Cla003783 (gene) Watermelon (97103) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cla003783
Type	gene
Organism	Citrullus. lanatus (Watermelon (97103) v1)
Description	Polypyrimidine tract-binding protein 3 (AHRD V1 -- A8MR27_ARATH)
Location	Chr8 : 10852640 .. 10853880 (+)

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.

ATGCCCCTCTCAGTGTGTGCCTCAGTGGTTATGGTGTGCACCTCAACATCTCAAGACTAACTTCCTATCCTCTTTTTTAGTTTTCCAAACTTTTAAGGAAGAAGCACCTGAATATTTTTTTAAAAGATATTCATTTTGCCCTAAAATCTCAAATAGAAGTTATATTTTCTTAAGTTCCATTTCGAGGTATTTCAAACTCTATTGAAGGGTATCTCTCTATCTAGATATTGCAGTTCAACTTTTATTTGTATTATTAACGAGTTAATGTGTATCTTTGCACATCTCCCATATCTCTTGATTTTTTTCTAAAAAAAACTCTGTACACTTTTGACATTCTTGCAGAACGATTTACTTCAGCTATTCCAGCCATTTGGTGTCATAACTAAGCTTGTGATGCTTCGTGCTAAAAATCAGGTTTGACTTCACTCTGATTCAGTGACATGTCTAAAGTTGTCTTATATCTGAGCTAAAGTGGAATATTAATTGTTTTGTCATTGTGTCATGAATTCAGGCACTTATGCAGATGCAAGATGTTCCCTCTGCAGTTAATGCTTTGCAGTTCTTTGCAAATGTTCAACCAAGCATTAGGTATTATTATGCCGTTAAAATTTATCCTTGAGAATTTGATTAGCCATTTTTTCTGTTAGTATTATCATAACTTGCAGTGGTATTAGCAAGAAGAGTGGAGGGTGCATCTGTTAAATAGTTAGGATGTCAAAATTTGTGGGTCCTAATGTAAGTTTGTAACTGAGAGTGTTCAAGTAATTGTGCGATCTTAGCTAGTACTTACGAAGGAGGACTATGGTAGAGAGAGGAGTTGCTTAGATCTGAATTCTCACCTTAGAGGAGAGTCTGGGATCTCTTGAATCTCTTTAATCACCCACTTGACTCTGTATTTTTGTCGCTCCAGTAAACAACAGAAGTTCTGGGTAGTGTTTTCATAATTATTTATTTATTTATTTTCAGATTAGTGTTTACTCAAGTTTATTGGGTTTAGTTTAATTTCACCCGTTTTTGGTTATGTTATGATACATTGGTACTCTTTTTATAAATCTCCATTTCATCAATGAAAAATTCTATTTCCTTAAATAAGGGAGGGAAACAAGATTAGATACACTCAAGGAAAAGATAGTAGGAGCACAAGAATCAATTCGGAGGAGTTTAATCAGTTGTTTAAAGAAGGAAGGGTGCAAGGTCAACTAACAAGAAGAATGGAAGATGAAGGGTATAGGGTCAACTAA

mRNA sequence

ATGCCCCTCTCAGTGTGTGCCTCAGTGGTTATGAACGATTTACTTCAGCTATTCCAGCCATTTGGTGTCATAACTAAGCTTGTGATGCTTCGTGCTAAAAATCAGGCACTTATGCAGATGCAAGATGTTCCCTCTGCAGTTAATGCTTTGCAGTTCTTTGCAAATGTTCAACCAAGCATTAGGGAGGGAAACAAGATTAGATACACTCAAGGAAAAGATAGTAGGAGCACAAGAATCAATTCGGAGGAGTTTAATCAGTTGTTTAAAGAAGGAAGGGTGCAAGGTCAACTAACAAGAAGAATGGAAGATGAAGGGTATAGGGTCAACTAA

Coding sequence (CDS)

