Csa7G004080 (gene) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Csa7G004080
Type	gene
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	RNA-binding protein, putative; contains IPR012677 (Nucleotide-binding, alpha-beta plait)
Location	Chr7 : 149676 .. 150491 (+)

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.

ATGGGAAAGAACAGAAGGCTTAAGGACGGCGCCGATAAGGGAGCCGCCGCCGGCGACCACTGCCCTTCCACAGTCTTTGTCAACAACTTCCCGTACTCGTTCACCAACTCACAGGTTCGTACTTCCTCTACTCCCTGCTTGTCTTCTTAGAAAATATATTGAGCTGAATAGTGTGAGACGTATGGGTTCTTTTTGTACTTTTCTTCTTGAGCTCGACTCATAGAAGCAAGCAATCGAATATTATTTTGGTTATGCAAGCAGTTCAGGAAATGCTTTGACTTTATTTCTTTCGGATTGTTTTGTTGTTCTATGCAATGTTAGTGAGCTTTCCTGTTTTCTCTATGTTCAATTAGCTTGAAGAAACATTCAGTGATGTTGGACCGGTCCGGCGGTGCTTCATGGTTACCCAAAAGGGTAAGTACGTCTGTGCATGATTATCTCGGATTCCCTTTCTTGCTTATTTGTTTATTTATTTATTTATTTTGCATTTCTTGTGCTTCTTGAGATGTCTGATGATTTGGTGATTTGGATACTATGAAGGAGCATTTGATCGAATAGATGGAGTGCTGTTATGAGATAATTGAATCGTGGCTTTATTGTTATTATTATCTTTTCATTGAAAAATCACTCGGCCAAAACTTCATTCTACATTTTCCTTTTTAGGGATCGTGTGGAAACCGAATGTTGTGTTCTACGTTTGTAAATTTTCAGATGTCATTTTGAGATATTTTTTTATTGAGAATGGTTTAAAACTTATCTTATTTTATGTCATCAGGTTCAACCGAGCATCGTGGTTTTGGATTCGTGCAGTTGTAA

mRNA sequence

ATGGGAAAGAACAGAAGGCTTAAGGACGGCGCCGATAAGGGAGCCGCCGCCGGCGACCACTGCCCTTCCACAGTCTTTGTCAACAACTTCCCGTACTCGTTCACCAACTCACAGCTTGAAGAAACATTCAGTGATGTTGGACCGGTCCGGCGGTGCTTCATGGTTACCCAAAAGGGTTCAACCGAGCATCGTGGTTTTGGATTCGTGCAGTTGTAA

Coding sequence (CDS)

ATGGGAAAGAACAGAAGGCTTAAGGACGGCGCCGATAAGGGAGCCGCCGCCGGCGACCACTGCCCTTCCACAGTCTTTGTCAACAACTTCCCGTACTCGTTCACCAACTCACAGCTTGAAGAAACATTCAGTGATGTTGGACCGGTCCGGCGGTGCTTCATGGTTACCCAAAAGGGTTCAACCGAGCATCGTGGTTTTGGATTCGTGCAGTTGTAA

Protein sequence

MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGSTEHRGFGFVQL*

Homology

[Close]

BLAST of Csa7G004080 vs. Swiss-Prot
Match: RBM28_MOUSE (RNA-binding protein 28 OS=Mus musculus GN=Rbm28 PE=1 SV=4)

HSP 1 Score: 58.9 bits (141), Expect = 2.6e-08
Identity = 27/46 (58.70%), Postives = 32/46 (69.57%), Query Frame = 1


Query: 24 TVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGSTEHRGFGFV 70
          T+FV   P S  + QLEE FS VGPV++CF+VT+KGS   RGFG+V
Sbjct: 5  TLFVGRLPPSARSDQLEELFSQVGPVKQCFVVTEKGSKACRGFGYV 50

[Close]

BLAST of Csa7G004080 vs. Swiss-Prot
Match: RBM28_HUMAN (RNA-binding protein 28 OS=Homo sapiens GN=RBM28 PE=1 SV=3)

HSP 1 Score: 58.9 bits (141), Expect = 2.6e-08
Identity = 27/46 (58.70%), Postives = 32/46 (69.57%), Query Frame = 1


Query: 24 TVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGSTEHRGFGFV 70
          T+FV   P S  + QLEE FS VGPV++CF+VT+KGS   RGFG+V
Sbjct: 5  TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKGSKACRGFGYV 50

[Close]

BLAST of Csa7G004080 vs. TrEMBL
Match: A0A0A0K0D5_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_7G004080 PE=4 SV=1)

