Csa1G690340 (gene) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Csa1G690340
Type	gene
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	DNA-directed RNA polymerase
Location	Chr1 : 27798112 .. 27798502 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDS

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

ATGTTAGATGATGATGGACTTGCTGCACTAGGAGAGATAATTGGACCAAGTGACGTTTATGTCAACAAACAATCCCCCATCATAATGAAAGGATCACCCTTACCAGGAATACCAGATAGTGCATATAGACCTTGTAGACAAGTATTTAAAGGTTCTGAAGGAGAGCCGACAGTGGTTGATGGGATGGCTCTTTCTACAGATAAGAATGACTGTTTATGTATCAAATTCTTCATTTGCCTGACCTGTAGACTAGAGCGGTGATAAGTTCAGTAGCAGACATATACAAAAAGGTGTATGTGGCACAATTGTGCAGCAAGAAGATTTCCCATTTTCTGCATGTGGAATTTCTGGATCTAATTATGAATCCTCATGGATTTCCGAGAAGTCATGA

mRNA sequence

ATGTTAGATGATGATGGACTTGCTGCACTAGGAGAGATAATTGGACCAAGTGACGTTTATGTCAACAAACAATCCCCCATCATAATGAAAGGATCACCCTTACCAGGAATACCAGATAGTGCATATAGACCTTGTAGACAAGTATTTAAAGGTTCTGAAGGAGAGCCGACAGTGCAAGAAGATTTCCCATTTTCTGCATGTGGAATTTCTGGATCTAATTATGAATCCTCATGGATTTCCGAGAAGTCATGA

Coding sequence (CDS)

ATGTTAGATGATGATGGACTTGCTGCACTAGGAGAGATAATTGGACCAAGTGACGTTTATGTCAACAAACAATCCCCCATCATAATGAAAGGATCACCCTTACCAGGAATACCAGATAGTGCATATAGACCTTGTAGACAAGTATTTAAAGGTTCTGAAGGAGAGCCGACAGTGCAAGAAGATTTCCCATTTTCTGCATGTGGAATTTCTGGATCTAATTATGAATCCTCATGGATTTCCGAGAAGTCATGA

Protein sequence

MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQEDFPFSACGISGSNYESSWISEKS*

Homology

[Close]

BLAST of Csa1G690340 vs. Swiss-Prot
Match: NRPC2_ARATH (DNA-directed RNA polymerase III subunit 2 OS=Arabidopsis thaliana GN=NRPC2 PE=2 SV=1)

HSP 1 Score: 65.1 bits (157), Expect = 4.2e-10
Identity = 31/58 (53.45%), Postives = 36/58 (62.07%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTV 59
           +LDDDGLA  GEII P+D+Y+NKQ P+         + DS YRP R+ FKG EGE  V
Sbjct: 827 ILDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQV 884

[Close]

BLAST of Csa1G690340 vs. TrEMBL
Match: A0A0A0M0Z5_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G690340 PE=4 SV=1)

HSP 1 Score: 174.1 bits (440), Expect = 7.2e-41
Identity = 83/83 (100.00%), Postives = 83/83 (100.00%), Query Frame = 1


Query: 1  MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE 60
          MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE
Sbjct: 1  MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE 60

Query: 61 DFPFSACGISGSNYESSWISEKS 84
          DFPFSACGISGSNYESSWISEKS
Sbjct: 61 DFPFSACGISGSNYESSWISEKS 83

[Close]

BLAST of Csa1G690340 vs. TrEMBL
Match: F6HVA6_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VIT_13s0084g00180 PE=4 SV=1)

HSP 1 Score: 81.6 bits (200), Expect = 4.9e-13
Identity = 41/61 (67.21%), Postives = 50/61 (81.97%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKG---SPLPGIPDSAYRPCRQVFKGSEGEPT 59
           +LDDDGLAA GEII P+D+Y+NK+SPII KG   SP+ G+PDSAY+P RQ FKG EGE +
Sbjct: 101 ILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPV-GLPDSAYKPSRQTFKGPEGEAS 160

[Close]

BLAST of Csa1G690340 vs. TrEMBL
Match: A5AMN9_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VITISV_031440 PE=4 SV=1)

HSP 1 Score: 81.6 bits (200), Expect = 4.9e-13
Identity = 41/61 (67.21%), Postives = 50/61 (81.97%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKG---SPLPGIPDSAYRPCRQVFKGSEGEPT 59
           +LDDDGLAA GEII P+D+Y+NK+SPII KG   SP+ G+PDSAY+P RQ FKG EGE +
Sbjct: 297 ILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPV-GLPDSAYKPSRQTFKGPEGEAS 356

[Close]

BLAST of Csa1G690340 vs. TrEMBL
Match: A0A059DCX6_EUCGR (DNA-directed RNA polymerase subunit beta (Fragment) OS=Eucalyptus grandis GN=EUGRSUZ_A007941 PE=3 SV=1)