ATGCCCCTCTCAGTGTGTGCCTCAGTGGTTATGAACGATTTACTTCAGCTATTCCAGCCATTTGGTGTCATAACTAAGCTTGTGATGCTTCGTGCTAAAAATCAGGCACTTATGCAGATGCAAGATGTTCCCTCTGCAGTTAATGCTTTGCAGTTCTTTGCAAATGTTCAACCAAGCATTAGGGAGGGAAACAAGATTAGATACACTCAAGGAAAAGATAGTAGGAGCACAAGAATCAATTCGGAGGAGTTTAATCAGTTGTTTAAAGAAGGAAGGGTGCAAGGTCAACTAACAAGAAGAATGGAAGATGAAGGGTATAGGGTCAACTAA

Protein sequence

MPLSVCASVVMNDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGNKIRYTQGKDSRSTRINSEEFNQLFKEGRVQGQLTRRMEDEGYRVN

Homology

[Close]

BLAST of Cla003783 vs. Swiss-Prot
Match: PTBP3_ARATH (Polypyrimidine tract-binding protein homolog 3 OS=Arabidopsis thaliana GN=At1g43190 PE=2 SV=1)

HSP 1 Score: 91.3 bits (225), Expect = 7.2e-18
Identity = 46/53 (86.79%), Postives = 47/53 (88.68%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDV SAV+ALQFF NVQP+IR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALLQMQDVSSAVSALQFFTNVQPTIRGRN 72

[Close]

BLAST of Cla003783 vs. TrEMBL
Match: A0A0R0HXC9_SOYBN (Uncharacterized protein OS=Glycine max GN=GLYMA_10G223300 PE=4 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 2.2e-18
Identity = 50/57 (87.72%), Postives = 54/57 (94.74%), Query Frame = 1


Query: 8  SVVMNDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          +V +NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDVPSAVNALQF+ANVQPSIR  N
Sbjct: 19 AVFLNDLLQLFQPFGVITKLVMLRAKNQALIQMQDVPSAVNALQFYANVQPSIRGRN 75

[Close]

BLAST of Cla003783 vs. TrEMBL
Match: A0A0A0KAL8_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G017000 PE=4 SV=1)

HSP 1 Score: 99.4 bits (246), Expect = 2.9e-18
Identity = 54/67 (80.60%), Postives = 56/67 (83.58%), Query Frame = 1


Query: 3  LSVCASVVM-----NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQ 62
          L +C S  M     NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFAN+Q
Sbjct: 21 LCLCLSFRMTEPSKNDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANLQ 80

Query: 63 PSIREGN 65
          PSIR  N
Sbjct: 81 PSIRGRN 87

[Close]

BLAST of Cla003783 vs. TrEMBL
Match: C0J4I8_CUCMA (RBP50 OS=Cucurbita maxima PE=2 SV=1)

HSP 1 Score: 98.6 bits (244), Expect = 5.0e-18
Identity = 50/53 (94.34%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDVPSAVNALQFFANVQPSIR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALIQMQDVPSAVNALQFFANVQPSIRGRN 72

[Close]

BLAST of Cla003783 vs. TrEMBL
Match: A0A0L9TZ49_PHAAN (Uncharacterized protein (Fragment) OS=Phaseolus angularis GN=LR48_Vigan02g201300 PE=4 SV=1)

HSP 1 Score: 97.4 bits (241), Expect = 1.1e-17
Identity = 48/53 (90.57%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDVPSAVNALQF+AN+QPSIR  N
Sbjct: 2  NDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAVNALQFYANIQPSIRGRN 54

[Close]

BLAST of Cla003783 vs. TrEMBL
Match: K7MHQ7_SOYBN (Uncharacterized protein OS=Glycine max GN=GLYMA_16G165000 PE=4 SV=1)

HSP 1 Score: 97.4 bits (241), Expect = 1.1e-17
Identity = 48/53 (90.57%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQAL+QMQD+PSAVNALQF+ANVQPSIR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALLQMQDIPSAVNALQFYANVQPSIRGRN 72

[Close]