HSP 1 Score: 151.8 bits (382), Expect = 3.3e-34
Identity = 71/71 (100.00%), Postives = 71/71 (100.00%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS
Sbjct: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQL 72
          TEHRGFGFVQL
Sbjct: 61 TEHRGFGFVQL 71

[Close]

BLAST of Csa7G004080 vs. TrEMBL
Match: F6I1A7_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VIT_03s0038g00110 PE=4 SV=1)

HSP 1 Score: 115.2 bits (287), Expect = 3.4e-23
Identity = 55/70 (78.57%), Postives = 59/70 (84.29%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGK    K+  + G A   HCPSTVFV+NFPYSFTNSQLEETFSDVGP+RRCFMVTQKGS
Sbjct: 1  MGK----KNKTEGGGARDQHCPSTVFVSNFPYSFTNSQLEETFSDVGPIRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFGFVQ
Sbjct: 61 TEHRGFGFVQ 66

[Close]

BLAST of Csa7G004080 vs. TrEMBL
Match: A0A0J8BDC2_BETVU (Uncharacterized protein OS=Beta vulgaris subsp. vulgaris GN=BVRB_3g067890 PE=4 SV=1)

HSP 1 Score: 112.8 bits (281), Expect = 1.7e-22
Identity = 51/70 (72.86%), Postives = 60/70 (85.71%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKN++LK+G        +HCP+TVFV+NFP+SFT SQLEETFSDVGP+RRCFMVT KGS
Sbjct: 1  MGKNKKLKEGQQS-----EHCPATVFVSNFPFSFTTSQLEETFSDVGPIRRCFMVTNKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFG+VQ
Sbjct: 61 TEHRGFGYVQ 65

[Close]

BLAST of Csa7G004080 vs. TrEMBL
Match: A0A0J8BFV6_BETVU (Uncharacterized protein OS=Beta vulgaris subsp. vulgaris GN=BVRB_3g067890 PE=4 SV=1)

HSP 1 Score: 112.8 bits (281), Expect = 1.7e-22
Identity = 51/70 (72.86%), Postives = 60/70 (85.71%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKN++LK+G        +HCP+TVFV+NFP+SFT SQLEETFSDVGP+RRCFMVT KGS
Sbjct: 1  MGKNKKLKEGQQS-----EHCPATVFVSNFPFSFTTSQLEETFSDVGPIRRCFMVTNKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFG+VQ
Sbjct: 61 TEHRGFGYVQ 65

[Close]

BLAST of Csa7G004080 vs. TrEMBL
Match: K4B3L2_SOLLC (Uncharacterized protein OS=Solanum lycopersicum PE=4 SV=1)

HSP 1 Score: 107.1 bits (266), Expect = 9.3e-21
Identity = 49/70 (70.00%), Postives = 56/70 (80.00%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKN++   G D       H PST+FVNN PYSFTN+QLEETFS+VGP+RRCFMVT KGS
Sbjct: 1  MGKNKKTMSGGDS-----QHSPSTIFVNNLPYSFTNAQLEETFSEVGPIRRCFMVTNKGS 60

Query: 61 TEHRGFGFVQ 71
          +EHRGFGFVQ
Sbjct: 61 SEHRGFGFVQ 65

[Close]

BLAST of Csa7G004080 vs. TAIR10
Match: AT2G21440.1 (AT2G21440.1 RNA-binding (RRM/RBD/RNP motifs) family protein)

HSP 1 Score: 87.4 bits (215), Expect = 3.8e-18
Identity = 44/71 (61.97%), Postives = 50/71 (70.42%), Query Frame = 1


Query: 1  MGKNRR-LKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKG 60
          MGKN+R  KDG +K      H  +TV V+  PYS TN+QLEE FS+VGPVRRCF+VT KG
Sbjct: 1  MGKNKRERKDGEEKSP----HAAATVCVSGLPYSITNAQLEEAFSEVGPVRRCFLVTNKG 60

Query: 61 STEHRGFGFVQ 71
          S EHRGF FV+
Sbjct: 61 SDEHRGFAFVK 67

[Close]

BLAST of Csa7G004080 vs. NCBI nr
Match: gi|700187922|gb|KGN43155.1| (hypothetical protein Csa_7G004080 [Cucumis sativus])

HSP 1 Score: 151.8 bits (382), Expect = 4.7e-34
Identity = 71/71 (100.00%), Postives = 71/71 (100.00%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS
Sbjct: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQL 72
          TEHRGFGFVQL
Sbjct: 61 TEHRGFGFVQL 71

[Close]

BLAST of Csa7G004080 vs. NCBI nr
Match: gi|449461647|ref|XP_004148553.1| (PREDICTED: RNA-binding protein 28 [Cucumis sativus])

