CsGy2G017100 (gene) Cucumber (Gy14) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CsGy2G017100
Type	gene
Organism	Cucumis sativus (Cucumber (Gy14) v2)
Description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
Location	Chr2 : 27318642 .. 27319226 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDS

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

ATGGAAAAGAAATACCAAAGGGGTCAAACCCTGGTTGGGATCGAGGCACGTAGGGTTGTGCAGAAAGCAGAAAGCGAAGATGATCATCCCAGTGCGTTGCTTCACTTGCGGGAAGGTAAGCTATGGACAACCATATTCAACATTGAGTTAAAGTTTCTTCTCAGAATTCCATTTTCCTGTTTTCTCTATCCTTCTATGTCCCACTGTCTTTGGGTTCTTGCCTACCCACCACCCCCAAAGTTTTCAATTACTCTCAACTCAACTCACCTCTTAGAACCCTTCGGTTTATATTTTTTTTTAGGTGATTGGAAACAAGTGGGATCATTACCTTGATATTCTACAGGCCGATTATTCAGAAGGGCAAGTGAGTGCAACACGTCACTTCATTTACATTTTGATTTCCGTCTTGGTTTCTTACAACATCCAAAAGCATACCTGTTTTACCTTGCCTTTTAGAAGAGATCCTAATGCATTTACTTTTCCCGTATTAGGGATGCACTTGATGCACTGGGTCTGGTTCGCTACTGCTGTAGACGAATGCTCATGACTCATGTTGACCTTATGAAAAGCTTCTTAATTACAATA

mRNA sequence

ATGGAAAAGAAATACCAAAGGGGTCAAACCCTGGTTGGGATCGAGGCACGTAGGGTTGTGCAGAAAGCAGAAAGCGAAGATGATCATCCCAGTGCGTTGCTTCACTTGCGGGAAGGTAAGCTATGGACAACCATATTCAACATTGAGTTAAAGTTTCTTCTCAGAATTCCATTTTCCTGTTTTCTCTATCCTTCTATGTCCCACTGTCTTTGGGTTCTTGCCTACCCACCACCCCCAAATGGGATCATTACCTTGATATTCTACAGGCCGATTATTCAGAAGGGCAAGGATGCACTTGATGCACTGGGTCTGGTTCGCTACTGCTGTAGACGAATGCTCATGACTCATGTTGACCTTATGAAAAGCTTCTTAATTACAATA

Coding sequence (CDS)

ATGGAAAAGAAATACCAAAGGGGTCAAACCCTGGTTGGGATCGAGGCACGTAGGGTTGTGCAGAAAGCAGAAAGCGAAGATGATCATCCCAGTGCGTTGCTTCACTTGCGGGAAGGTAAGCTATGGACAACCATATTCAACATTGAGTTAAAGTTTCTTCTCAGAATTCCATTTTCCTGTTTTCTCTATCCTTCTATGTCCCACTGTCTTTGGGTTCTTGCCTACCCACCACCCCCAAATGGGATCATTACCTTGATATTCTACAGGCCGATTATTCAGAAGGGCAAGGATGCACTTGATGCACTGGGTCTGGTTCGCTACTGCTGTAGACGAATGCTCATGACTCATGTTGACCTTATGAAAAGCTTCTTAATTACAATA

Protein sequence

MEKKYQRGQTLVGIEARRVVQKAESEDDHPSALLHLREGKLWTTIFNIELKFLLRIPFSCFLYPSMSHCLWVLAYPPPPNGIITLIFYRPIIQKGKDALDALGLVRYCCRRMLMTHVDLMKSFLITI

Homology

[Close]

BLAST of CsGy2G017100 vs. NCBI nr
Match: CDY25312.1 (BnaC01g29810D [Brassica napus])

HSP 1 Score: 56.6 bits (135), Expect = 7.1e-05
Identity = 31/63 (49.21%), Postives = 38/63 (60.32%), Query Frame = 0


