CmoCh13G000890 (gene) Cucurbita moschata (Rifu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmoCh13G000890
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu))
Description	DNA-directed RNA polymerases I and III subunit RPAC2
Location	Cmo_Chr13 : 534477 .. 536000 (-)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSexonthree_prime_UTR

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

ATGCCTCTTTTAGGAGTAACATCCGGACGGGTAAAGTTTGTAAGGATAGTAATATAGTCCGGAAGAAATAACTAATCAAAAGCTTCTCCTTCAAGCTAAAACAACAATTAACTATGACTCTTGACCTAGATAACGTCCTAGACATAGGAGAGATTGGTGCAAGAGGGAATGCCTAGACGACGTTTTTCTTATTGAGCAGCTGAAAGTAGATCTATGGGTCCTTCCGTCCCTTGCTCCTGAATAAGGGTACGGATAGTTTTGTATACTTTTAAATGACTTGTTACATCATCTCGTAGTCTAAGAGTGACATTTTGTGGTTACAACATTCCTCATTCTTAGAGTCTAGACAACAAGTAATATTTTGAGGTAGTTTAACTCTCTAAAGTGCAAGAGATCGGTTCTCATTTTTAGTGTTTTTAATGATTAGACTTGTTCTGGCCTGTTTTTCTTCTTTATACACATCCAATTTATGCATTCATGAGAAATATAGTCTATGGCTCTATGCGAAATGTGATCCTTTTCTAAAGAACACAAGTTGGATCCTTGTAGCTTTGCTAGAACCCCATCCATCTTGGAACTTGATTTATGGATCGTGACTATTTAGTTTCATAACTTAAACAAGATTTATAAGGTGGCTATCTTGTTCTTACTATGGATACTAGCATCTCAATATTGATGTGACGTGCGTATTAGATAGACGTTAGTTGATTTGACGATAGAAAAATAGTTGGAAGTGACCAAGCATTAGCATTAGAGATACTGATGAGAAGGGTTTTGATGGAACATGACAGGTGATCCTGCAAGAGAGGTTCTGAAAGATGCGTGTCAGAACTTCATGGTGGTCTGCCACCATGTGAGGAACACATTCGACAAGGTTGTGCTTGATTTCAAACCCACCAATCCTGTGGGGAACATTAATATCAATTAGAATGGGACCCTTTTTCTCTTTCAACTTGTAACTTTCTTTCTTAGGCTCATCTATATTGCAGTTTACAGGTGATTGAGTTGGTTAGCTAATGGTGAGATTCCACATCGGTTGGAGAGGGAAACGAACCATTCCTTATAAGAGTGTGAAAATTTCTTCCTAGTAAATACGTTTTAAAACCGTGAGGCTGAAGACGATACGTAATGGGCTAAAGCAGACAATATTTGTTAATGATGAGTTTGGGCTGTTTCAAATGGGATTAGAGTTAGACGCTGGGCAATGTGCCAACGAGGACACTAGGCCCTCAAAGGGTAGATCGTGAGATCCCACATTGGTTGGAGAGAGGAAGAAACATTCCTTGTAAAGATGTGGAAATCTCTCCTTAGTAGACGCGTTTTAAAACTGTGAGGTTGATGAGCTTGGACTGTTACAAATGGCTTCTAGAACAGATTCGTTTCGTTGAATTTTGCTTGCTTTTACTGTTGAGATGCCTATGCACAGGGATTTCACGTTAATTATTGTATATTGTAGATCCATGTGAAAAGTAAAAGAAACAGGTATGATCGAATTTGATTGGATGTTTATGTGAGAAATCTCCC

mRNA sequence

ATGCCTCTTTTAGGAGTAACATCCGGACGGAGTCTAGACAACAAACTTGTTCTGGCCTGTTTTTCTTCTTTATACACATCCAATTTATGCATTCATGAGAAATATAGTCTATGGCTCTATGCGAAATGTGATCCTTTTCTAAAGAACACAAGTGATCCTGCAAGAGAGGTTCTGAAAGATGCGTGTCAGAACTTCATGGTGGTCTGCCACCATGTGAGGAACACATTCGACAAGGTTGTGCTTGATTTCAAACCCACCAATCCTGTGGGGAACATTAATATCAATTAGAATGGGACCCTTTTTCTCTTTCAACTTGTAACTTTCTTTCTTAGGCTCATCTATATTGCAGTTTACAGGTGATTGAGTTGGTTAGCTAATGGTGAGATTCCACATCGGTTGGAGAGGGAAACGAACCATTCCTTATAAGAGTGTGAAAATTTCTTCCTAGTAAATACGTTTTAAAACCGTGAGGCTGAAGACGATACGTAATGGGCTAAAGCAGACAATATTTGTTAATGATGAGTTTGGGCTGTTTCAAATGGGATTAGAGTTAGACGCTGGGCAATGTGCCAACGAGGACACTAGGCCCTCAAAGGGTAGATCGTGAGATCCCACATTGGTTGGAGAGAGGAAGAAACATTCCTTGTAAAGATGTGGAAATCTCTCCTTAGTAGACGCGTTTTAAAACTGTGAGGTTGATGAGCTTGGACTGTTACAAATGGCTTCTAGAACAGATTCGTTTCGTTGAATTTTGCTTGCTTTTACTGTTGAGATGCCTATGCACAGGGATTTCACGTTAATTATTGTATATTGTAGATCCATGTGAAAAGTAAAAGAAACAGGTATGATCGAATTTGATTGGATGTTTATGTGAGAAATCTCCC