HSP 1 Score: 79.7 bits (195), Expect = 1.8e-12
Identity = 43/78 (55.13%), Postives = 54/78 (69.23%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSP-LPGIPDSAYRPCRQVFKGSEGEPTVQ 60
           +LD+DG+AA GEII P+DVY+NK+SPII KG+P L G+ DS Y+P RQ FKG+EGE  V 
Sbjct: 409 ILDNDGIAAPGEIIRPNDVYINKESPIITKGNPKLGGLKDSDYKPSRQTFKGAEGESCVV 468

Query: 61  EDFPFSACGISGSNYESS 78
           +    S    S  NY  S
Sbjct: 469 DRVTLS----SDKNYNLS 482

[Close]

BLAST of Csa1G690340 vs. TrEMBL
Match: W9RD68_9ROSA (DNA-directed RNA polymerase III subunit RPC2 OS=Morus notabilis GN=L484_011540 PE=4 SV=1)

HSP 1 Score: 73.9 bits (180), Expect = 1.0e-10
Identity = 35/58 (60.34%), Postives = 42/58 (72.41%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTV 59
           +LDDDGLAA GEII P+D+Y+NKQSP + KG    G+ DS Y+P  Q FKG EGE  V
Sbjct: 105 VLDDDGLAAPGEIIRPNDIYINKQSPKVTKGPMRTGLTDSDYKPACQTFKGPEGESCV 162

[Close]

BLAST of Csa1G690340 vs. TAIR10
Match: AT5G45140.1 (AT5G45140.1 nuclear RNA polymerase C2)

HSP 1 Score: 65.1 bits (157), Expect = 2.4e-11
Identity = 31/58 (53.45%), Postives = 36/58 (62.07%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTV 59
           +LDDDGLA  GEII P+D+Y+NKQ P+         + DS YRP R+ FKG EGE  V
Sbjct: 827 ILDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQV 884

[Close]

BLAST of Csa1G690340 vs. NCBI nr
Match: gi|700211701|gb|KGN66797.1| (hypothetical protein Csa_1G690340 [Cucumis sativus])

HSP 1 Score: 174.1 bits (440), Expect = 1.0e-40
Identity = 83/83 (100.00%), Postives = 83/83 (100.00%), Query Frame = 1


Query: 1  MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE 60
          MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE
Sbjct: 1  MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTVQE 60

Query: 61 DFPFSACGISGSNYESSWISEKS 84
          DFPFSACGISGSNYESSWISEKS
Sbjct: 61 DFPFSACGISGSNYESSWISEKS 83

[Close]

BLAST of Csa1G690340 vs. NCBI nr
Match: gi|659124980|ref|XP_008462447.1| (PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Cucumis melo])

HSP 1 Score: 110.9 bits (276), Expect = 1.1e-21
Identity = 52/58 (89.66%), Postives = 55/58 (94.83%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTV 59
           +LDDDGLAA GEII P+DVYVNKQSPII KGSPLPGIPDSAYRPCRQ+FKGSEGEPTV
Sbjct: 824 ILDDDGLAAPGEIIRPNDVYVNKQSPIITKGSPLPGIPDSAYRPCRQIFKGSEGEPTV 881

[Close]

BLAST of Csa1G690340 vs. NCBI nr
Match: gi|778730035|ref|XP_004141655.2| (PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Cucumis sativus])

HSP 1 Score: 109.4 bits (272), Expect = 3.1e-21
Identity = 50/58 (86.21%), Postives = 55/58 (94.83%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKGSPLPGIPDSAYRPCRQVFKGSEGEPTV 59
           +LDDDGLAA GEII P+D+YVNKQSPII KGSPLPGIPD+AYRPCRQ+FKGSEGEPTV
Sbjct: 824 ILDDDGLAAPGEIIRPNDIYVNKQSPIITKGSPLPGIPDNAYRPCRQIFKGSEGEPTV 881

[Close]

BLAST of Csa1G690340 vs. NCBI nr
Match: gi|147819201|emb|CAN62632.1| (hypothetical protein VITISV_031440 [Vitis vinifera])

HSP 1 Score: 81.6 bits (200), Expect = 7.0e-13
Identity = 41/61 (67.21%), Postives = 50/61 (81.97%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKG---SPLPGIPDSAYRPCRQVFKGSEGEPT 59
           +LDDDGLAA GEII P+D+Y+NK+SPII KG   SP+ G+PDSAY+P RQ FKG EGE +
Sbjct: 297 ILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPV-GLPDSAYKPSRQTFKGPEGEAS 356

[Close]

BLAST of Csa1G690340 vs. NCBI nr
Match: gi|296087814|emb|CBI35070.3| (unnamed protein product [Vitis vinifera])

HSP 1 Score: 81.6 bits (200), Expect = 7.0e-13
Identity = 41/61 (67.21%), Postives = 50/61 (81.97%), Query Frame = 1