HSP 1 Score: 150.2 bits (378), Expect = 1.4e-33
Identity = 70/70 (100.00%), Postives = 70/70 (100.00%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS
Sbjct: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFGFVQ
Sbjct: 61 TEHRGFGFVQ 70

[Close]

BLAST of Csa7G004080 vs. NCBI nr
Match: gi|659094468|ref|XP_008448076.1| (PREDICTED: RNA-binding protein 28 [Cucumis melo])

HSP 1 Score: 143.3 bits (360), Expect = 1.7e-31
Identity = 67/70 (95.71%), Postives = 67/70 (95.71%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGKNRRLKDGADKGAAAGDHCPS VFV N PYSFTNSQLEETFSDVGPVRRCFMVTQKGS
Sbjct: 1  MGKNRRLKDGADKGAAAGDHCPSKVFVKNLPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFGFVQ
Sbjct: 61 TEHRGFGFVQ 70

[Close]

BLAST of Csa7G004080 vs. NCBI nr
Match: gi|297744765|emb|CBI38027.3| (unnamed protein product [Vitis vinifera])

HSP 1 Score: 115.2 bits (287), Expect = 4.9e-23
Identity = 55/70 (78.57%), Postives = 59/70 (84.29%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGK    K+  + G A   HCPSTVFV+NFPYSFTNSQLEETFSDVGP+RRCFMVTQKGS
Sbjct: 1  MGK----KNKTEGGGARDQHCPSTVFVSNFPYSFTNSQLEETFSDVGPIRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFGFVQ
Sbjct: 61 TEHRGFGFVQ 66

[Close]

BLAST of Csa7G004080 vs. NCBI nr
Match: gi|731383175|ref|XP_010647689.1| (PREDICTED: RNA-binding protein 28 isoform X2 [Vitis vinifera])

HSP 1 Score: 115.2 bits (287), Expect = 4.9e-23
Identity = 55/70 (78.57%), Postives = 59/70 (84.29%), Query Frame = 1


Query: 1  MGKNRRLKDGADKGAAAGDHCPSTVFVNNFPYSFTNSQLEETFSDVGPVRRCFMVTQKGS 60
          MGK    K+  + G A   HCPSTVFV+NFPYSFTNSQLEETFSDVGP+RRCFMVTQKGS
Sbjct: 1  MGK----KNKTEGGGARDQHCPSTVFVSNFPYSFTNSQLEETFSDVGPIRRCFMVTQKGS 60

Query: 61 TEHRGFGFVQ 71
          TEHRGFGFVQ
Sbjct: 61 TEHRGFGFVQ 66

The following BLAST results are available for this feature:

BLAST of Csa7G004080 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RBM28_MOUSE	2.6e-08	58.70	RNA-binding protein 28 OS=Mus musculus GN=Rbm28 PE=1 SV=4	[more]
RBM28_HUMAN	2.6e-08	58.70	RNA-binding protein 28 OS=Homo sapiens GN=RBM28 PE=1 SV=3	[more]

BLAST of Csa7G004080 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0K0D5_CUCSA	3.3e-34	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_7G004080 PE=4 SV=1	[more]
F6I1A7_VITVI	3.4e-23	78.57	Putative uncharacterized protein OS=Vitis vinifera GN=VIT_03s0038g00110 PE=4 SV=...	[more]
A0A0J8BDC2_BETVU	1.7e-22	72.86	Uncharacterized protein OS=Beta vulgaris subsp. vulgaris GN=BVRB_3g067890 PE=4 S...	[more]
A0A0J8BFV6_BETVU	1.7e-22	72.86	Uncharacterized protein OS=Beta vulgaris subsp. vulgaris GN=BVRB_3g067890 PE=4 S...	[more]
K4B3L2_SOLLC	9.3e-21	70.00	Uncharacterized protein OS=Solanum lycopersicum PE=4 SV=1	[more]

BLAST of Csa7G004080 vs. TAIR10


Match Name	E-value	Identity	Description
AT2G21440.1	3.8e-18	61.97	RNA-binding (RRM/RBD/RNP motifs) family protein	[more]

BLAST of Csa7G004080 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700187922\|gb\|KGN43155.1\|	4.7e-34	100.00	hypothetical protein Csa_7G004080 [Cucumis sativus]	[more]
gi\|449461647\|ref\|XP_004148553.1\|	1.4e-33	100.00	PREDICTED: RNA-binding protein 28 [Cucumis sativus]	[more]
gi\|659094468\|ref\|XP_008448076.1\|	1.7e-31	95.71	PREDICTED: RNA-binding protein 28 [Cucumis melo]	[more]
gi\|297744765\|emb\|CBI38027.3\|	4.9e-23	78.57	unnamed protein product [Vitis vinifera]	[more]
gi\|731383175\|ref\|XP_010647689.1\|	4.9e-23	78.57	PREDICTED: RNA-binding protein 28 isoform X2 [Vitis vinifera]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR000504	RRM_dom
IPR012677	Nucleotide-bd_a/b_plait_sf