Coding sequence (CDS)

ATGCCTCTTTTAGGAGTAACATCCGGACGGAGTCTAGACAACAAACTTGTTCTGGCCTGTTTTTCTTCTTTATACACATCCAATTTATGCATTCATGAGAAATATAGTCTATGGCTCTATGCGAAATGTGATCCTTTTCTAAAGAACACAAGTGATCCTGCAAGAGAGGTTCTGAAAGATGCGTGTCAGAACTTCATGGTGGTCTGCCACCATGTGAGGAACACATTCGACAAGGTTGTGCTTGATTTCAAACCCACCAATCCTGTGGGGAACATTAATATCAATTAG

Homology

[Close]

BLAST of CmoCh13G000890 vs. TrEMBL
Match: A0A0A0LUT5_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G095010 PE=4 SV=1)

HSP 1 Score: 81.3 bits (199), Expect = 7.2e-13
Identity = 37/48 (77.08%), Postives = 40/48 (83.33%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNINI 95
           ++ T DPAREVLKDACQN MVVC HVRNTFDK VLD K TNPV +INI
Sbjct: 56  VQTTGDPAREVLKDACQNLMVVCQHVRNTFDKAVLDVKLTNPVRDINI 103

[Close]

BLAST of CmoCh13G000890 vs. TrEMBL
Match: A0A0A0LV21_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G527910 PE=4 SV=1)

HSP 1 Score: 77.0 bits (188), Expect = 1.4e-11
Identity = 37/52 (71.15%), Postives = 40/52 (76.92%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPT----NPVGNINI 95
           ++ T DPAREVLKDACQN MVVC HVRNTFDK VLDF  T     PVG+INI
Sbjct: 56  VQTTGDPAREVLKDACQNLMVVCQHVRNTFDKAVLDFNLTKPKEKPVGDINI 107

[Close]

BLAST of CmoCh13G000890 vs. TrEMBL
Match: A0A0D2QSH4_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_003G126400 PE=4 SV=1)

HSP 1 Score: 68.6 bits (166), Expect = 4.8e-09
Identity = 30/49 (61.22%), Postives = 38/49 (77.55%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNININ 96
           ++ T DPAREVLKDACQN M++C HVR+TFDK V DFK +N V  + I+
Sbjct: 56  VQTTGDPAREVLKDACQNLMLMCRHVRSTFDKAVEDFKASNAVKAMKID 104

[Close]

BLAST of CmoCh13G000890 vs. TrEMBL
Match: A0A0B0MTD7_GOSAR (DNA-directed RNA polymerases I and III subunit RPAC2 OS=Gossypium arboreum GN=F383_24198 PE=4 SV=1)

HSP 1 Score: 67.4 bits (163), Expect = 1.1e-08
Identity = 29/49 (59.18%), Postives = 38/49 (77.55%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNININ 96
           ++ T DPAREVLKDACQN M++C HVR+TFDK V DF+ +N V  + I+
Sbjct: 56  VQTTGDPAREVLKDACQNLMLMCRHVRSTFDKAVEDFRASNAVKAMKID 104

[Close]

BLAST of CmoCh13G000890 vs. TrEMBL
Match: A0A0D2SWK1_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_008G072300 PE=4 SV=1)

HSP 1 Score: 67.0 bits (162), Expect = 1.4e-08
Identity = 30/49 (61.22%), Postives = 37/49 (75.51%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNININ 96
           ++ T DPAREVLKDACQN M++C HVR TFDK V DFK +N V  + I+
Sbjct: 87  VQTTGDPAREVLKDACQNLMLMCRHVRCTFDKAVEDFKASNAVKAMKID 135

[Close]

BLAST of CmoCh13G000890 vs. TAIR10
Match: AT2G29540.3 (AT2G29540.3 RNApolymerase 14 kDa subunit)

