CmaCh04G012260 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh04G012260
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	Serine/arginine-rich splicing factor 4
Location	Cma_Chr04 : 6254625 .. 6256472 (+)

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.

ATGCAATCAGTCCAAAGCACACATAAAAGGGATGGATTCGAACTGAAGTTTTATCGGAGAGGGAAAGAGATTCAGAAAAGCGTCGGAAACCGAGGGAAATCTTTGGAAGTGGAGGGGGATGATTATTTTTAGTTTGGTATTCTTTTGCCCTTTTCCGTTTTTCTCTTGCAAAATCTTCCTTTTGCGTCTTAAAACGCATTGACTATTTTATTTATACGAACAGTTGTATCAGTCAAATTGCATTTTCGCTTTTTATTTTTTCTTTTGTGTATTAAATTATACAAAATCGCCCCTAGGTTTTCATTATTGGGCTTAAAATTTGTTTTTTTTAATTAAATATAATATATAAAAAATTGATATATTTTTTACCATTTATTTTATCTTAAAATATATCTTATTTATTTACGTAAAATAAATCATAAATATGTCATCATTAAAGGGTTATAAATAGAAACAAATTCGTTCGTACTATCAGTAGAGTTTGTAAGACCGCGATGGATCCTTAGTACAAAAACTTACCTTAAATCAAACTTGTCTAGTCTATAAATATTTTGTATTTTAATATTTTTTAAATTGACTTAAAAATAATTATACATTTTTTAGTTCAACGATATACCTTATATTTCTCCGTGTTTTATTAATTCAACAATATACCTTATATTTCTACGTGTTTATTAATAAATAAGTGAAAAGTACCAAATCTAGACCCATTTGGATTTTAATTTTTAATTTTTGAAAATTAAATTTATAATCCATGTCAAATTTTTAAACCTAAAAATACAAGAATACCAAATAGTCTATTGGGCTTAAAAGTAGCCCAATCAACCTATTTTAGGCGGCGCAGCCCACAAGAATTGAGCCCAAAACAATTATTCTGTAAAATTGGGCCTACGGCTGTTCCAGAAAAAGAAATCACTATAAGAATATCTGGAGCGGCTTACGGAAATCATTTTGTTTATGCTAAAGACGTGAAATTTAGGGTTTCGTATTCTTTCCAGGTGCGCCTCCTTCGAATTTTCTAGGTTTGCTCTCCTCGAAGCATTCGACTCAAAATTCATGGCATTTTTCTATTGATTTTTTTTTTTAGCGCAATAAGGTTCTGTATAGTCTCTATTTAGATTAAACAAATAGTTACTGGTTTGTTAATACTGTCACTGATTGTGGTGGTACTGCGATTGTCAATTGTAGACAAAATGCCAAGGTACGACGATCGTTATGGTGGTACTCGGCTCTACGTTGGGCGCCTGTCTTCACGGACGAGGTCCCGTGATCTGGATGACTTGTTCGGTCGTTATGGAAGGTATGCAGAATCTAGCCGGATGTACCGTACCGTTCAGCCGTGGTCGAATTTGTATGCTAACATTAATTTGTTGAATTCGTTAAGTGTATGTGTGTTTAGCTATGCTGTATTTTACAGATGTAGATTCTAGCCGGATATACTGTTCATCTTTGGTTGAATTTGTGTGCCAACATTAATTTGTTGAATTCGAAATGTGTATGCGTGTTTAGTTATGCCTCGTTTACTTCTTTTGTCCCGGTTATGCTATTGCCAACATCATTATCAGAGTAAATTATTAATTGACACTTCTCTCGAGACCTCTTGAGGCATTTACCAAGCCCTATTTTTGGGTGCACGACTGTAAATGTGTATTTTGATATATCCGTGAAAGTGTGGATTGTTGATGGGTCTGTGTGGTTTAACTTGAGTGATCTTGTTGAAGGTTTTTTGGCTTATGTCAAACCTGGAGGTCTATGGTGAGAGGGTTCCCTTGGTGGATTTGGCGAGTCTTTCTATTATGTTATTGCCTGTTTTTATGGAAATGCCAAGAATCTCAGAATGGTGTTTAG

