Spg017782 (gene) Sponge gourd (cylindrica) v1

Overview


Name	Spg017782
Type	gene
Organism	Luffa cylindrica (Sponge gourd (cylindrica) v1)
Description	U6 snRNA-associated Sm-like protein LSm4
Location	scaffold9: 33876684 .. 33877261 (-)
RNA-Seq Expression	Spg017782
Synteny	Spg017782

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: polypeptideCDS

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

TCCCCTTCGCTCCTAAAGATCGCTCAAGGGCATCCAATGGTAAGGGTCTCATTTCAATATACGTGTAAATATGGGTGAGCTTATAGCACCTCAACTAAGTTCAAGAGAGAGACTTAAATTTGATCGTCAAGAAACTTAAAGATTTTATATCTAGATAGGGGGCCTCAATATGTAATGCATAATAGGTTGCATTCTGCTTAAACCCTTCCTTCGAGTTTGTTTTTTTGTAGTATGCCATTTTATTCTTTCATAAATGAAATTTCGGTTTCTTACCAAAATAATAATAACAACAACAGCAACAACTTTCATGTTAGGAATTTGCTTTTGAATTTATTTCAAGAATGTAAAATTCGTTGTTGCAACAGTTGGTGGAACTGAAAAATGGTGAGACTTACAACGGCCATTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGGGAAGTCATCTGCACTTCCAAAGTAATGAACTTTTATTTCAGTGATGAATTTTTCTCTTTTTCATTTGCTTTTACTTTTTATGAGAGAATGGGTAACAGTTTTCTATATCAAATGTAGGATTTGGCGGATGTCTGA

mRNA sequence

TCCCCTTCGCTCCTAAAGATCGCTCAAGGGCATCCAATGTTGGTGGAACTGAAAAATGGTGAGACTTACAACGGCCATTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGGGAAGTCATCTGCACTTCCAAAGATTTGGCGGATGTCTGA

Coding sequence (CDS)

TCCCCTTCGCTCCTAAAGATCGCTCAAGGGCATCCAATGTTGGTGGAACTGAAAAATGGTGAGACTTACAACGGCCATTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGGGAAGTCATCTGCACTTCCAAAGATTTGGCGGATGTCTGA

Protein sequence

SPSLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDLADV

Homology

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BLAST of Spg017782 vs. NCBI nr
Match: XP_022770923.1 (probable U6 snRNA-associated Sm-like protein LSm4 isoform X1 [Durio zibethinus] >XP_022770924.1 probable U6 snRNA-associated Sm-like protein LSm4 isoform X1 [Durio zibethinus])

HSP 1 Score: 99.8 bits (247), Expect = 7.4e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 34 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 78

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BLAST of Spg017782 vs. NCBI nr
Match: XP_039129750.1 (probable U6 snRNA-associated Sm-like protein LSm4 [Dioscorea cayenensis subsp. rotundata])

HSP 1 Score: 99.8 bits (247), Expect = 7.4e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. NCBI nr
Match: KAF2315001.1 (hypothetical protein GH714_037497 [Hevea brasiliensis])

HSP 1 Score: 99.8 bits (247), Expect = 7.4e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3   SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
           SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 877 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 921

[Close]

BLAST of Spg017782 vs. NCBI nr
Match: XP_002283804.1 (PREDICTED: probable U6 snRNA-associated Sm-like protein LSm4 [Vitis vinifera])

HSP 1 Score: 99.8 bits (247), Expect = 7.4e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. NCBI nr
Match: XP_022926288.1 (sm-like protein LSM4 isoform X1 [Cucurbita moschata] >XP_022981642.1 sm-like protein LSM4 isoform X1 [Cucurbita maxima] >XP_022981643.1 sm-like protein LSM4 isoform X1 [Cucurbita maxima] >XP_023523329.1 sm-like protein LSM4 isoform X1 [Cucurbita pepo subsp. pepo] >KAG7037244.1 hypothetical protein SDJN02_00867 [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 99.8 bits (247), Expect = 7.4e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