BLAST of Cla003783 vs. NCBI nr
Match: gi|947086396|gb|KRH35117.1| (hypothetical protein GLYMA_10G223300 [Glycine max])

HSP 1 Score: 99.8 bits (247), Expect = 3.2e-18
Identity = 50/57 (87.72%), Postives = 54/57 (94.74%), Query Frame = 1


Query: 8  SVVMNDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          +V +NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDVPSAVNALQF+ANVQPSIR  N
Sbjct: 19 AVFLNDLLQLFQPFGVITKLVMLRAKNQALIQMQDVPSAVNALQFYANVQPSIRGRN 75

[Close]

BLAST of Cla003783 vs. NCBI nr
Match: gi|700190680|gb|KGN45884.1| (hypothetical protein Csa_6G017000 [Cucumis sativus])

HSP 1 Score: 99.4 bits (246), Expect = 4.2e-18
Identity = 54/67 (80.60%), Postives = 56/67 (83.58%), Query Frame = 1


Query: 3  LSVCASVVM-----NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQ 62
          L +C S  M     NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFAN+Q
Sbjct: 21 LCLCLSFRMTEPSKNDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANLQ 80

Query: 63 PSIREGN 65
          PSIR  N
Sbjct: 81 PSIRGRN 87

[Close]

BLAST of Cla003783 vs. NCBI nr
Match: gi|778709849|ref|XP_011656467.1| (PREDICTED: polypyrimidine tract-binding protein homolog 3 [Cucumis sativus])

HSP 1 Score: 99.0 bits (245), Expect = 5.5e-18
Identity = 50/53 (94.34%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFAN+QPSIR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANLQPSIRGRN 72

[Close]

BLAST of Cla003783 vs. NCBI nr
Match: gi|659126205|ref|XP_008463064.1| (PREDICTED: polypyrimidine tract-binding protein homolog 3 [Cucumis melo])

HSP 1 Score: 99.0 bits (245), Expect = 5.5e-18
Identity = 50/53 (94.34%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFAN+QPSIR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANLQPSIRGRN 72

[Close]

BLAST of Cla003783 vs. NCBI nr
Match: gi|209362272|gb|ACI43571.1| (RBP50 [Cucurbita maxima])

HSP 1 Score: 98.6 bits (244), Expect = 7.2e-18
Identity = 50/53 (94.34%), Postives = 51/53 (96.23%), Query Frame = 1


Query: 12 NDLLQLFQPFGVITKLVMLRAKNQALMQMQDVPSAVNALQFFANVQPSIREGN 65
          NDLLQLFQPFGVITKLVMLRAKNQAL+QMQDVPSAVNALQFFANVQPSIR  N
Sbjct: 20 NDLLQLFQPFGVITKLVMLRAKNQALIQMQDVPSAVNALQFFANVQPSIRGRN 72

The following BLAST results are available for this feature:

BLAST of Cla003783 vs. Swiss-Prot


Match Name	E-value	Identity	Description
PTBP3_ARATH	7.2e-18	86.79	Polypyrimidine tract-binding protein homolog 3 OS=Arabidopsis thaliana GN=At1g43...	[more]

BLAST of Cla003783 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0R0HXC9_SOYBN	2.2e-18	87.72	Uncharacterized protein OS=Glycine max GN=GLYMA_10G223300 PE=4 SV=1	[more]
A0A0A0KAL8_CUCSA	2.9e-18	80.60	Uncharacterized protein OS=Cucumis sativus GN=Csa_6G017000 PE=4 SV=1	[more]
C0J4I8_CUCMA	5.0e-18	94.34	RBP50 OS=Cucurbita maxima PE=2 SV=1	[more]
A0A0L9TZ49_PHAAN	1.1e-17	90.57	Uncharacterized protein (Fragment) OS=Phaseolus angularis GN=LR48_Vigan02g201300...	[more]
K7MHQ7_SOYBN	1.1e-17	90.57	Uncharacterized protein OS=Glycine max GN=GLYMA_16G165000 PE=4 SV=1	[more]