mRNA sequence

ATGCAATCAGTCCAAAGCACACATAAAAGGGATGGATTCGAACTGAAGTTTTATCGGAGAGGGAAAGAGATTCAGAAAAGCGTCGGAAACCGAGGGAAATCTTTGGAAGGTTTCGTATTCTTTCCAGGTGCGCCTCCTTCGAATTTTCTAGACAAAATGCCAAGGTACGACGATCGTTATGGTGGTACTCGGCTCTACGTTGGGCGCCTGTCTTCACGGACGAGGTCCCGTGATCTGGATGACTTGTTCGGTCGTTATGGAAGGTTTTTTGGCTTATGTCAAACCTGGAGGTCTATGGTGAGAGGGTTCCCTTGGTGGATTTGGCGAGTCTTTCTATTATGTTATTGCCTGTTTTTATGGAAATGCCAAGAATCTCAGAATGGTGTTTAG

Coding sequence (CDS)

ATGCAATCAGTCCAAAGCACACATAAAAGGGATGGATTCGAACTGAAGTTTTATCGGAGAGGGAAAGAGATTCAGAAAAGCGTCGGAAACCGAGGGAAATCTTTGGAAGGTTTCGTATTCTTTCCAGGTGCGCCTCCTTCGAATTTTCTAGACAAAATGCCAAGGTACGACGATCGTTATGGTGGTACTCGGCTCTACGTTGGGCGCCTGTCTTCACGGACGAGGTCCCGTGATCTGGATGACTTGTTCGGTCGTTATGGAAGGTTTTTTGGCTTATGTCAAACCTGGAGGTCTATGGTGAGAGGGTTCCCTTGGTGGATTTGGCGAGTCTTTCTATTATGTTATTGCCTGTTTTTATGGAAATGCCAAGAATCTCAGAATGGTGTTTAG

Protein sequence

MQSVQSTHKRDGFELKFYRRGKEIQKSVGNRGKSLEGFVFFPGAPPSNFLDKMPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRGFPWWIWRVFLLCYCLFLWKCQESQNGV

Homology

[Close]

BLAST of CmaCh04G012260 vs. Swiss-Prot
Match: RSZ32_ARATH (Serine/arginine-rich splicing factor RS2Z32 OS=Arabidopsis thaliana GN=RS2Z32 PE=1 SV=1)

HSP 1 Score: 69.3 bits (168), Expect = 3.4e-11
Identity = 31/36 (86.11%), Postives = 33/36 (91.67%), Query Frame = 1


Query: 53 MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGR 89
          MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGR
Sbjct: 1  MPRYDDRYGNTRLYVGRLSSRTRTRDLERLFSRYGR 36

[Close]

BLAST of CmaCh04G012260 vs. Swiss-Prot
Match: RSZ33_ARATH (Serine/arginine-rich splicing factor RS2Z33 OS=Arabidopsis thaliana GN=RS2Z33 PE=1 SV=1)

HSP 1 Score: 69.3 bits (168), Expect = 3.4e-11
Identity = 31/36 (86.11%), Postives = 33/36 (91.67%), Query Frame = 1


Query: 53 MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGR 89
          MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGR
Sbjct: 1  MPRYDDRYGNTRLYVGRLSSRTRTRDLERLFSRYGR 36

[Close]

BLAST of CmaCh04G012260 vs. TrEMBL
Match: D7TQD0_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VIT_08s0040g02850 PE=4 SV=1)

HSP 1 Score: 99.4 bits (246), Expect = 3.5e-18
Identity = 43/54 (79.63%), Postives = 46/54 (85.19%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRGFPWW 107
           MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGRF G C TWRSMV G+ WW
Sbjct: 1   MPRYDDRYGNTRLYVGRLSSRTRTRDLESLFSRYGRFLGFCLTWRSMVGGWNWW 54

[Close]

BLAST of CmaCh04G012260 vs. TrEMBL
Match: M1HA94_MAIZE (Arginine/serine-rich splicing factor RS2Z39 transcript V OS=Zea mays GN=RS2Z39 PE=2 SV=1)

HSP 1 Score: 96.3 bits (238), Expect = 2.9e-17
Identity = 43/56 (76.79%), Postives = 48/56 (85.71%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRGFPWWIW 109
           MPRYDDRYGGTRLYVGRL++RTRSRDL+ LFGRYGRFFG  +  RS+V G PWW W
Sbjct: 1   MPRYDDRYGGTRLYVGRLATRTRSRDLEHLFGRYGRFFGFYR--RSLVEGCPWWTW 54

