Lsi08G005370 (gene) Bottle gourd (USVL1VR-Ls) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Lsi08G005370
Type	gene
Organism	Lagenaria siceraria (Bottle gourd (USVL1VR-Ls))
Description	RNA-binding with multiple splicing
Location	chr08 : 13351148 .. 13353651 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSthree_prime_UTR

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

ATGCAGTTAGAGCAGTGCTCGGAGATGTGTGGTTAGACTTCAATATAAATATAAGGAATTTTCAAGATTACAAGACATGCAGTTCTCTACAAATTGTACTGGGTTTTTATGACTCCAGCTTTTCTGAGATAGTCTTGTAATTTCATCTGATTAATGAAATTTTGTTTCCTATTAAAGAAAATATCTAGGTGCATGTTTAATTAATTTTTCTGCTATAAATGGAAGTAGTTTCATCATTCATGTGACAACTTCTTTATGTTTAGTTTTTGTTCAGATAATACACGATAGATTTGCTAAACAAGTATCTGATTTGCACAGGTTATAAAATGGACGAACAAGATCCCGAATCTAATTATTTGCGACTACAGTTCTCACGACATCCAGGTCCGAGGTCTGGTTCAGGAACTGTGGCAAAAGGTGAATAAGCTATAGAGACAGGATGACCAATTTAAATGGGAGACGTATCATCTTCTAGTGCACATTTTACTAGCTGCTTATGCATCCATTATATGTTATTAGACATGCTGTTGTTAAGATAGGCAAATTGTAGCCGACCCCACTGAATATTAAAGTTGCTTGTAAATTTAAGGGGATTAGATTCAGAGTGTTTCAATAGTCAACTGTGCAATTGAATTTTGATGTACAATTATGTCAATGCTTCATAATTCGAAGATATACCTGGTACAATTTTTATAAACTGTTGGTTCTTTACCCCCCACAAACAGTAAATACGCTCCCACAAATTCTGGCATGGTGGATTAATATTCTGAACTCCATTATTTATGACATATTAAAAGGCTAGTATTTGGTTTTATAACAAAAGTTAATTTAGGTTATCCTTTGAAAATTGCTCACAGGTTTGATGTATTTTTACTCATTGCATCCCAATTGTTAGGAATATTGAATTAGTGGAAATATTTTTATGAATGGAGCAAAAGGGTTGATAACAAGTAATTAGCTCAAGGAGGTACATGTCTTAGTTGCTCGAATTACATAACATTGTTTTTACTCTATTTGCTAAATCAATTAGTACAATTTTTTATTCAATTTTTTTGATTGCTATAATTTTTGCATGGTAAGATTCATTCAGGTACTATAGCAGGAATTTGGAGAGTTCCTGTACCCTCCAACACACCAAAATCAGCCTATTCCGCTGGTCATTCCTCCCATACCAATATGCAATACCTCAGGTAACTAGCTTTCTAAAATTTTGCTCAACTGTATAACCACCATATGCAATAAAGTCCTATACTAAGATAGTTTGTGACAGCAAAATCTTCCTCTTGGAATATGATATATTTTTCTCTCTGTAAAAGAAAATCATTTGAATAATATATTGTAAGTTTCCTGGCTATCATCTACTGGGAAAGTAGATGTAAAGTTGTGGCTAATTAATCACTATATAGATGTCAAGAGGCGACTGGTGAGTTGTTAAGTTGGTTGTTTGTTTTTCTTGGTGTTTGAATTAATATTAAATATGATGATTCTGAATTTTCCATGGTTTTTGGCCCCAGCTATTAATGAGTCATTCTCCCCCTCTTCATGTGAGAGTGTGATGGTGGTAAAAGGTTGGCCCCAGTGTTGATTTTGCATCCCAAACAGTTCTGATTTGAACTTTCTATAGGTTTTTAGACCCACACCATAGAAAAAACTTCATGAAAACTTAATAAGTGCCAGAGGCCAAGTTTTGAAGCAGAACTAAAAGCCCATTTGCTTGGAATTGGAGGGAAAAAAGGGTTCTTCAACTGCAACTGCAATGCCCCCCTTTGTTATCTACCTTCTCCTTGCACTGGTGTATTTGAATCTGCCATCAAAATTTAGTGCAGATGCAGAATATGTTCATTATCCACCTCCTTTACAAAAAAGGCATAAGCAATCAGAGCAGTCAGTGCCACAACCCCCTGTTTCTGAGCCAATAGTTCCCTATTTTCCCTTTGTATACAGTCCAATCCCATCCCCATCTGAGAGGCCTTATGAACCACCCTCATCACCACCACTAAAGCAGTCCCAACCGCCATTATCTCCATTTTCCGAGCCTCTAGTTCCTTATTTTCCTTTTGTATATATACCAACACCATCCCCAGCTCAAAAGCCTTATGAAGATGCATCACCTTCCCCATCTCCTGTGTTCACAAGACCTGTAGTTCCTTATTATCCCTTCTGATTTCCACCTCCTTCCCCTTGAAAACACCTCTATCCTCCAAATCCGATCGACCACCTTCAATCGCCTTCACCTCTGCCTCCGCCTCCTTACTAAACACTACTATTTGCATCCACAACATGATGATATCTATGATAAAAGCTTACTTCTTCCTGGAAGATGTTTAGTTTTTGCTGTTATTGATATATTTATATGCTCATTGCACTCGAATCTCTCTGGCTTTCGGGTTATGTTCTTATTCTCTGCATTAAGTTTGTATTGTTCTTGTCACCCTGTTTGTATTGTACATACTGATTCTGGAAATATTTCTTATCCAAGAATAATAATAATGTATCTTACCTCG