Query: 1   MLDDDGLAALGEIIGPSDVYVNKQSPIIMKG---SPLPGIPDSAYRPCRQVFKGSEGEPT 59
           +LDDDGLAA GEII P+D+Y+NK+SPII KG   SP+ G+PDSAY+P RQ FKG EGE +
Sbjct: 125 ILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISPV-GLPDSAYKPSRQTFKGPEGEAS 184

The following BLAST results are available for this feature:

BLAST of Csa1G690340 vs. Swiss-Prot


Match Name	E-value	Identity	Description
NRPC2_ARATH	4.2e-10	53.45	DNA-directed RNA polymerase III subunit 2 OS=Arabidopsis thaliana GN=NRPC2 PE=2 ...	[more]

BLAST of Csa1G690340 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0M0Z5_CUCSA	7.2e-41	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G690340 PE=4 SV=1	[more]
F6HVA6_VITVI	4.9e-13	67.21	Putative uncharacterized protein OS=Vitis vinifera GN=VIT_13s0084g00180 PE=4 SV=...	[more]
A5AMN9_VITVI	4.9e-13	67.21	Putative uncharacterized protein OS=Vitis vinifera GN=VITISV_031440 PE=4 SV=1	[more]
A0A059DCX6_EUCGR	1.8e-12	55.13	DNA-directed RNA polymerase subunit beta (Fragment) OS=Eucalyptus grandis GN=EUG...	[more]
W9RD68_9ROSA	1.0e-10	60.34	DNA-directed RNA polymerase III subunit RPC2 OS=Morus notabilis GN=L484_011540 P...	[more]

BLAST of Csa1G690340 vs. TAIR10


Match Name	E-value	Identity	Description
AT5G45140.1	2.4e-11	53.45	nuclear RNA polymerase C2	[more]

BLAST of Csa1G690340 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700211701\|gb\|KGN66797.1\|	1.0e-40	100.00	hypothetical protein Csa_1G690340 [Cucumis sativus]	[more]
gi\|659124980\|ref\|XP_008462447.1\|	1.1e-21	89.66	PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Cucumis melo]	[more]
gi\|778730035\|ref\|XP_004141655.2\|	3.1e-21	86.21	PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Cucumis sativus]	[more]
gi\|147819201\|emb\|CAN62632.1\|	7.0e-13	67.21	hypothetical protein VITISV_031440 [Vitis vinifera]	[more]
gi\|296087814\|emb\|CBI35070.3\|	7.0e-13	67.21	unnamed protein product [Vitis vinifera]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR014724	RNA_pol_RPB2_OB-fold

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

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:0001522	pseudouridine synthesis
biological_process	GO:0009451	RNA modification
cellular_component	GO:0005730	nucleolus
molecular_function	GO:0003899	DNA-directed RNA polymerase activity
molecular_function	GO:1901363	heterocyclic compound binding
molecular_function	GO:0097159	organic cyclic compound binding
molecular_function	GO:0009982	pseudouridine synthase activity
molecular_function	GO:0003723	RNA binding

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
CU176807	cucumber EST collection version 3.0	transcribed_cluster

Relationships

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


Feature Name	Unique Name	Type
Csa1G690340.1	Csa1G690340.1	mRNA

The following transcribed_cluster feature(s) are associated with this gene:


Feature Name	Unique Name	Type
CU176807	CU176807	transcribed_cluster

InterPro

Analysis Name: InterPro Annotations of cucumber (Chinese Long)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR014724	RNA polymerase Rpb2, OB-fold	GENE3D	G3DSA:2.40.50.150		coord: 2..32 score: 1.

Synteny

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

None

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Csa1G690340	Cucurbita pepo (Zucchini)	cpecuB639
Csa1G690340	Cucurbita pepo (Zucchini)	cpecuB701
Csa1G690340	Bottle gourd (USVL1VR-Ls)	culsiB058
Csa1G690340	Bottle gourd (USVL1VR-Ls)	culsiB080
Csa1G690340	Cucumber (Gy14) v2	cgybcuB002
Csa1G690340	Melon (DHL92) v3.6.1	cumedB037
Csa1G690340	Silver-seed gourd	carcuB0016
Csa1G690340	Silver-seed gourd	carcuB0927
Csa1G690340	Watermelon (97103) v2	cuwmbB075
Csa1G690340	Watermelon (97103) v2	cuwmbB082
Csa1G690340	Wax gourd	cuwgoB113
Csa1G690340	Cucumber (Gy14) v1	cgycuB417
Csa1G690340	Cucurbita maxima (Rimu)	cmacuB064
Csa1G690340	Cucurbita maxima (Rimu)	cmacuB085
Csa1G690340	Cucurbita moschata (Rifu)	cmocuB075
Csa1G690340	Cucurbita moschata (Rifu)	cmocuB054
Csa1G690340	Melon (DHL92) v3.5.1	cumeB045
Csa1G690340	Watermelon (Charleston Gray)	cuwcgB077
Csa1G690340	Watermelon (Charleston Gray)	cuwcgB085
Csa1G690340	Watermelon (97103) v1	cuwmB090