[Close]

BLAST of CmaCh04G012260 vs. TrEMBL
Match: A0A061ERP0_THECC (RNA-binding family protein with retrovirus zinc finger-like domain, putative OS=Theobroma cacao GN=TCM_022039 PE=4 SV=1)

HSP 1 Score: 87.4 bits (215), Expect = 1.4e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           MPR+D RYG TRLYVGRLSSRTR+RDL+ +F RYGRF G C TWR MVRG
Sbjct: 1   MPRFDGRYGTTRLYVGRLSSRTRARDLEHIFSRYGRFLGFCLTWRPMVRG 50

[Close]

BLAST of CmaCh04G012260 vs. TrEMBL
Match: A0A0B0MR15_GOSAR (Serine/arginine-rich splicing factor 6 OS=Gossypium arboreum GN=F383_06032 PE=4 SV=1)

HSP 1 Score: 85.5 bits (210), Expect = 5.2e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           M RYDDRY  TRLYVGR+SSRTR+RDL+ LF RYGRF G CQTWR +VRG
Sbjct: 1   MRRYDDRYCHTRLYVGRISSRTRTRDLERLFSRYGRFLGFCQTWRPVVRG 50

[Close]

BLAST of CmaCh04G012260 vs. TrEMBL
Match: A0A0B0MIH0_GOSAR (Serine/arginine-rich splicing factor 4 OS=Gossypium arboreum GN=F383_06032 PE=4 SV=1)

HSP 1 Score: 85.5 bits (210), Expect = 5.2e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           M RYDDRY  TRLYVGR+SSRTR+RDL+ LF RYGRF G CQTWR +VRG
Sbjct: 1   MRRYDDRYCHTRLYVGRISSRTRTRDLERLFSRYGRFLGFCQTWRPVVRG 50

[Close]

BLAST of CmaCh04G012260 vs. TAIR10
Match: AT2G37340.1 (AT2G37340.1 arginine/serine-rich zinc knuckle-containing protein 33)

HSP 1 Score: 69.3 bits (168), Expect = 1.9e-12
Identity = 31/36 (86.11%), Postives = 33/36 (91.67%), Query Frame = 1


Query: 53 MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGR 89
          MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGR
Sbjct: 1  MPRYDDRYGNTRLYVGRLSSRTRTRDLERLFSRYGR 36

[Close]

BLAST of CmaCh04G012260 vs. TAIR10
Match: AT3G53500.2 (AT3G53500.2 RNA-binding (RRM/RBD/RNP motifs) family protein with retrovirus zinc finger-like domain)

HSP 1 Score: 69.3 bits (168), Expect = 1.9e-12
Identity = 31/36 (86.11%), Postives = 33/36 (91.67%), Query Frame = 1


Query: 53 MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGR 89
          MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGR
Sbjct: 1  MPRYDDRYGNTRLYVGRLSSRTRTRDLERLFSRYGR 36

[Close]

BLAST of CmaCh04G012260 vs. NCBI nr
Match: gi|297741518|emb|CBI32650.3| (unnamed protein product [Vitis vinifera])

HSP 1 Score: 99.4 bits (246), Expect = 5.0e-18
Identity = 43/54 (79.63%), Postives = 46/54 (85.19%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRGFPWW 107
           MPRYDDRYG TRLYVGRLSSRTR+RDL+ LF RYGRF G C TWRSMV G+ WW
Sbjct: 1   MPRYDDRYGNTRLYVGRLSSRTRTRDLESLFSRYGRFLGFCLTWRSMVGGWNWW 54

[Close]

BLAST of CmaCh04G012260 vs. NCBI nr
Match: gi|448878168|gb|AGE46047.1| (arginine/serine-rich splicing factor RS2Z39 transcript V [Zea mays])

HSP 1 Score: 96.3 bits (238), Expect = 4.2e-17
Identity = 43/56 (76.79%), Postives = 48/56 (85.71%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRGFPWWIW 109
           MPRYDDRYGGTRLYVGRL++RTRSRDL+ LFGRYGRFFG  +  RS+V G PWW W
Sbjct: 1   MPRYDDRYGGTRLYVGRLATRTRSRDLEHLFGRYGRFFGFYR--RSLVEGCPWWTW 54

