Cla013820 (gene) Watermelon (97103) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cla013820
Type	gene
Organism	Citrullus. lanatus (Watermelon (97103) v1)
Description	U6 snRNA-associated Sm-like protein LSm3 (AHRD V1 **-- F1LDH2_ASCSU); contains Interpro domain(s) IPR001163 Like-Sm ribonucleoprotein, core
Location	Chr8 : 16205311 .. 16205861 (-)

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.

ATGGCGACCGAAGAAGAAAGCACTGTCAAGGAGCCACTGGATCTCATAAGGTTGAGTCTTGACGAACGTATTTACGTCAAGCTTCGCTCTGACCGCGAACTCCGCGGCAAACTCCATGTATATCCTCCTTCATTACTTCTTCTTTTCCCCCCCCCCCCCCCCTTTTTTTTTCTTTTTTTTCCCTGTTTCATTACGTTGTCTCTCTATCTCTCTATCTACCCCTTTAATCGAATGCCCCCAATTGTTGGTTTATCTAGTGATTTTTTTTTCTTTCGGTCAAATGAATATCCTGGAGAATTAGGGTTTTGTTATCGTTTGAGTTTCTTGATGGGGTTCCCTGAAATTTGTTTACACTCATTTTCTTGAAAAAAAGGCTACACTTTAGTTGCTCCCAGTAACCCAATTGAGTTTTTGAGTTTGGGATGGGGCAGGGGCTGGTTTCGAACTTCTCTATTTTTGCGGTAATGAAATTGGATGAATCCGGAAGAAGTGCCCTAACGGTGAAAAGTGTCAAAGTCAGAGATCTCTGCTCTTACCCATTGGAAATTTAG

mRNA sequence

ATGGCGACCGAAGAAGAAAGCACTGTCAAGGAGCCACTGGATCTCATAAGGTTGAGTCTTGACGAACGTATTTACGTCAAGCTTCGCTCTGACCGCGAACTCCGCGGCAAACTCCATGGGCTGGTTTCGAACTTCTCTATTTTTGCGGTAATGAAATTGGATGAATCCGGAAGAAGTGCCCTAACGGTGAAAAGTGTCAAAGTCAGAGATCTCTGCTCTTACCCATTGGAAATTTAG

Coding sequence (CDS)

ATGGCGACCGAAGAAGAAAGCACTGTCAAGGAGCCACTGGATCTCATAAGGTTGAGTCTTGACGAACGTATTTACGTCAAGCTTCGCTCTGACCGCGAACTCCGCGGCAAACTCCATGGGCTGGTTTCGAACTTCTCTATTTTTGCGGTAATGAAATTGGATGAATCCGGAAGAAGTGCCCTAACGGTGAAAAGTGTCAAAGTCAGAGATCTCTGCTCTTACCCATTGGAAATTTAG

Protein sequence

MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLHGLVSNFSIFAVMKLDESGRSALTVKSVKVRDLCSYPLEI

Homology

[Close]

BLAST of Cla013820 vs. Swiss-Prot
Match: LSM3B_ARATH (Sm-like protein LSM3B OS=Arabidopsis thaliana GN=LSM3B PE=1 SV=1)

HSP 1 Score: 72.0 bits (175), Expect = 3.2e-12
Identity = 35/39 (89.74%), Postives = 36/39 (92.31%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          M+ EEE+TV+EPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MSGEEEATVREPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. Swiss-Prot
Match: LSM3A_ARATH (Sm-like protein LSM3A OS=Arabidopsis thaliana GN=LSM3A PE=1 SV=1)

HSP 1 Score: 69.3 bits (168), Expect = 2.1e-11
Identity = 32/39 (82.05%), Postives = 36/39 (92.31%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          M+ EE++TV+EPLDLIRLS++ERIYVKLRSDRELRGKLH
Sbjct: 1  MSVEEDATVREPLDLIRLSIEERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. Swiss-Prot
Match: LSM3_DICDI (Probable U6 snRNA-associated Sm-like protein LSm3 OS=Dictyostelium discoideum GN=lsm3 PE=3 SV=1)

HSP 1 Score: 64.7 bits (156), Expect = 5.1e-10
Identity = 31/39 (79.49%), Postives = 32/39 (82.05%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          M   EE TV+EPLDLIRLSLDERI+VK+R DRELRGKLH
Sbjct: 1  MDKREEGTVEEPLDLIRLSLDERIFVKMRQDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. Swiss-Prot
Match: LSM3_BOVIN (U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus GN=LSM3 PE=3 SV=3)

HSP 1 Score: 61.2 bits (147), Expect = 5.7e-09
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


Query: 7  STVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          +TV+EPLDLIRLSLDERIYVK+R+DRELRG+LH
Sbjct: 12 NTVEEPLDLIRLSLDERIYVKMRNDRELRGRLH 44