mRNA sequence

ATGCAGTTAGAGCAGTGCTCGGAGATGTGTGGTTATAAAATGGACGAACAAGATCCCGAATCTAATTATTTGCGACTACAGTTCTCACGACATCCAGGTCCGAGGTCTGGTTCAGGAACTGTGGCAAAAGGTTTGATGTATTTTTACTCATTGCATCCCAATTGTACTATAGCAGGAATTTGGAGAGTTCCTGTACCCTCCAACACACCAAAATCAGCCTATTCCGCTGGTCATTCCTCCCATACCAATATGCAATACCTCAGATGTCAAGAGGCGACTGCTATTAATGAGTCATTCTCCCCCTCTTCATGTGAGAGTGTGATGGTGGTAAAAGGTTGGCCCCAGTGTTGATTTTGCATCCCAAACAGTTCTGATTTGAACTTTCTATAGGTTTTTAGACCCACACCATAGAAAAAACTTCATGAAAACTTAATAAGTGCCAGAGGCCAAGTTTTGAAGCAGAACTAAAAGCCCATTTGCTTGGAATTGGAGGGAAAAAAGGGTTCTTCAACTGCAACTGCAATGCCCCCCTTTGTTATCTACCTTCTCCTTGCACTGGTGTATTTGAATCTGCCATCAAAATTTAGTGCAGATGCAGAATATGTTCATTATCCACCTCCTTTACAAAAAAGGCATAAGCAATCAGAGCAGTCAGTGCCACAACCCCCTGTTTCTGAGCCAATAGTTCCCTATTTTCCCTTTGTATACAGTCCAATCCCATCCCCATCTGAGAGGCCTTATGAACCACCCTCATCACCACCACTAAAGCAGTCCCAACCGCCATTATCTCCATTTTCCGAGCCTCTAGTTCCTTATTTTCCTTTTGTATATATACCAACACCATCCCCAGCTCAAAAGCCTTATGAAGATGCATCACCTTCCCCATCTCCTGTGTTCACAAGACCTGTAGTTCCTTATTATCCCTTCTGATTTCCACCTCCTTCCCCTTGAAAACACCTCTATCCTCCAAATCCGATCGACCACCTTCAATCGCCTTCACCTCTGCCTCCGCCTCCTTACTAAACACTACTATTTGCATCCACAACATGATGATATCTATGATAAAAGCTTACTTCTTCCTGGAAGATGTTTAGTTTTTGCTGTTATTGATATATTTATATGCTCATTGCACTCGAATCTCTCTGGCTTTCGGGTTATGTTCTTATTCTCTGCATTAAGTTTGTATTGTTCTTGTCACCCTGTTTGTATTGTACATACTGATTCTGGAAATATTTCTTATCCAAGAATAATAATAATGTATCTTACCTCG

Coding sequence (CDS)

