CsaV3_7G005520 (gene) Cucumber (Chinese Long) v3 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CsaV3_7G005520
Type	gene
Organism	Cucumis sativus (Cucumber (Chinese Long) v3)
Description	Splicing factor 3b subunit 3
Location	chr7 : 3266178 .. 3266766 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: polypeptideexonCDS

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

ATGGCGGTTTCGGAGGAGGAATGTTCATCTGCGAAATCGCGATCTTCATCTTCCACTTCTAGTTCCACGTATTACTTGGCTAAGTGCGTTCTCAGAGGCAGTGTTGTTCTCCAGGTTCTTTACGGTCACATACGCTCTCCGAGCTCTCTCGATGTCGTCTTTGGCAAGGTTTGTTCTGTATTTTGTTGTTAATGAACTCTTCTTCATTTTTGAAGTGTTTCGTTATGCTTTATTGATAGGCATTGGTGTAGTTGTTTGGACTTACGGAACCAATTGGTTAAATAGAGCAATCAGCTGTTCTGTACTTTTATTTGATTGAAGCTCGTTTCCTCTCGGTAATTATTTAACTTCTGGTATAGGTTTGCATCGTGTTTTTTCCTCTTATTCAAGTAGTGAATGAAGAGTGTTGTTCCTTGCTTCAGAAATCAGAGGCATTTCGATACTTGGTTTGTTGGCGTGGGTATTTTAATGTTAGGATGTAGGTTTATCGTTTACAGGACTTTAATTTCTCTAATGGAGTAAAAATGTGAATCTCATGCATCCTGCCAATTGCTGTCTGCAATGGAGGGAGTTCATTTCATTTTAAATC

mRNA sequence

ATGGCGGTTTCGGAGGAGGAATGTTCATCTGCGAAATCGCGATCTTCATCTTCCACTTCTAGTTCCACGTATTACTTGGCTAAGTGCGTTCTCAGAGGCAGTGTTGTTCTCCAGGTTCTTTACGGTCACATACGCTCTCCGAGCTCTCTCGATGTCGTCTTTGGCAAGGTTTGCATCGTGTTTTTTCCTCTTATTCAAGTAGTGAATGAAGAGTGTTGTTCCTTGCTTCAGAAATCAGAGGCATTTCGATACTTGGTTTGTTGGCGTGGGTATTTTAATGTTAGGATGTAG

Coding sequence (CDS)

ATGGCGGTTTCGGAGGAGGAATGTTCATCTGCGAAATCGCGATCTTCATCTTCCACTTCTAGTTCCACGTATTACTTGGCTAAGTGCGTTCTCAGAGGCAGTGTTGTTCTCCAGGTTCTTTACGGTCACATACGCTCTCCGAGCTCTCTCGATGTCGTCTTTGGCAAGGTTTGCATCGTGTTTTTTCCTCTTATTCAAGTAGTGAATGAAGAGTGTTGTTCCTTGCTTCAGAAATCAGAGGCATTTCGATACTTGGTTTGTTGGCGTGGGTATTTTAATGTTAGGATGTAG

Protein sequence

MAVSEEECSSAKSRSSSSTSSSTYYLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGKVCIVFFPLIQVVNEECCSLLQKSEAFRYLVCWRGYFNVRM

Homology

[Close]

BLAST of CsaV3_7G005520 vs. NCBI nr
Match: XP_004136549.1 (PREDICTED: splicing factor 3B subunit 3 [Cucumis sativus] >KGN59264.1 hypothetical protein Csa_3G792040 [Cucumis sativus])

HSP 1 Score: 74.3 bits (181), Expect = 2.5e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. NCBI nr
Match: XP_008443005.1 (PREDICTED: pre-mRNA-splicing factor RSE1 [Cucumis melo])

HSP 1 Score: 74.3 bits (181), Expect = 2.5e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. NCBI nr
Match: XP_022934513.1 (pre-mRNA-splicing factor RSE1 [Cucurbita moschata])

HSP 1 Score: 74.3 bits (181), Expect = 2.5e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. NCBI nr
Match: XP_023526646.1 (splicing factor 3B subunit 3 [Cucurbita pepo subsp. pepo])

HSP 1 Score: 74.3 bits (181), Expect = 2.5e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. NCBI nr
Match: XP_015898900.1 (uncharacterized protein LOC107432303 isoform X1 [Ziziphus jujuba])

HSP 1 Score: 73.2 bits (178), Expect = 5.6e-10
Identity = 53/56 (94.64%), Postives = 54/56 (96.43%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEEC XXXXXXXXXXXXXXX LAKCVLRGSVVLQV+YGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECSXXXXXXXXXXXXXXXYLAKCVLRGSVVLQVVYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. TAIR10
Match: AT3G11960.1 (Cleavage and polyadenylation specificity factor (CPSF) A subunit protein)

HSP 1 Score: 52.4 bits (124), Expect = 1.8e-07
Identity = 26/35 (74.29%), Postives = 29/35 (82.86%), Query Frame = 0