Query: 62  LYPSMSHCLWVLAYPPPPNGIITLIFYRPIIQKGKDALDALGLVRYCCRRMLMTHVDLMK 121
           LY   S C W           I+ + + P+  K  DALDA+GLVRYCCRRMLMTHVDL++
Sbjct: 35  LYDGFSGCYWCF----DSVVCISSLIFIPLCVK-LDALDAIGLVRYCCRRMLMTHVDLIE 92

Query: 122 SFL 125
             L
Sbjct: 95  KLL 92

[Close]

BLAST of CsGy2G017100 vs. NCBI nr
Match: XP_019240650.1 (PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 10-like [Nicotiana attenuata])

HSP 1 Score: 54.7 bits (130), Expect = 2.7e-04
Identity = 24/29 (82.76%), Postives = 27/29 (93.10%), Query Frame = 0


Query: 96  KDALDALGLVRYCCRRMLMTHVDLMKSFL 125
           K+ALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 32  KEALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. NCBI nr
Match: ABF70104.1 (DNA-directed RNA polymerase II 8.2 kDa polypeptide, putative [Musa balbisiana])

HSP 1 Score: 53.9 bits (128), Expect = 4.6e-04
Identity = 24/28 (85.71%), Postives = 26/28 (92.86%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. NCBI nr
Match: XP_015618232.1 (DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Oryza sativa Japonica Group] >BAF29331.1 Os12g0180400 [Oryza sativa Japonica Group])

HSP 1 Score: 53.9 bits (128), Expect = 4.6e-04
Identity = 24/28 (85.71%), Postives = 26/28 (92.86%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. NCBI nr
Match: ABK20909.1 (unknown [Picea sitchensis] >ABK22149.1 unknown [Picea sitchensis] >ABK25286.1 unknown [Picea sitchensis])

HSP 1 Score: 53.9 bits (128), Expect = 4.6e-04
Identity = 24/28 (85.71%), Postives = 26/28 (92.86%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. TAIR10
Match: AT1G61700.1 (RNA polymerases N / 8 kDa subunit)

HSP 1 Score: 53.9 bits (128), Expect = 8.3e-08
Identity = 24/28 (85.71%), Postives = 26/28 (92.86%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. TAIR10
Match: AT1G11475.1 (RNA polymerases N / 8 kDa subunit)

HSP 1 Score: 50.8 bits (120), Expect = 7.0e-07
Identity = 23/28 (82.14%), Postives = 25/28 (89.29%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDAL LVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALQLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. Swiss-Prot
Match: sp|Q9SYA6|RPBAL_ARATH (DNA-directed RNA polymerase subunit 10-like protein OS=Arabidopsis thaliana OX=3702 GN=NRPB10L PE=1 SV=1)

HSP 1 Score: 53.9 bits (128), Expect = 1.5e-06
Identity = 24/28 (85.71%), Postives = 26/28 (92.86%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALGLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. Swiss-Prot
Match: sp|Q39290|RPAB5_BRANA (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Brassica napus OX=3708 PE=3 SV=1)

HSP 1 Score: 51.6 bits (122), Expect = 7.4e-06
Identity = 23/28 (82.14%), Postives = 25/28 (89.29%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDAL LVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALNLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. Swiss-Prot
Match: sp|Q8LFJ6|NRPBA_ARATH (DNA-directed RNA polymerases II, IV and V subunit 10 OS=Arabidopsis thaliana OX=3702 GN=NRPB10 PE=1 SV=1)

HSP 1 Score: 50.8 bits (120), Expect = 1.3e-05
Identity = 23/28 (82.14%), Postives = 25/28 (89.29%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDAL LVRYCCRRMLMTHVDL++  L
Sbjct: 33  DALDALQLVRYCCRRMLMTHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. Swiss-Prot
Match: sp|Q32P78|RPAB5_BOVIN (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus OX=9913 GN=POLR2L PE=1 SV=1)