ATGCAGTTAGAGCAGTGCTCGGAGATGTGTGGTTATAAAATGGACGAACAAGATCCCGAATCTAATTATTTGCGACTACAGTTCTCACGACATCCAGGTCCGAGGTCTGGTTCAGGAACTGTGGCAAAAGGTTTGATGTATTTTTACTCATTGCATCCCAATTGTACTATAGCAGGAATTTGGAGAGTTCCTGTACCCTCCAACACACCAAAATCAGCCTATTCCGCTGGTCATTCCTCCCATACCAATATGCAATACCTCAGATGTCAAGAGGCGACTGCTATTAATGAGTCATTCTCCCCCTCTTCATGTGAGAGTGTGATGGTGGTAAAAGGTTGGCCCCAGTGTTGA

Protein sequence

MQLEQCSEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAKGLMYFYSLHPNCTIAGIWRVPVPSNTPKSAYSAGHSSHTNMQYLRCQEATAINESFSPSSCESVMVVKGWPQC

Homology

[Close]

BLAST of Lsi08G005370 vs. Swiss-Prot
Match: RBP1_MEDTR (RNA-binding protein 1 OS=Medicago truncatula GN=RBP1 PE=2 SV=1)

HSP 1 Score: 53.9 bits (128), Expect = 1.3e-06
Identity = 24/38 (63.16%), Postives = 31/38 (81.58%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAKG 45
           S + GYK+DE +PES++LRLQFSR+PGPRSG G  + G
Sbjct: 212 SALQGYKVDEINPESSHLRLQFSRYPGPRSGGGPRSSG 249

[Close]

BLAST of Lsi08G005370 vs. TrEMBL
Match: A0A0A0KCN5_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G338020 PE=4 SV=1)

HSP 1 Score: 100.1 bits (248), Expect = 1.8e-18
Identity = 50/80 (62.50%), Postives = 59/80 (73.75%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAKG--LMYFYSLHPNCTIAGIWRVP 66
           S + GYKMDEQDPESNYLRLQFSRHPGPRSGSG+  K   ++   +      IAGIWRVP
Sbjct: 228 SALQGYKMDEQDPESNYLRLQFSRHPGPRSGSGSGGKSGTIVTNRATWLTSAIAGIWRVP 287

Query: 67  VPSNTPKSAYSAGHSSHTNM 85
             SNTPKSAY  GHS++ ++
Sbjct: 288 ASSNTPKSAYIVGHSTYESV 307

[Close]

BLAST of Lsi08G005370 vs. TrEMBL
Match: A0A0B0PU61_GOSAR (RNA-binding with multiple splicing OS=Gossypium arboreum GN=F383_10922 PE=4 SV=1)

HSP 1 Score: 61.6 bits (148), Expect = 7.2e-07
Identity = 27/34 (79.41%), Postives = 30/34 (88.24%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGT 41
           S + GYKMDE DP+SNYLRLQFSR+PGPRSG GT
Sbjct: 248 SALQGYKMDEHDPDSNYLRLQFSRYPGPRSGPGT 281

[Close]

BLAST of Lsi08G005370 vs. TrEMBL
Match: A0A061FI30_THECC (Nucleotide binding,nucleic acid binding OS=Theobroma cacao GN=TCM_035511 PE=4 SV=1)

HSP 1 Score: 60.8 bits (146), Expect = 1.2e-06
Identity = 31/48 (64.58%), Postives = 35/48 (72.92%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAKGLMYFYSLHPN 55
           S + GYKMDE DP+SNYLRLQFSR+PGPRS SG  A+G     S H N
Sbjct: 216 SALQGYKMDEHDPDSNYLRLQFSRYPGPRSSSG--ARGRRVLRSGHFN 261

[Close]

BLAST of Lsi08G005370 vs. TrEMBL
Match: A0A0D2TWR8_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_009G284800 PE=4 SV=1)

HSP 1 Score: 60.5 bits (145), Expect = 1.6e-06
Identity = 26/34 (76.47%), Postives = 30/34 (88.24%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGT 41
           S + GYKMDE DP+SNYL+LQFSR+PGPRSG GT
Sbjct: 216 SALQGYKMDEHDPDSNYLKLQFSRYPGPRSGPGT 249

[Close]

BLAST of Lsi08G005370 vs. TrEMBL
Match: A0A0D2S9U1_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_009G284800 PE=4 SV=1)