Query: 26 LAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK-VCI 60
          LAKC+LR SVVLQV YG+ RSPSS D+VFGK  CI
Sbjct: 37 LAKCILRPSVVLQVAYGYFRSPSSRDIVFGKETCI 71

[Close]

BLAST of CsaV3_7G005520 vs. TrEMBL
Match: tr|A0A1S3B741|A0A1S3B741_CUCME (pre-mRNA-splicing factor RSE1 OS=Cucumis melo OX=3656 GN=LOC103486735 PE=4 SV=1)

HSP 1 Score: 74.3 bits (181), Expect = 1.7e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. TrEMBL
Match: tr|A0A0A0LEB2|A0A0A0LEB2_CUCSA (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_3G792040 PE=4 SV=1)

HSP 1 Score: 74.3 bits (181), Expect = 1.7e-10
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK
Sbjct: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. TrEMBL
Match: tr|A0A2C9VD89|A0A2C9VD89_MANES (Uncharacterized protein OS=Manihot esculenta OX=3983 GN=MANES_08G040000 PE=4 SV=1)

HSP 1 Score: 68.9 bits (167), Expect = 7.0e-09
Identity = 35/56 (62.50%), Postives = 37/56 (66.07%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEEC                 LAKCVLRGSVVLQV+YGH RSPSS D+VFGK
Sbjct: 1  MAVSEEECSNAKSRSSSPSANGAYYLAKCVLRGSVVLQVVYGHFRSPSSSDIVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. TrEMBL
Match: tr|V7D0H9|V7D0H9_PHAVU (Uncharacterized protein OS=Phaseolus vulgaris OX=3885 GN=PHAVU_001G200200g PE=4 SV=1)

HSP 1 Score: 67.8 bits (164), Expect = 1.5e-08
Identity = 35/56 (62.50%), Postives = 37/56 (66.07%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEEC                 L+KCVLRGSVVLQVLY HIRSPSS D+VFGK
Sbjct: 1  MAVSEEECSSAKSGSSSFSSASRYYLSKCVLRGSVVLQVLYAHIRSPSSNDIVFGK 56

[Close]

BLAST of CsaV3_7G005520 vs. TrEMBL
Match: tr|A0A0L9U9W7|A0A0L9U9W7_PHAAN (Uncharacterized protein OS=Phaseolus angularis OX=3914 GN=LR48_Vigan03g291500 PE=4 SV=1)

HSP 1 Score: 67.4 bits (163), Expect = 2.0e-08
Identity = 34/56 (60.71%), Postives = 37/56 (66.07%), Query Frame = 0


Query: 1  MAVSEEECXXXXXXXXXXXXXXXXXLAKCVLRGSVVLQVLYGHIRSPSSLDVVFGK 57
          MAVSEEEC                 L+KCVLRGSVVLQVLY HIRSPSS D++FGK
Sbjct: 1  MAVSEEECSSAKSGPSSSSSASRYYLSKCVLRGSVVLQVLYAHIRSPSSNDIIFGK 56

The following BLAST results are available for this feature:

BLAST of CsaV3_7G005520 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_004136549.1	2.5e-10	100.00	PREDICTED: splicing factor 3B subunit 3 [Cucumis sativus] >KGN59264.1 hypothetic...	[more]
XP_008443005.1	2.5e-10	100.00	PREDICTED: pre-mRNA-splicing factor RSE1 [Cucumis melo]	[more]
XP_022934513.1	2.5e-10	100.00	pre-mRNA-splicing factor RSE1 [Cucurbita moschata]	[more]
XP_023526646.1	2.5e-10	100.00	splicing factor 3B subunit 3 [Cucurbita pepo subsp. pepo]	[more]
XP_015898900.1	5.6e-10	94.64	uncharacterized protein LOC107432303 isoform X1 [Ziziphus jujuba]	[more]

BLAST of CsaV3_7G005520 vs. TAIR10


Match Name	E-value	Identity	Description
AT3G11960.1	1.8e-07	74.29	Cleavage and polyadenylation specificity factor (CPSF) A subunit protein	[more]

BLAST of CsaV3_7G005520 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CsaV3_7G005520 vs. TrEMBL


Match Name	E-value	Identity	Description
tr\|A0A1S3B741\|A0A1S3B741_CUCME	1.7e-10	100.00	pre-mRNA-splicing factor RSE1 OS=Cucumis melo OX=3656 GN=LOC103486735 PE=4 SV=1	[more]
tr\|A0A0A0LEB2\|A0A0A0LEB2_CUCSA	1.7e-10	100.00	Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_3G792040 PE=4 SV=1	[more]
tr\|A0A2C9VD89\|A0A2C9VD89_MANES	7.0e-09	62.50	Uncharacterized protein OS=Manihot esculenta OX=3983 GN=MANES_08G040000 PE=4 SV=...	[more]
tr\|V7D0H9\|V7D0H9_PHAVU	1.5e-08	62.50	Uncharacterized protein OS=Phaseolus vulgaris OX=3885 GN=PHAVU_001G200200g PE=4 ...	[more]
tr\|A0A0L9U9W7\|A0A0L9U9W7_PHAAN	2.0e-08	60.71	Uncharacterized protein OS=Phaseolus angularis OX=3914 GN=LR48_Vigan03g291500 PE...	[more]