[Close]

BLAST of CmaCh04G012260 vs. NCBI nr
Match: gi|590630022|ref|XP_007027153.1| (RNA-binding family protein with retrovirus zinc finger-like domain, putative [Theobroma cacao])

HSP 1 Score: 87.4 bits (215), Expect = 2.0e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           MPR+D RYG TRLYVGRLSSRTR+RDL+ +F RYGRF G C TWR MVRG
Sbjct: 1   MPRFDGRYGTTRLYVGRLSSRTRARDLEHIFSRYGRFLGFCLTWRPMVRG 50

[Close]

BLAST of CmaCh04G012260 vs. NCBI nr
Match: gi|728815732|gb|KHG01944.1| (Serine/arginine-rich splicing factor 6 [Gossypium arboreum])

HSP 1 Score: 85.5 bits (210), Expect = 7.4e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           M RYDDRY  TRLYVGR+SSRTR+RDL+ LF RYGRF G CQTWR +VRG
Sbjct: 1   MRRYDDRYCHTRLYVGRISSRTRTRDLERLFSRYGRFLGFCQTWRPVVRG 50

[Close]

BLAST of CmaCh04G012260 vs. NCBI nr
Match: gi|728815731|gb|KHG01943.1| (Serine/arginine-rich splicing factor 4 [Gossypium arboreum])

HSP 1 Score: 85.5 bits (210), Expect = 7.4e-14
Identity = 38/50 (76.00%), Postives = 42/50 (84.00%), Query Frame = 1


Query: 53  MPRYDDRYGGTRLYVGRLSSRTRSRDLDDLFGRYGRFFGLCQTWRSMVRG 103
           M RYDDRY  TRLYVGR+SSRTR+RDL+ LF RYGRF G CQTWR +VRG
Sbjct: 1   MRRYDDRYCHTRLYVGRISSRTRTRDLERLFSRYGRFLGFCQTWRPVVRG 50

The following BLAST results are available for this feature:

BLAST of CmaCh04G012260 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RSZ32_ARATH	3.4e-11	86.11	Serine/arginine-rich splicing factor RS2Z32 OS=Arabidopsis thaliana GN=RS2Z32 PE...	[more]
RSZ33_ARATH	3.4e-11	86.11	Serine/arginine-rich splicing factor RS2Z33 OS=Arabidopsis thaliana GN=RS2Z33 PE...	[more]

BLAST of CmaCh04G012260 vs. TrEMBL


Match Name	E-value	Identity	Description
D7TQD0_VITVI	3.5e-18	79.63	Putative uncharacterized protein OS=Vitis vinifera GN=VIT_08s0040g02850 PE=4 SV=...	[more]
M1HA94_MAIZE	2.9e-17	76.79	Arginine/serine-rich splicing factor RS2Z39 transcript V OS=Zea mays GN=RS2Z39 P...	[more]
A0A061ERP0_THECC	1.4e-14	76.00	RNA-binding family protein with retrovirus zinc finger-like domain, putative OS=...	[more]
A0A0B0MR15_GOSAR	5.2e-14	76.00	Serine/arginine-rich splicing factor 6 OS=Gossypium arboreum GN=F383_06032 PE=4 ...	[more]
A0A0B0MIH0_GOSAR	5.2e-14	76.00	Serine/arginine-rich splicing factor 4 OS=Gossypium arboreum GN=F383_06032 PE=4 ...	[more]

BLAST of CmaCh04G012260 vs. TAIR10


Match Name	E-value	Identity	Description
AT2G37340.1	1.9e-12	86.11	arginine/serine-rich zinc knuckle-containing protein 33	[more]
AT3G53500.2	1.9e-12	86.11	RNA-binding (RRM/RBD/RNP motifs) family protein with retrovirus zinc...	[more]