HSP 1 Score: 48.5 bits (114), Expect = 6.3e-05
Identity = 21/28 (75.00%), Postives = 24/28 (85.71%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGL RYCCRRML+ HVDL++  L
Sbjct: 33  DALDALGLKRYCCRRMLLAHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. Swiss-Prot
Match: sp|Q6QN04|RPAB5_CHILA (DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Chinchilla lanigera OX=34839 GN=POLR2L PE=3 SV=1)

HSP 1 Score: 48.5 bits (114), Expect = 6.3e-05
Identity = 21/28 (75.00%), Postives = 24/28 (85.71%), Query Frame = 0


Query: 97  DALDALGLVRYCCRRMLMTHVDLMKSFL 125
           DALDALGL RYCCRRML+ HVDL++  L
Sbjct: 33  DALDALGLKRYCCRRMLLAHVDLIEKLL 60

[Close]

BLAST of CsGy2G017100 vs. TrEMBL
Match: tr|A0A287QVX2|A0A287QVX2_HORVV (Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1)

HSP 1 Score: 57.4 bits (137), Expect = 2.7e-05
Identity = 25/30 (83.33%), Postives = 28/30 (93.33%), Query Frame = 0


Query: 95  GKDALDALGLVRYCCRRMLMTHVDLMKSFL 125
           G+DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 1   GRDALDALGLVRYCCRRMLMTHVDLIEKLL 30

[Close]

BLAST of CsGy2G017100 vs. TrEMBL
Match: tr|A0A078GJE9|A0A078GJE9_BRANA (BnaC01g29810D protein OS=Brassica napus OX=3708 GN=BnaC01g29810D PE=4 SV=1)

HSP 1 Score: 56.6 bits (135), Expect = 4.7e-05
Identity = 31/63 (49.21%), Postives = 38/63 (60.32%), Query Frame = 0


Query: 62  LYPSMSHCLWVLAYPPPPNGIITLIFYRPIIQKGKDALDALGLVRYCCRRMLMTHVDLMK 121
           LY   S C W           I+ + + P+  K  DALDA+GLVRYCCRRMLMTHVDL++
Sbjct: 35  LYDGFSGCYWCF----DSVVCISSLIFIPLCVK-LDALDAIGLVRYCCRRMLMTHVDLIE 92

Query: 122 SFL 125
             L
Sbjct: 95  KLL 92

[Close]

BLAST of CsGy2G017100 vs. TrEMBL
Match: tr|A0A0D3HS23|A0A0D3HS23_9ORYZ (Uncharacterized protein OS=Oryza barthii OX=65489 PE=3 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 6.1e-05
Identity = 25/40 (62.50%), Postives = 31/40 (77.50%), Query Frame = 0


Query: 85  LIFYRPIIQKGKDALDALGLVRYCCRRMLMTHVDLMKSFL 125
           ++ Y  +  +  DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 52  MVCYADLSMRTWDALDALGLVRYCCRRMLMTHVDLIEKLL 91

[Close]

BLAST of CsGy2G017100 vs. TrEMBL
Match: tr|A0A287QVY9|A0A287QVY9_HORVV (Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1)

HSP 1 Score: 55.1 bits (131), Expect = 1.4e-04
Identity = 24/29 (82.76%), Postives = 27/29 (93.10%), Query Frame = 0


Query: 96  KDALDALGLVRYCCRRMLMTHVDLMKSFL 125
           +DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 3   RDALDALGLVRYCCRRMLMTHVDLIEKLL 31

[Close]

BLAST of CsGy2G017100 vs. TrEMBL
Match: tr|A0A287QVN9|A0A287QVN9_HORVV (Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1)

HSP 1 Score: 55.1 bits (131), Expect = 1.4e-04
Identity = 24/29 (82.76%), Postives = 27/29 (93.10%), Query Frame = 0