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:0048825	cotyledon development
biological_process	GO:0009755	hormone-mediated signaling pathway
biological_process	GO:0000956	nuclear-transcribed mRNA catabolic process
biological_process	GO:0006486	protein glycosylation
biological_process	GO:0010182	sugar mediated signaling pathway
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0005634	nucleus
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0005515	protein binding

Relationships

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


Feature Name	Unique Name	Type
CsaV3_7G005520.1	CsaV3_7G005520.1	mRNA

InterPro

Analysis Name: InterPro Annotations of cucumber chineselong genome (v3)
Date Performed: 2019-03-04


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 8..23
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 1..23
None	No IPR available	PANTHER	PTHR10644	DNA REPAIR/RNA PROCESSING CPSF FAMILY	coord: 15..60
None	No IPR available	PANTHER	PTHR10644:SF6	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR CPSF A SUBUNIT PROTEIN	coord: 15..60

Synteny

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


Gene	Orthologue	Organism	Block
CsaV3_7G005520	CSPI03G36130	Wild cucumber (PI 183967)	cpicucB194
CsaV3_7G005520	Cucsa.242390	Cucumber (Gy14) v1	cgycucB368
CsaV3_7G005520	CsGy3G033570	Cucumber (Gy14) v2	cgybcucB157
CsaV3_7G005520	Carg03593	Silver-seed gourd	carcucB0283
CsaV3_7G005520	Cla017574	Watermelon (97103) v1	cucwmB603
CsaV3_7G005520	ClCG10G017810	Watermelon (Charleston Gray)	cucwcgB557
CsaV3_7G005520	Lsi03G017680	Bottle gourd (USVL1VR-Ls)	cuclsiB556
CsaV3_7G005520	Cla97C10G200760	Watermelon (97103) v2	cucwmbB538
CsaV3_7G005520	Bhi11G002083	Wax gourd	cucwgoB673

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


Gene	Paralogue	Organism	Block
CsaV3_7G005520	CsaV3_3G038490	Cucumber (Chinese Long) v3	cuccucB157

The following block(s) are covering this gene:


Gene	Organism	Block
CsaV3_7G005520	Cucumber (Gy14) v2	cgybcucB348
CsaV3_7G005520	Cucumber (Gy14) v1	cgycucB226
CsaV3_7G005520	Cucurbita maxima (Rimu)	cmacucB0172
CsaV3_7G005520	Cucurbita maxima (Rimu)	cmacucB0638
CsaV3_7G005520	Cucurbita maxima (Rimu)	cmacucB0686
CsaV3_7G005520	Cucurbita maxima (Rimu)	cmacucB0768
CsaV3_7G005520	Cucurbita maxima (Rimu)	cmacucB1002
CsaV3_7G005520	Cucurbita moschata (Rifu)	cmocucB0155
CsaV3_7G005520	Cucurbita moschata (Rifu)	cmocucB0259
CsaV3_7G005520	Cucurbita moschata (Rifu)	cmocucB0622
CsaV3_7G005520	Cucurbita moschata (Rifu)	cmocucB0754
CsaV3_7G005520	Cucurbita moschata (Rifu)	cmocucB0987
CsaV3_7G005520	Cucurbita pepo (Zucchini)	cpecucB0322
CsaV3_7G005520	Cucurbita pepo (Zucchini)	cpecucB0656
CsaV3_7G005520	Cucurbita pepo (Zucchini)	cpecucB0863
CsaV3_7G005520	Cucurbita pepo (Zucchini)	cpecucB0946
CsaV3_7G005520	Cucurbita pepo (Zucchini)	cpecucB1082
CsaV3_7G005520	Wild cucumber (PI 183967)	cpicucB415
CsaV3_7G005520	Bottle gourd (USVL1VR-Ls)	cuclsiB529
CsaV3_7G005520	Melon (DHL92) v3.5.1	cucmeB548
CsaV3_7G005520	Melon (DHL92) v3.5.1	cucmeB574
CsaV3_7G005520	Melon (DHL92) v3.6.1	cucmedB536
CsaV3_7G005520	Melon (DHL92) v3.6.1	cucmedB560
CsaV3_7G005520	Watermelon (Charleston Gray)	cucwcgB564
CsaV3_7G005520	Watermelon (Charleston Gray)	cucwcgB597
CsaV3_7G005520	Watermelon (97103) v1	cucwmB614
CsaV3_7G005520	Watermelon (97103) v1	cucwmB627
CsaV3_7G005520	Watermelon (97103) v2	cucwmbB542
CsaV3_7G005520	Watermelon (97103) v2	cucwmbB574
CsaV3_7G005520	Wax gourd	cucwgoB687
CsaV3_7G005520	Wax gourd	cucwgoB707
CsaV3_7G005520	Silver-seed gourd	carcucB0717
CsaV3_7G005520	Silver-seed gourd	carcucB0758
CsaV3_7G005520	Silver-seed gourd	carcucB0915