), Expect = 5.7e-32
Identity = 68/71 (95.77%), Postives = 69/71 (97.18%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLFLY 85
          NYNSN SL L+
Sbjct: 61 NYNSNPSLSLF 71

[Close]

BLAST of MS000901 vs. ExPASy TrEMBL
Match: A0A5N5N9W5 (Uncharacterized protein OS=Salix brachista OX=2182728 GN=DKX38_004359 PE=3 SV=1)

HSP 1 Score: 146.0 bits (367), Expect = 7.5e-32
Identity = 67/70 (95.71%), Postives = 68/70 (97.14%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNSNFSLFL 84
          NYNSNFS FL
Sbjct: 61 NYNSNFSFFL 70

[Close]

BLAST of MS000901 vs. ExPASy TrEMBL
Match: A0A453FTM1 (Uncharacterized protein OS=Aegilops tauschii subsp. strangulata OX=200361 PE=3 SV=1)

HSP 1 Score: 144.8 bits (364), Expect = 1.7e-31
Identity = 65/71 (91.55%), Postives = 69/71 (97.18%), Query Frame = 0


Query: 7   GLGQKAKMIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHV 66
           G G+ +KMIIPVRCFTCGKVIGNKWDHYLDLLQADY+EGDALDALGLVRYCCRRMLMTHV
Sbjct: 38  GGGRGSKMIIPVRCFTCGKVIGNKWDHYLDLLQADYTEGDALDALGLVRYCCRRMLMTHV 97

Query: 67  DLIEKLLNYNS 78
           DLIEKLLNYN+
Sbjct: 98  DLIEKLLNYNT 108

[Close]

BLAST of MS000901 vs. ExPASy TrEMBL
Match: M8D4I9 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Aegilops tauschii OX=37682 GN=F775_26628 PE=3 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 2.2e-31
Identity = 65/70 (92.86%), Postives = 68/70 (97.14%), Query Frame = 0


Query: 7   GLGQKAKMIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHV 66
           G G+ +KMIIPVRCFTCGKVIGNKWDHYLDLLQADY+EGDALDALGLVRYCCRRMLMTHV
Sbjct: 133 GGGRGSKMIIPVRCFTCGKVIGNKWDHYLDLLQADYTEGDALDALGLVRYCCRRMLMTHV 192

Query: 67  DLIEKLLNYN 77
           DLIEKLLNYN
Sbjct: 193 DLIEKLLNYN 202

[Close]

BLAST of MS000901 vs. ExPASy TrEMBL
Match: A0A446NTG8 (Uncharacterized protein OS=Triticum turgidum subsp. durum OX=4567 GN=TRITD_3Av1G210240 PE=3 SV=1)

HSP 1 Score: 142.9 bits (359), Expect = 6.3e-31
Identity = 64/69 (92.75%), Postives = 67/69 (97.10%), Query Frame = 0


Query: 9   GQKAKMIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDL 68
           G  +KMIIPVRCFTCGKVIGNKWDHYLDLLQADY+EGDALDALGLVRYCCRRMLMTHVDL
Sbjct: 38  GGGSKMIIPVRCFTCGKVIGNKWDHYLDLLQADYTEGDALDALGLVRYCCRRMLMTHVDL 97

Query: 69  IEKLLNYNS 78
           IEKLLNYN+
Sbjct: 98  IEKLLNYNT 106

[Close]

BLAST of MS000901 vs. TAIR 10
Match: AT1G61700.1 (RNA polymerases N / 8 kDa subunit )

HSP 1 Score: 134.0 bits (336), Expect = 5.6e-32
Identity = 59/64 (92.19%), Postives = 63/64 (98.44%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MI+PVRCFTCGKVIGNKWD YL+LLQADY+EGDALDALGLVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIVPVRCFTCGKVIGNKWDTYLELLQADYAEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNS 78
          NYN+
Sbjct: 61 NYNT 64

[Close]

BLAST of MS000901 vs. TAIR 10
Match: AT1G11475.1 (RNA polymerases N / 8 kDa subunit )

HSP 1 Score: 131.7 bits (330), Expect = 2.8e-31
Identity = 59/64 (92.19%), Postives = 61/64 (95.31%), Query Frame = 0