Query: 96  KDALDALGLVRYCCRRMLMTHVDLMKSFL 125
           +DALDALGLVRYCCRRMLMTHVDL++  L
Sbjct: 2   RDALDALGLVRYCCRRMLMTHVDLIEKLL 30

The following BLAST results are available for this feature:

BLAST of CsGy2G017100 vs. NCBI nr


Match Name	E-value	Identity	Description
CDY25312.1	7.1e-05	49.21	BnaC01g29810D [Brassica napus]	[more]
XP_019240650.1	2.7e-04	82.76	PREDICTED: DNA-directed RNA polymerases II, IV and V subunit 10-like [Nicotiana ...	[more]
ABF70104.1	4.6e-04	85.71	DNA-directed RNA polymerase II 8.2 kDa polypeptide, putative [Musa balbisiana]	[more]
XP_015618232.1	4.6e-04	85.71	DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Oryza sativa Japonic...	[more]
ABK20909.1	4.6e-04	85.71	unknown [Picea sitchensis] >ABK22149.1 unknown [Picea sitchensis] >ABK25286.1 un...	[more]

BLAST of CsGy2G017100 vs. TAIR10


Match Name	E-value	Identity	Description
AT1G61700.1	8.3e-08	85.71	RNA polymerases N / 8 kDa subunit	[more]
AT1G11475.1	7.0e-07	82.14	RNA polymerases N / 8 kDa subunit	[more]

BLAST of CsGy2G017100 vs. Swiss-Prot


Match Name	E-value	Identity	Description
sp\|Q9SYA6\|RPBAL_ARATH	1.5e-06	85.71	DNA-directed RNA polymerase subunit 10-like protein OS=Arabidopsis thaliana OX=3...	[more]
sp\|Q39290\|RPAB5_BRANA	7.4e-06	82.14	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Brassica napus OX=...	[more]
sp\|Q8LFJ6\|NRPBA_ARATH	1.3e-05	82.14	DNA-directed RNA polymerases II, IV and V subunit 10 OS=Arabidopsis thaliana OX=...	[more]
sp\|Q32P78\|RPAB5_BOVIN	6.3e-05	75.00	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus OX=9913...	[more]
sp\|Q6QN04\|RPAB5_CHILA	6.3e-05	75.00	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Chinchilla laniger...	[more]

BLAST of CsGy2G017100 vs. TrEMBL


Match Name	E-value	Identity	Description
tr\|A0A287QVX2\|A0A287QVX2_HORVV	2.7e-05	83.33	Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1	[more]
tr\|A0A078GJE9\|A0A078GJE9_BRANA	4.7e-05	49.21	BnaC01g29810D protein OS=Brassica napus OX=3708 GN=BnaC01g29810D PE=4 SV=1	[more]
tr\|A0A0D3HS23\|A0A0D3HS23_9ORYZ	6.1e-05	62.50	Uncharacterized protein OS=Oryza barthii OX=65489 PE=3 SV=1	[more]
tr\|A0A287QVY9\|A0A287QVY9_HORVV	1.4e-04	82.76	Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1	[more]
tr\|A0A287QVN9\|A0A287QVN9_HORVV	1.4e-04	82.76	Uncharacterized protein OS=Hordeum vulgare subsp. vulgare OX=112509 PE=4 SV=1	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **Molecular Function**
Term	Definition
GO:0003677	DNA binding
GO:0003899	DNA-directed RNA polymerase activity

Vocabulary: **Biological Process**
Term	Definition
GO:0006351	transcription, DNA-templated

Vocabulary: **INTERPRO**
Term	Definition
IPR023580	RNA_pol_su_RPB10
IPR000268	RNAP_N/Rpb10

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0008150	biological_process
biological_process	GO:0006351	transcription, DNA-templated
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0003677	DNA binding
molecular_function	GO:0003899	DNA-directed RNA polymerase activity