HSP 1 Score: 51.2 bits (121), Expect = 4.0e-07
Identity = 21/38 (55.26%), Postives = 27/38 (71.05%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFK 85
           ++ T DPAREV KDACQ  M +  HVR+ FDK V ++K
Sbjct: 73  VQTTGDPAREVFKDACQELMQMNRHVRSVFDKAVAEYK 110

[Close]

BLAST of CmoCh13G000890 vs. NCBI nr
Match: gi|778659017|ref|XP_004147276.2| (PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis sativus])

HSP 1 Score: 81.3 bits (199), Expect = 1.0e-12
Identity = 37/48 (77.08%), Postives = 40/48 (83.33%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNINI 95
           ++ T DPAREVLKDACQN MVVC HVRNTFDK VLD K TNPV +INI
Sbjct: 56  VQTTGDPAREVLKDACQNLMVVCQHVRNTFDKAVLDVKLTNPVRDINI 103

[Close]

BLAST of CmoCh13G000890 vs. NCBI nr
Match: gi|449455052|ref|XP_004145267.1| (PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis sativus])

HSP 1 Score: 77.0 bits (188), Expect = 1.9e-11
Identity = 37/52 (71.15%), Postives = 40/52 (76.92%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPT----NPVGNINI 95
           ++ T DPAREVLKDACQN MVVC HVRNTFDK VLDF  T     PVG+INI
Sbjct: 56  VQTTGDPAREVLKDACQNLMVVCQHVRNTFDKAVLDFNLTKPKEKPVGDINI 107

[Close]

BLAST of CmoCh13G000890 vs. NCBI nr
Match: gi|659115158|ref|XP_008457416.1| (PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis melo])

HSP 1 Score: 74.7 bits (182), Expect = 9.7e-11
Identity = 36/52 (69.23%), Postives = 39/52 (75.00%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPT----NPVGNINI 95
           ++ T DPAREVLKDACQN MVVC HVRNTFDK VLDF  T     P G+INI
Sbjct: 56  VQTTGDPAREVLKDACQNLMVVCQHVRNTFDKAVLDFNLTKAKEEPEGDINI 107

[Close]

BLAST of CmoCh13G000890 vs. NCBI nr
Match: gi|823142887|ref|XP_012471245.1| (PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2-like [Gossypium raimondii])

HSP 1 Score: 68.6 bits (166), Expect = 6.9e-09
Identity = 30/49 (61.22%), Postives = 38/49 (77.55%), Query Frame = 1


Query: 47  LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPVGNININ 96
           ++ T DPAREVLKDACQN M++C HVR+TFDK V DFK +N V  + I+
Sbjct: 56  VQTTGDPAREVLKDACQNLMLMCRHVRSTFDKAVEDFKASNAVKAMKID 104

[Close]

BLAST of CmoCh13G000890 vs. NCBI nr
Match: gi|1000963455|ref|XP_015575526.1| (PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Ricinus communis])

HSP 1 Score: 68.2 bits (165), Expect = 9.0e-09
Identity = 28/43 (65.12%), Postives = 33/43 (76.74%), Query Frame = 1


Query: 47 LKNTSDPAREVLKDACQNFMVVCHHVRNTFDKVVLDFKPTNPV 90
          ++ T DPAREVLKD CQN M +C HVR+TFDK V D+K  NPV
Sbjct: 56 VQTTGDPAREVLKDGCQNLMFMCEHVRSTFDKAVSDYKANNPV 98

The following BLAST results are available for this feature:

BLAST of CmoCh13G000890 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CmoCh13G000890 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0LUT5_CUCSA	7.2e-13	77.08	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G095010 PE=4 SV=1	[more]
A0A0A0LV21_CUCSA	1.4e-11	71.15	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G527910 PE=4 SV=1	[more]
A0A0D2QSH4_GOSRA	4.8e-09	61.22	Uncharacterized protein OS=Gossypium raimondii GN=B456_003G126400 PE=4 SV=1	[more]
A0A0B0MTD7_GOSAR	1.1e-08	59.18	DNA-directed RNA polymerases I and III subunit RPAC2 OS=Gossypium arboreum GN=F3...	[more]
A0A0D2SWK1_GOSRA	1.4e-08	61.22	Uncharacterized protein OS=Gossypium raimondii GN=B456_008G072300 PE=4 SV=1	[more]

BLAST of CmoCh13G000890 vs. TAIR10


Match Name	E-value	Identity	Description
AT2G29540.3	4.0e-07	55.26	RNApolymerase 14 kDa subunit	[more]

BLAST of CmoCh13G000890 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|778659017\|ref\|XP_004147276.2\|	1.0e-12	77.08	PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis sativus...	[more]
gi\|449455052\|ref\|XP_004145267.1\|	1.9e-11	71.15	PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis sativus...	[more]
gi\|659115158\|ref\|XP_008457416.1\|	9.7e-11	69.23	PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Cucumis melo]	[more]
gi\|823142887\|ref\|XP_012471245.1\|	6.9e-09	61.22	PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2-like [Gossypium ...	[more]
gi\|1000963455\|ref\|XP_015575526.1\|	9.0e-09	65.12	PREDICTED: DNA-directed RNA polymerases I and III subunit RPAC2 [Ricinus communi...	[more]