BLAST of Cla003783 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|947086396\|gb\|KRH35117.1\|	3.2e-18	87.72	hypothetical protein GLYMA_10G223300 [Glycine max]	[more]
gi\|700190680\|gb\|KGN45884.1\|	4.2e-18	80.60	hypothetical protein Csa_6G017000 [Cucumis sativus]	[more]
gi\|778709849\|ref\|XP_011656467.1\|	5.5e-18	94.34	PREDICTED: polypyrimidine tract-binding protein homolog 3 [Cucumis sativus]	[more]
gi\|659126205\|ref\|XP_008463064.1\|	5.5e-18	94.34	PREDICTED: polypyrimidine tract-binding protein homolog 3 [Cucumis melo]	[more]
gi\|209362272\|gb\|ACI43571.1\|	7.2e-18	94.34	RBP50 [Cucurbita maxima]	[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:0006397	mRNA processing
biological_process	GO:0055114	oxidation-reduction process
biological_process	GO:0045595	regulation of cell differentiation
biological_process	GO:0043484	regulation of RNA splicing
biological_process	GO:0006417	regulation of translation
biological_process	GO:0008150	biological_process
cellular_component	GO:0005634	nucleus
cellular_component	GO:0000932	cytoplasmic mRNA processing body
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0000166	nucleotide binding
molecular_function	GO:0003723	RNA binding
molecular_function	GO:0032440	2-alkenal reductase [NAD(P)] activity
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0003729	mRNA binding
molecular_function	GO:0030170	pyridoxal phosphate binding
molecular_function	GO:0008483	transaminase activity

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
WMU08968	watermelon unigene v2 vs TrEMBL	transcribed_cluster

Relationships

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


Feature Name	Unique Name	Type
Cla003783	Cla003783.1	mRNA

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


Feature Name	Unique Name	Type
WMU08968	WMU08968	transcribed_cluster

InterPro

Analysis Name: InterPro Annotations of watermelon (97103)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR012677	Nucleotide-binding alpha-beta plait domain	GENE3D	G3DSA:3.30.70.330		coord: 8..62 score: 1.4
IPR012677	Nucleotide-binding alpha-beta plait domain	unknown	SSF54928	RNA-binding domain, RBD	coord: 9..60 score: 6.3

Synteny

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


Gene	Orthologue	Organism	Block
Cla003783	Cla97C08G146530	Watermelon (97103) v2	wmwmbB103
Cla003783	Csa6G017000	Cucumber (Chinese Long) v2	cuwmB462
Cla003783	MELO3C024993	Melon (DHL92) v3.5.1	mewmB303
Cla003783	ClCG08G002590	Watermelon (Charleston Gray)	wcgwmB403
Cla003783	CSPI06G02570	Wild cucumber (PI 183967)	cpiwmB479
Cla003783	CmaCh09G012850	Cucurbita maxima (Rimu)	cmawmB018
Cla003783	CmoCh09G012430	Cucurbita moschata (Rifu)	cmowmB010
Cla003783	Lsi08G002430	Bottle gourd (USVL1VR-Ls)	lsiwmB470
Cla003783	CsGy6G002630	Cucumber (Gy14) v2	cgybwmB434
Cla003783	MELO3C024993.2	Melon (DHL92) v3.6.1	medwmB307
Cla003783	Carg24108	Silver-seed gourd	carwmB0675
Cla003783	CsaV3_6G002770	Cucumber (Chinese Long) v3	cucwmB490
Cla003783	Bhi04G001757	Wax gourd	wgowmB323

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cla003783	Cucumber (Gy14) v1	cgywmB656
Cla003783	Wild cucumber (PI 183967)	cpiwmB490
Cla003783	Watermelon (Charleston Gray)	wcgwmB410
Cla003783	Cucumber (Chinese Long) v2	cuwmB475
Cla003783	Cucumber (Gy14) v2	cgybwmB446
Cla003783	Cucumber (Chinese Long) v3	cucwmB501