[Close]

BLAST of Cla013820 vs. Swiss-Prot
Match: LSM3_HUMAN (U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens GN=LSM3 PE=1 SV=2)

HSP 1 Score: 61.2 bits (147), Expect = 5.7e-09
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


Query: 7  STVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          +TV+EPLDLIRLSLDERIYVK+R+DRELRG+LH
Sbjct: 12 NTVEEPLDLIRLSLDERIYVKMRNDRELRGRLH 44

[Close]

BLAST of Cla013820 vs. TrEMBL
Match: A0A0A0K8S0_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_6G057110 PE=4 SV=1)

HSP 1 Score: 78.2 bits (191), Expect = 5.0e-12
Identity = 39/39 (100.00%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. TrEMBL
Match: A0A0B0PV80_GOSAR (U6 snRNA-associated Sm-like protein LSm3 OS=Gossypium arboreum GN=F383_15446 PE=4 SV=1)

HSP 1 Score: 77.0 bits (188), Expect = 1.1e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEE+STVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEDSTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. TrEMBL
Match: M0T1T6_MUSAM (Uncharacterized protein OS=Musa acuminata subsp. malaccensis PE=4 SV=1)

HSP 1 Score: 76.6 bits (187), Expect = 1.5e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MA+EEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MASEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. TrEMBL
Match: A0A151RN45_CAJCA (U6 snRNA-associated Sm-like protein LSm3 OS=Cajanus cajan GN=KK1_034588 PE=4 SV=1)

HSP 1 Score: 76.3 bits (186), Expect = 1.9e-11
Identity = 38/39 (97.44%), Postives = 38/39 (97.44%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEEES VKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. TrEMBL
Match: A0A0S3TAL4_PHAAN (Uncharacterized protein OS=Vigna angularis var. angularis GN=Vigan.11G146700 PE=4 SV=1)

HSP 1 Score: 76.3 bits (186), Expect = 1.9e-11
Identity = 38/39 (97.44%), Postives = 38/39 (97.44%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEEES VKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. NCBI nr
Match: gi|659081800|ref|XP_008441520.1| (PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Cucumis melo])

HSP 1 Score: 78.2 bits (191), Expect = 7.2e-12
Identity = 39/39 (100.00%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. NCBI nr
Match: gi|728848891|gb|KHG28334.1| (U6 snRNA-associated Sm-like protein LSm3 [Gossypium arboreum])

HSP 1 Score: 77.0 bits (188), Expect = 1.6e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MATEE+STVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MATEEDSTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. NCBI nr
Match: gi|1009125356|ref|XP_015879569.1| (PREDICTED: sm-like protein LSM3B [Ziziphus jujuba])

HSP 1 Score: 76.6 bits (187), Expect = 2.1e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MA+EEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MASEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. NCBI nr
Match: gi|672125005|ref|XP_008785908.1| (PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Phoenix dactylifera])

HSP 1 Score: 76.6 bits (187), Expect = 2.1e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MA+EEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MASEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

[Close]

BLAST of Cla013820 vs. NCBI nr
Match: gi|695030348|ref|XP_009402631.1| (PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Musa acuminata subsp. malaccensis])

HSP 1 Score: 76.6 bits (187), Expect = 2.1e-11
Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 1


Query: 1  MATEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 40
          MA+EEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH
Sbjct: 1  MASEEESTVKEPLDLIRLSLDERIYVKLRSDRELRGKLH 39

The following BLAST results are available for this feature:

BLAST of Cla013820 vs. Swiss-Prot


Match Name	E-value	Identity	Description
LSM3B_ARATH	3.2e-12	89.74	Sm-like protein LSM3B OS=Arabidopsis thaliana GN=LSM3B PE=1 SV=1	[more]
LSM3A_ARATH	2.1e-11	82.05	Sm-like protein LSM3A OS=Arabidopsis thaliana GN=LSM3A PE=1 SV=1	[more]
LSM3_DICDI	5.1e-10	79.49	Probable U6 snRNA-associated Sm-like protein LSm3 OS=Dictyostelium discoideum GN...	[more]
LSM3_BOVIN	5.7e-09	84.85	U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus GN=LSM3 PE=3 SV=3	[more]
LSM3_HUMAN	5.7e-09	84.85	U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens GN=LSM3 PE=1 SV=2	[more]