Vocabulary: **Molecular Function**
Term	Definition
GO:0003676	nucleic acid binding
GO:0000166	nucleotide binding

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0008150	biological_process
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0000785	chromatin
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0000166	nucleotide binding
molecular_function	GO:0003682	chromatin binding
molecular_function	GO:0005515	protein binding
molecular_function	GO:0008270	zinc ion binding
molecular_function	GO:0003723	RNA binding

Relationships

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


Feature Name	Unique Name	Type
Csa7G004080.1	Csa7G004080.1	mRNA

InterPro

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


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000504	RNA recognition motif domain	PFAM	PF00076	RRM_1	coord: 25..70 score: 3.7
IPR000504	RNA recognition motif domain	PROFILE	PS50102	RRM	coord: 23..71 score: 11
IPR012677	Nucleotide-binding alpha-beta plait domain	GENE3D	G3DSA:3.30.70.330		coord: 23..70 score: 6.8
IPR012677	Nucleotide-binding alpha-beta plait domain	unknown	SSF54928	RNA-binding domain, RBD	coord: 16..70 score: 8.06
None	No IPR available	PANTHER	PTHR24012	FAMILY NOT NAMED	coord: 1..70 score: 1.2
None	No IPR available	PANTHER	PTHR24012:SF411	EXPRESSED PROTEIN	coord: 1..70 score: 1.2

Synteny

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


Gene	Orthologue	Organism	Block
Csa7G004080	Cla015904	Watermelon (97103) v1	cuwmB604
Csa7G004080	MELO3C013443	Melon (DHL92) v3.5.1	cumeB531
Csa7G004080	ClCG02G004760	Watermelon (Charleston Gray)	cuwcgB546
Csa7G004080	Lsi11G011240	Bottle gourd (USVL1VR-Ls)	culsiB494
Csa7G004080	MELO3C013443.2	Melon (DHL92) v3.6.1	cumedB510
Csa7G004080	Cla97C02G031740	Watermelon (97103) v2	cuwmbB529
Csa7G004080	Bhi05G001124	Wax gourd	cuwgoB668
Csa7G004080	CmoCh19G006940	Cucurbita moschata (Rifu)	cmocuB518
Csa7G004080	Cp4.1LG15g05540	Cucurbita pepo (Zucchini)	cpecuB257
Csa7G004080	CsGy7G000170	Cucumber (Gy14) v2	cgybcuB324
Csa7G004080	Carg19396	Silver-seed gourd	carcuB0342

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Csa7G004080	Wax gourd	cuwgoB681
Csa7G004080	Cucumber (Chinese Long) v2	cucuB077
Csa7G004080	Cucumber (Gy14) v1	cgycuB136
Csa7G004080	Cucumber (Gy14) v1	cgycuB528
Csa7G004080	Cucurbita maxima (Rimu)	cmacuB152
Csa7G004080	Cucurbita maxima (Rimu)	cmacuB575
Csa7G004080	Cucurbita maxima (Rimu)	cmacuB644
Csa7G004080	Cucurbita moschata (Rifu)	cmocuB139
Csa7G004080	Cucurbita moschata (Rifu)	cmocuB561
Csa7G004080	Cucurbita moschata (Rifu)	cmocuB633
Csa7G004080	Melon (DHL92) v3.5.1	cumeB513
Csa7G004080	Watermelon (Charleston Gray)	cuwcgB534
Csa7G004080	Watermelon (97103) v1	cuwmB609
Csa7G004080	Cucurbita pepo (Zucchini)	cpecuB301
Csa7G004080	Cucurbita pepo (Zucchini)	cpecuB696
Csa7G004080	Cucurbita pepo (Zucchini)	cpecuB766
Csa7G004080	Cucurbita pepo (Zucchini)	cpecuB847
Csa7G004080	Bottle gourd (USVL1VR-Ls)	culsiB489
Csa7G004080	Cucumber (Gy14) v2	cgybcuB088
Csa7G004080	Melon (DHL92) v3.6.1	cumedB493
Csa7G004080	Silver-seed gourd	carcuB0194
Csa7G004080	Silver-seed gourd	carcuB0997
Csa7G004080	Watermelon (97103) v2	cuwmbB519