Query: 14 MIIPVRCFTCGKVIGNKWDHYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLL 73
          MIIPVRCFTCGKVIGNKWD YLDLLQ DY+EGDALDAL LVRYCCRRMLMTHVDLIEKLL
Sbjct: 1  MIIPVRCFTCGKVIGNKWDQYLDLLQLDYTEGDALDALQLVRYCCRRMLMTHVDLIEKLL 60

Query: 74 NYNS 78
          NYN+
Sbjct: 61 NYNT 64

The following BLAST results are available for this feature:

BLAST of MS000901 vs. NCBI nr


Match Name	E-value	Identity	Description
KAG6782578.1	1.2e-31	97.10	hypothetical protein POTOM_011988 [Populus tomentosa]	[more]
KAA0057130.1	1.2e-31	95.77	DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Cucumis melo var. ma...	[more]
KAF9825663.1	1.2e-31	97.10	hypothetical protein H0E87_032116, partial [Populus deltoides]	[more]
KAB5564305.1	1.5e-31	95.71	hypothetical protein DKX38_004359 [Salix brachista]	[more]
KAF9685616.1	4.5e-31	97.06	hypothetical protein SADUNF_Sadunf03G0073100 [Salix dunnii]	[more]

BLAST of MS000901 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q9SYA6	7.9e-31	92.19	DNA-directed RNA polymerase subunit 10-like protein OS=Arabidopsis thaliana OX=3...	[more]
Q8LFJ6	3.9e-30	92.19	DNA-directed RNA polymerases II, IV and V subunit 10 OS=Arabidopsis thaliana OX=...	[more]
Q39290	3.9e-30	92.19	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Brassica napus OX=...	[more]
Q55AB6	4.1e-27	88.71	DNA-directed RNA polymerases I, II, and III subunit rpabc5 OS=Dictyostelium disc...	[more]
Q32P78	7.0e-27	83.87	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus OX=9913...	[more]

BLAST of MS000901 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A5A7UPU3	5.7e-32	95.77	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Cucumis melo var. ...	[more]
A0A5N5N9W5	7.5e-32	95.71	Uncharacterized protein OS=Salix brachista OX=2182728 GN=DKX38_004359 PE=3 SV=1	[more]
A0A453FTM1	1.7e-31	91.55	Uncharacterized protein OS=Aegilops tauschii subsp. strangulata OX=200361 PE=3 S...	[more]
M8D4I9	2.2e-31	92.86	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Aegilops tauschii ...	[more]
A0A446NTG8	6.3e-31	92.75	Uncharacterized protein OS=Triticum turgidum subsp. durum OX=4567 GN=TRITD_3Av1G...	[more]

BLAST of MS000901 vs. TAIR 10


Match Name	E-value	Identity	Description
AT1G61700.1	5.6e-32	92.19	RNA polymerases N / 8 kDa subunit	[more]
AT1G11475.1	2.8e-31	92.19	RNA polymerases N / 8 kDa subunit	[more]

InterPro

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

Position :

Zoom :

x 1


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	PFAM	PF01194	RNA_pol_N	coord: 14..72 e-value: 9.2E-32 score: 109.1
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	PANTHER	PTHR23431	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 FAMILY MEMBER	coord: 14..77
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	HAMAP	MF_00250	RNApol_arch_N	coord: 14..76 score: 19.33688
None	No IPR available	GENE3D	1.10.10.60		coord: 14..78 e-value: 2.8E-39 score: 135.1
None	No IPR available	PANTHER	PTHR23431:SF6	SUBFAMILY NOT NAMED	coord: 14..77
IPR020789	RNA polymerases, subunit N, zinc binding site	PROSITE	PS01112	RNA_POL_N_8KD	coord: 15..24
IPR023580	RNA polymerase subunit RPB10	SUPERFAMILY	46924	RNA polymerase subunit RPB10	coord: 14..76

Relationships

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


Feature Name	Unique Name	Type
MS000901.1	MS000901.1	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:0003677	DNA binding
molecular_function	GO:0003899	DNA-directed 5'-3' RNA polymerase activity
molecular_function	GO:0008270	zinc ion binding