BLAST of Cla013820 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0K8S0_CUCSA	5.0e-12	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_6G057110 PE=4 SV=1	[more]
A0A0B0PV80_GOSAR	1.1e-11	97.44	U6 snRNA-associated Sm-like protein LSm3 OS=Gossypium arboreum GN=F383_15446 PE=...	[more]
M0T1T6_MUSAM	1.5e-11	97.44	Uncharacterized protein OS=Musa acuminata subsp. malaccensis PE=4 SV=1	[more]
A0A151RN45_CAJCA	1.9e-11	97.44	U6 snRNA-associated Sm-like protein LSm3 OS=Cajanus cajan GN=KK1_034588 PE=4 SV=...	[more]
A0A0S3TAL4_PHAAN	1.9e-11	97.44	Uncharacterized protein OS=Vigna angularis var. angularis GN=Vigan.11G146700 PE=...	[more]

BLAST of Cla013820 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|659081800\|ref\|XP_008441520.1\|	7.2e-12	100.00	PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Cucumis melo]	[more]
gi\|728848891\|gb\|KHG28334.1\|	1.6e-11	97.44	U6 snRNA-associated Sm-like protein LSm3 [Gossypium arboreum]	[more]
gi\|1009125356\|ref\|XP_015879569.1\|	2.1e-11	97.44	PREDICTED: sm-like protein LSM3B [Ziziphus jujuba]	[more]
gi\|672125005\|ref\|XP_008785908.1\|	2.1e-11	97.44	PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Phoenix dactylifera]	[more]
gi\|695030348\|ref\|XP_009402631.1\|	2.1e-11	97.44	PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Musa acuminata subsp. malac...	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR010920	LSM_dom_sf

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:0033962	cytoplasmic mRNA processing body assembly
biological_process	GO:0000398	mRNA splicing, via spliceosome
biological_process	GO:0000956	nuclear-transcribed mRNA catabolic process
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0030529	intracellular ribonucleoprotein complex
cellular_component	GO:0019013	viral nucleocapsid
cellular_component	GO:0071013	catalytic step 2 spliceosome
cellular_component	GO:0000932	cytoplasmic mRNA processing body
cellular_component	GO:1990726	Lsm1-7-Pat1 complex
cellular_component	GO:0071011	precatalytic spliceosome
cellular_component	GO:0046540	U4/U6 x U5 tri-snRNP complex
cellular_component	GO:0005688	U6 snRNP
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0003723	RNA binding

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
WMU29443	watermelon unigene v2 vs TrEMBL	transcribed_cluster

Relationships

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


Feature Name	Unique Name	Type
Cla013820	Cla013820.1	mRNA

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


Feature Name	Unique Name	Type
WMU29443	WMU29443	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
IPR010920	LSM domain	unknown	SSF50182	Sm-like ribonucleoproteins	coord: 10..41 score: 1.4
None	No IPR available	GENE3D	G3DSA:2.30.30.100		coord: 3..40 score: 8.
None	No IPR available	PANTHER	PTHR13110	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3	coord: 1..39 score: 3.1
None	No IPR available	PANTHER	PTHR13110:SF2	SUBFAMILY NOT NAMED	coord: 1..39 score: 3.1

Synteny

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


Gene	Orthologue	Organism	Block
Cla013820	Cla97C08G149660	Watermelon (97103) v2	wmwmbB100
Cla013820	Csa6G057110	Cucumber (Chinese Long) v2	cuwmB470
Cla013820	MELO3C008344	Melon (DHL92) v3.5.1	mewmB309
Cla013820	ClCG08G006960	Watermelon (Charleston Gray)	wcgwmB400
Cla013820	CSPI06G04950	Wild cucumber (PI 183967)	cpiwmB485
Cla013820	Cucsa.363670	Cucumber (Gy14) v1	cgywmB654
Cla013820	CmaCh04G024470	Cucurbita maxima (Rimu)	cmawmB666
Cla013820	CmaCh15G005990	Cucurbita maxima (Rimu)	cmawmB260
Cla013820	CmoCh04G025620	Cucurbita moschata (Rifu)	cmowmB661
Cla013820	CmoCh15G006050	Cucurbita moschata (Rifu)	cmowmB250
Cla013820	Lsi08G005530	Bottle gourd (USVL1VR-Ls)	lsiwmB466
Cla013820	Cp4.1LG01g21160	Cucurbita pepo (Zucchini)	cpewmB393
Cla013820	CsGy6G004860	Cucumber (Gy14) v2	cgybwmB441
Cla013820	MELO3C008344.2	Melon (DHL92) v3.6.1	medwmB301
Cla013820	Carg15789	Silver-seed gourd	carwmB0064
Cla013820	CsaV3_1G019700	Cucumber (Chinese Long) v3	cucwmB010
Cla013820	Bhi04G001366	Wax gourd	wgowmB309

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cla013820	Silver-seed gourd	carwmB0824
Cla013820	Cucumber (Chinese Long) v3	cucwmB496
Cla013820	Cucurbita pepo (Zucchini)	cpewmB170