BLAST of CmaCh04G012260 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|297741518\|emb\|CBI32650.3\|	5.0e-18	79.63	unnamed protein product [Vitis vinifera]	[more]
gi\|448878168\|gb\|AGE46047.1\|	4.2e-17	76.79	arginine/serine-rich splicing factor RS2Z39 transcript V [Zea mays]	[more]
gi\|590630022\|ref\|XP_007027153.1\|	2.0e-14	76.00	RNA-binding family protein with retrovirus zinc finger-like domain, putative [Th...	[more]
gi\|728815732\|gb\|KHG01944.1\|	7.4e-14	76.00	Serine/arginine-rich splicing factor 6 [Gossypium arboreum]	[more]
gi\|728815731\|gb\|KHG01943.1\|	7.4e-14	76.00	Serine/arginine-rich splicing factor 4 [Gossypium arboreum]	[more]

Annotated Terms

The following terms have been associated with this gene:

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

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

Relationships

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


Feature Name	Unique Name	Type
CmaCh04G012260.1	CmaCh04G012260.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Cucurbita maxima
Date Performed: 2017-05-20


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR012677	Nucleotide-binding alpha-beta plait domain	GENE3D	G3DSA:3.30.70.330		coord: 54..89 score: 1.
IPR012677	Nucleotide-binding alpha-beta plait domain	unknown	SSF54928	RNA-binding domain, RBD	coord: 26..89 score: 1.1

Synteny

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


Gene	Orthologue	Organism	Block
CmaCh04G012260	CmoCh04G012970	Cucurbita moschata (Rifu)	cmacmoB728
CmaCh04G012260	CsaV3_5G006510	Cucumber (Chinese Long) v3	cmacucB0884
CmaCh04G012260	Carg26905	Silver-seed gourd	carcmaB1040
CmaCh04G012260	Carg23771	Silver-seed gourd	carcmaB1199

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh04G012260	Melon (DHL92) v3.6.1	cmamedB739
CmaCh04G012260	Melon (DHL92) v3.6.1	cmamedB771
CmaCh04G012260	Silver-seed gourd	carcmaB0428
CmaCh04G012260	Cucumber (Chinese Long) v3	cmacucB0832
CmaCh04G012260	Cucumber (Chinese Long) v3	cmacucB0853
CmaCh04G012260	Cucumber (Chinese Long) v3	cmacucB0916
CmaCh04G012260	Watermelon (97103) v2	cmawmbB719
CmaCh04G012260	Watermelon (97103) v2	cmawmbB740
CmaCh04G012260	Watermelon (97103) v2	cmawmbB742
CmaCh04G012260	Wax gourd	cmawgoB0825
CmaCh04G012260	Wax gourd	cmawgoB0892
CmaCh04G012260	Cucurbita maxima (Rimu)	cmacmaB272
CmaCh04G012260	Cucurbita maxima (Rimu)	cmacmaB487
CmaCh04G012260	Cucurbita maxima (Rimu)	cmacmaB531
CmaCh04G012260	Cucumber (Gy14) v1	cgycmaB0472
CmaCh04G012260	Cucumber (Gy14) v1	cgycmaB1049
CmaCh04G012260	Cucurbita moschata (Rifu)	cmacmoB720
CmaCh04G012260	Cucurbita moschata (Rifu)	cmacmoB723
CmaCh04G012260	Cucurbita moschata (Rifu)	cmacmoB731
CmaCh04G012260	Wild cucumber (PI 183967)	cmacpiB756
CmaCh04G012260	Cucumber (Chinese Long) v2	cmacuB746
CmaCh04G012260	Melon (DHL92) v3.5.1	cmameB652
CmaCh04G012260	Watermelon (Charleston Gray)	cmawcgB641
CmaCh04G012260	Watermelon (97103) v1	cmawmB723
CmaCh04G012260	Cucurbita pepo (Zucchini)	cmacpeB720
CmaCh04G012260	Cucurbita pepo (Zucchini)	cmacpeB723
CmaCh04G012260	Cucurbita pepo (Zucchini)	cmacpeB752
CmaCh04G012260	Bottle gourd (USVL1VR-Ls)	cmalsiB631
CmaCh04G012260	Bottle gourd (USVL1VR-Ls)	cmalsiB666
CmaCh04G012260	Bottle gourd (USVL1VR-Ls)	cmalsiB676
CmaCh04G012260	Cucumber (Gy14) v2	cgybcmaB412
CmaCh04G012260	Cucumber (Gy14) v2	cgybcmaB555
CmaCh04G012260	Cucumber (Gy14) v2	cgybcmaB673