HSP 1 Score: 60.5 bits (145), Expect = 1.6e-06
Identity = 26/34 (76.47%), Postives = 30/34 (88.24%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGT 41
           S + GYKMDE DP+SNYL+LQFSR+PGPRSG GT
Sbjct: 175 SALQGYKMDEHDPDSNYLKLQFSRYPGPRSGPGT 208

[Close]

BLAST of Lsi08G005370 vs. NCBI nr
Match: gi|700192266|gb|KGN47470.1| (hypothetical protein Csa_6G338020 [Cucumis sativus])

HSP 1 Score: 100.1 bits (248), Expect = 2.6e-18
Identity = 50/80 (62.50%), Postives = 59/80 (73.75%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAKG--LMYFYSLHPNCTIAGIWRVP 66
           S + GYKMDEQDPESNYLRLQFSRHPGPRSGSG+  K   ++   +      IAGIWRVP
Sbjct: 228 SALQGYKMDEQDPESNYLRLQFSRHPGPRSGSGSGGKSGTIVTNRATWLTSAIAGIWRVP 287

Query: 67  VPSNTPKSAYSAGHSSHTNM 85
             SNTPKSAY  GHS++ ++
Sbjct: 288 ASSNTPKSAYIVGHSTYESV 307

[Close]

BLAST of Lsi08G005370 vs. NCBI nr
Match: gi|449462154|ref|XP_004148806.1| (PREDICTED: U1 small nuclear ribonucleoprotein A [Cucumis sativus])

HSP 1 Score: 68.2 bits (165), Expect = 1.1e-08
Identity = 31/37 (83.78%), Postives = 33/37 (89.19%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAK 44
           S + GYKMDEQDPESNYLRLQFSRHPGPRSGSG+  K
Sbjct: 220 SALQGYKMDEQDPESNYLRLQFSRHPGPRSGSGSGGK 256

[Close]

BLAST of Lsi08G005370 vs. NCBI nr
Match: gi|659081831|ref|XP_008441534.1| (PREDICTED: uncharacterized protein LOC103485638 [Cucumis melo])

HSP 1 Score: 66.2 bits (160), Expect = 4.2e-08
Identity = 30/37 (81.08%), Postives = 32/37 (86.49%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAK 44
           S + GYKMDEQDPESNYLRLQFSRHPGPRSG G+  K
Sbjct: 220 SALQGYKMDEQDPESNYLRLQFSRHPGPRSGFGSSGK 256

[Close]

BLAST of Lsi08G005370 vs. NCBI nr
Match: gi|823228735|ref|XP_012447111.1| (PREDICTED: cell wall integrity protein scw1-like isoform X1 [Gossypium raimondii])

HSP 1 Score: 62.8 bits (151), Expect = 4.6e-07
Identity = 30/60 (50.00%), Postives = 40/60 (66.67%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGTVAK----GLMYFYSLHPNCTIAGIWR 63
           S + GYKMDE DP+SNYL+LQFSR+PGPRSG GT  +       +F+ ++      G+WR
Sbjct: 216 SALQGYKMDEHDPDSNYLKLQFSRYPGPRSGPGTRGRRFTVEFFFFFEIY-----FGLWR 270

[Close]

BLAST of Lsi08G005370 vs. NCBI nr
Match: gi|728848531|gb|KHG27974.1| (RNA-binding with multiple splicing [Gossypium arboreum])

HSP 1 Score: 61.6 bits (148), Expect = 1.0e-06
Identity = 27/34 (79.41%), Postives = 30/34 (88.24%), Query Frame = 1


Query: 7   SEMCGYKMDEQDPESNYLRLQFSRHPGPRSGSGT 41
           S + GYKMDE DP+SNYLRLQFSR+PGPRSG GT
Sbjct: 248 SALQGYKMDEHDPDSNYLRLQFSRYPGPRSGPGT 281

The following BLAST results are available for this feature:

BLAST of Lsi08G005370 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RBP1_MEDTR	1.3e-06	63.16	RNA-binding protein 1 OS=Medicago truncatula GN=RBP1 PE=2 SV=1	[more]