Relationships

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


Feature Name	Unique Name	Type
CsGy2G017100.1	CsGy2G017100.1	mRNA

InterPro

Analysis Name: InterPro Annotations of cucumber Gy14 genome (v2)
Date Performed: 2018-09-25


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	GENE3D	G3DSA:1.10.10.60		coord: 85..126 e-value: 1.5E-11 score: 46.2
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	PFAM	PF01194	RNA_pol_N	coord: 94..121 e-value: 1.1E-10 score: 41.6
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	PANTHER	PTHR23431	FAMILY NOT NAMED	coord: 96..119
IPR000268	DNA-directed RNA polymerase, subunit N/Rpb10	PRODOM	PD006539		coord: 97..124 e-value: 2.0E-5 score: 109.0
IPR023580	RNA polymerase subunit RPB10	SUPERFAMILY	SSF46924	RNA polymerase subunit RPB10	coord: 95..123

Synteny

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


Gene	Orthologue	Organism	Block
CsGy2G017100	CsaV3_2G024730	Cucumber (Chinese Long) v3	cgybcucB065
CsGy2G017100	Bhi04G000542	Wax gourd	cgybwgoB150

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CsGy2G017100	Watermelon (97103) v2	cgybwmbB125
CsGy2G017100	Watermelon (97103) v2	cgybwmbB156
CsGy2G017100	Wax gourd	cgybwgoB188
CsGy2G017100	Cucumber (Gy14) v2	cgybcgybB059
CsGy2G017100	Cucurbita maxima (Rimu)	cgybcmaB170
CsGy2G017100	Cucurbita maxima (Rimu)	cgybcmaB198
CsGy2G017100	Cucurbita maxima (Rimu)	cgybcmaB244
CsGy2G017100	Cucurbita maxima (Rimu)	cgybcmaB250
CsGy2G017100	Cucurbita moschata (Rifu)	cgybcmoB162
CsGy2G017100	Cucurbita moschata (Rifu)	cgybcmoB191
CsGy2G017100	Cucurbita moschata (Rifu)	cgybcmoB232
CsGy2G017100	Cucurbita moschata (Rifu)	cgybcmoB238
CsGy2G017100	Cucurbita pepo (Zucchini)	cgybcpeB154
CsGy2G017100	Cucurbita pepo (Zucchini)	cgybcpeB161
CsGy2G017100	Cucurbita pepo (Zucchini)	cgybcpeB210
CsGy2G017100	Cucurbita pepo (Zucchini)	cgybcpeB263
CsGy2G017100	Cucumber (Chinese Long) v2	cgybcuB057
CsGy2G017100	Cucumber (Chinese Long) v2	cgybcuB076
CsGy2G017100	Bottle gourd (USVL1VR-Ls)	cgyblsiB105
CsGy2G017100	Melon (DHL92) v3.6.1	cgybmedB101
CsGy2G017100	Bottle gourd (USVL1VR-Ls)	cgyblsiB129
CsGy2G017100	Melon (DHL92) v3.5.1	cgybmeB077
CsGy2G017100	Melon (DHL92) v3.5.1	cgybmeB102
CsGy2G017100	Melon (DHL92) v3.6.1	cgybmedB073
CsGy2G017100	Watermelon (Charleston Gray)	cgybwcgB130
CsGy2G017100	Watermelon (Charleston Gray)	cgybwcgB155
CsGy2G017100	Watermelon (97103) v1	cgybwmB098
CsGy2G017100	Watermelon (97103) v1	cgybwmB118
CsGy2G017100	Wild cucumber (PI 183967)	cgybcpiB057
CsGy2G017100	Wild cucumber (PI 183967)	cgybcpiB077
CsGy2G017100	Silver-seed gourd	carcgybB0506
CsGy2G017100	Silver-seed gourd	carcgybB0622
CsGy2G017100	Silver-seed gourd	carcgybB0718
CsGy2G017100	Cucumber (Chinese Long) v3	cgybcucB083