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006144	purine nucleobase metabolic process
biological_process	GO:0006206	pyrimidine nucleobase metabolic process
biological_process	GO:0006351	transcription, DNA-templated
biological_process	GO:0008150	biological_process
biological_process	GO:0006383	transcription from RNA polymerase III promoter
biological_process	GO:0006360	transcription from RNA polymerase I promoter
cellular_component	GO:0005730	nucleolus
cellular_component	GO:0005666	DNA-directed RNA polymerase III complex
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0005736	DNA-directed RNA polymerase I complex
molecular_function	GO:0003677	DNA binding
molecular_function	GO:0003899	DNA-directed RNA polymerase activity
molecular_function	GO:0046983	protein dimerization activity
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0001054	RNA polymerase I activity
molecular_function	GO:0001056	RNA polymerase III activity

Relationships

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


Feature Name	Unique Name	Type
CmoCh13G000890.1	CmoCh13G000890.1	mRNA

Synteny

The following gene(s) are orthologous to this gene:


Gene	Orthologue	Organism	Block
CmoCh13G000890	Cucsa.146730	Cucumber (Gy14) v1	cgycmoB0402
CmoCh13G000890	CmaCh13G000930	Cucurbita maxima (Rimu)	cmacmoB218
CmoCh13G000890	CmaCh01G006380	Cucurbita maxima (Rimu)	cmacmoB458
CmoCh13G000890	Cla008195	Watermelon (97103) v1	cmowmB173
CmoCh13G000890	Csa1G527910	Cucumber (Chinese Long) v2	cmocuB204
CmoCh13G000890	ClCG03G001080	Watermelon (Charleston Gray)	cmowcgB184
CmoCh13G000890	CSPI01G23560	Wild cucumber (PI 183967)	cmocpiB206
CmoCh13G000890	Lsi02G013160	Bottle gourd (USVL1VR-Ls)	cmolsiB191
CmoCh13G000890	Cp4.1LG02g11650	Cucurbita pepo (Zucchini)	cmocpeB207
CmoCh13G000890	CsaV3_1G035860	Cucumber (Chinese Long) v3	cmocucB0236
CmoCh13G000890	Cla97C03G051910	Watermelon (97103) v2	cmowmbB209
CmoCh13G000890	CsGy1G023030	Cucumber (Gy14) v2	cgybcmoB069
CmoCh13G000890	Carg12407	Silver-seed gourd	carcmoB0594

The following gene(s) are paralogous to this gene:


Gene	Paralogue	Organism	Block
CmoCh13G000890	CmoCh01G006700	Cucurbita moschata (Rifu)	cmocmoB173

The following block(s) are covering this gene:


Gene	Organism	Block
CmoCh13G000890	Cucurbita pepo (Zucchini)	cmocpeB211
CmoCh13G000890	Cucurbita pepo (Zucchini)	cmocpeB202
CmoCh13G000890	Bottle gourd (USVL1VR-Ls)	cmolsiB186
CmoCh13G000890	Melon (DHL92) v3.6.1	cmomedB198
CmoCh13G000890	Melon (DHL92) v3.6.1	cmomedB203
CmoCh13G000890	Silver-seed gourd	carcmoB0212
CmoCh13G000890	Silver-seed gourd	carcmoB0517
CmoCh13G000890	Cucumber (Chinese Long) v3	cmocucB0253
CmoCh13G000890	Watermelon (97103) v2	cmowmbB204
CmoCh13G000890	Wax gourd	cmowgoB0238
CmoCh13G000890	Wax gourd	cmowgoB0245
CmoCh13G000890	Cucurbita moschata (Rifu)	cmocmoB180
CmoCh13G000890	Cucurbita moschata (Rifu)	cmocmoB189
CmoCh13G000890	Cucumber (Gy14) v1	cgycmoB0384
CmoCh13G000890	Cucurbita maxima (Rimu)	cmacmoB577
CmoCh13G000890	Wild cucumber (PI 183967)	cmocpiB214
CmoCh13G000890	Wild cucumber (PI 183967)	cmocpiB217
CmoCh13G000890	Cucumber (Chinese Long) v2	cmocuB214
CmoCh13G000890	Melon (DHL92) v3.5.1	cmomeB178
CmoCh13G000890	Melon (DHL92) v3.5.1	cmomeB181
CmoCh13G000890	Watermelon (Charleston Gray)	cmowcgB180
CmoCh13G000890	Watermelon (97103) v1	cmowmB197