BLAST of Lsi08G005370 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KCN5_CUCSA	1.8e-18	62.50	Uncharacterized protein OS=Cucumis sativus GN=Csa_6G338020 PE=4 SV=1	[more]
A0A0B0PU61_GOSAR	7.2e-07	79.41	RNA-binding with multiple splicing OS=Gossypium arboreum GN=F383_10922 PE=4 SV=1	[more]
A0A061FI30_THECC	1.2e-06	64.58	Nucleotide binding,nucleic acid binding OS=Theobroma cacao GN=TCM_035511 PE=4 SV...	[more]
A0A0D2TWR8_GOSRA	1.6e-06	76.47	Uncharacterized protein OS=Gossypium raimondii GN=B456_009G284800 PE=4 SV=1	[more]
A0A0D2S9U1_GOSRA	1.6e-06	76.47	Uncharacterized protein OS=Gossypium raimondii GN=B456_009G284800 PE=4 SV=1	[more]

BLAST of Lsi08G005370 vs. TAIR10


Match Name	E-value	Identity	Description

BLAST of Lsi08G005370 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700192266\|gb\|KGN47470.1\|	2.6e-18	62.50	hypothetical protein Csa_6G338020 [Cucumis sativus]	[more]
gi\|449462154\|ref\|XP_004148806.1\|	1.1e-08	83.78	PREDICTED: U1 small nuclear ribonucleoprotein A [Cucumis sativus]	[more]
gi\|659081831\|ref\|XP_008441534.1\|	4.2e-08	81.08	PREDICTED: uncharacterized protein LOC103485638 [Cucumis melo]	[more]
gi\|823228735\|ref\|XP_012447111.1\|	4.6e-07	50.00	PREDICTED: cell wall integrity protein scw1-like isoform X1 [Gossypium raimondii...	[more]
gi\|728848531\|gb\|KHG27974.1\|	1.0e-06	79.41	RNA-binding with multiple splicing [Gossypium arboreum]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **Molecular Function**
Term	Definition
GO:0017069	snRNA binding

Vocabulary: **Biological Process**
Term	Definition
GO:0000398	mRNA splicing, via spliceosome

Vocabulary: **INTERPRO**
Term	Definition
IPR024888	U1 small nuclear ribonucleoprotein A/U2 small nuclear ribonucleoprotein B''

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0000398	mRNA splicing, via spliceosome
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0000166	nucleotide binding
molecular_function	GO:0017069	snRNA binding

Relationships

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


Feature Name	Unique Name	Type
Lsi08G005370.1	Lsi08G005370.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Lagenaria siceraria
Date Performed: 2017-09-18


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR024888	U1 small nuclear ribonucleoprotein A/U2 small nuclear ribonucleoprotein B''	PANTHER	PTHR10501	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B	coord: 11..44 score: 2.6
None	No IPR available	PANTHER	PTHR10501:SF20	NUCLEIC ACID/NUCLEOTIDE BINDING PROTEIN	coord: 11..44 score: 2.6

Synteny

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


Gene	Orthologue	Organism	Block
Lsi08G005370	MELO3C029972.2	Melon (DHL92) v3.6.1	lsimedB494

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Lsi08G005370	Bottle gourd (USVL1VR-Ls)	lsilsiB122
Lsi08G005370	Cucurbita maxima (Rimu)	cmalsiB294
Lsi08G005370	Cucurbita maxima (Rimu)	cmalsiB703
Lsi08G005370	Cucurbita moschata (Rifu)	cmolsiB282
Lsi08G005370	Cucurbita moschata (Rifu)	cmolsiB697
Lsi08G005370	Cucurbita pepo (Zucchini)	cpelsiB158
Lsi08G005370	Cucurbita pepo (Zucchini)	cpelsiB382
Lsi08G005370	Melon (DHL92) v3.5.1	lsimeB475
Lsi08G005370	Watermelon (Charleston Gray)	lsiwcgB439
Lsi08G005370	Watermelon (97103) v1	lsiwmB466
Lsi08G005370	Cucumber (Gy14) v2	cgyblsiB447
Lsi08G005370	Melon (DHL92) v3.6.1	lsimedB487
Lsi08G005370	Silver-seed gourd	carlsiB059
Lsi08G005370	Silver-seed gourd	carlsiB758
Lsi08G005370	Cucumber (Chinese Long) v3	cuclsiB512
Lsi08G005370	Cucumber (Chinese Long) v3	cuclsiB572
Lsi08G005370	Watermelon (97103) v2	lsiwmbB445
Lsi08G005370	Wax gourd	lsiwgoB602