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BLAST of Spg017782 vs. ExPASy Swiss-Prot
Match: F4K4E3 (Sm-like protein LSM4 OS=Arabidopsis thaliana OX=3702 GN=LSM4 PE=1 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 9.7e-21
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy Swiss-Prot
Match: Q9LGE6 (Probable U6 snRNA-associated Sm-like protein LSm4 OS=Oryza sativa subsp. japonica OX=39947 GN=Os01g0256900 PE=2 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 9.7e-21
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy Swiss-Prot
Match: Q43582 (Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum OX=4097 PE=2 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 9.7e-21
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy Swiss-Prot
Match: Q9ZRU9 (Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica OX=28930 GN=LSM4 PE=2 SV=1)

HSP 1 Score: 97.8 bits (242), Expect = 3.7e-20
Identity = 43/45 (95.56%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELK+GETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKSGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy Swiss-Prot
Match: Q3ZBK6 (U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus OX=9913 GN=LSM4 PE=2 SV=1)

HSP 1 Score: 89.7 bits (221), Expect = 1.0e-17
Identity = 39/45 (86.67%), Postives = 42/45 (93.33%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQ HPMLVELKNGETYNGHLV+CD WMNI+LREVICTS+D
Sbjct: 5  SLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRD 49

[Close]

BLAST of Spg017782 vs. ExPASy TrEMBL
Match: A0A2G9IAA6 (U6 snRNA-associated Sm-like protein LSm4 OS=Handroanthus impetiginosus OX=429701 GN=LSM4 PE=3 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.6e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy TrEMBL
Match: A0A5D2E990 (U6 snRNA-associated Sm-like protein LSm4 OS=Gossypium darwinii OX=34276 GN=LSM4 PE=3 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.6e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy TrEMBL
Match: A0A059A9J1 (U6 snRNA-associated Sm-like protein LSm4 OS=Eucalyptus grandis OX=71139 GN=LSM4 PE=3 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.6e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy TrEMBL
Match: A0A1U7WYS5 (U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana sylvestris OX=4096 GN=LOC104231212 PE=3 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.6e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. ExPASy TrEMBL
Match: A0A1U8KMG3 (U6 snRNA-associated Sm-like protein LSm4 OS=Gossypium hirsutum OX=3635 GN=LOC107917334 PE=3 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.6e-18
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. TAIR 10
Match: AT5G27720.1 (Small nuclear ribonucleoprotein family protein )

HSP 1 Score: 99.8 bits (247), Expect = 6.9e-22
Identity = 44/45 (97.78%), Postives = 44/45 (97.78%), Query Frame = 0


Query: 3  SLLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          SLLK AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD
Sbjct: 5  SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 49

[Close]

BLAST of Spg017782 vs. TAIR 10
Match: AT1G20580.1 (Small nuclear ribonucleoprotein family protein )

HSP 1 Score: 44.7 bits (104), Expect = 2.6e-05
Identity = 19/44 (43.18%), Postives = 27/44 (61.36%), Query Frame = 0


Query: 4  LLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          LL  A GH + VELK+GE Y G ++ C+   N  L ++  T+KD
Sbjct: 11 LLHEASGHIVTVELKSGELYRGSMIECEDNWNCQLEDITYTAKD 54

[Close]

BLAST of Spg017782 vs. TAIR 10
Match: AT1G76300.1 (snRNP core protein SMD3 )

HSP 1 Score: 41.6 bits (96), Expect = 2.2e-04
Identity = 17/44 (38.64%), Postives = 26/44 (59.09%), Query Frame = 0


Query: 4  LLKIAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD 48
          LL  + GH + VE+K+GE Y G ++ C+   N  L  +  T+KD
Sbjct: 11 LLHESSGHIVSVEMKSGELYRGSMIECEDNWNCQLENITYTAKD 54

The following BLAST results are available for this feature:

BLAST of Spg017782 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_022770923.1	7.4e-18	97.78	probable U6 snRNA-associated Sm-like protein LSm4 isoform X1 [Durio zibethinus] ...	[more]
XP_039129750.1	7.4e-18	97.78	probable U6 snRNA-associated Sm-like protein LSm4 [Dioscorea cayenensis subsp. r...	[more]
KAF2315001.1	7.4e-18	97.78	hypothetical protein GH714_037497 [Hevea brasiliensis]	[more]
XP_002283804.1	7.4e-18	97.78	PREDICTED: probable U6 snRNA-associated Sm-like protein LSm4 [Vitis vinifera]	[more]
XP_022926288.1	7.4e-18	97.78	sm-like protein LSM4 isoform X1 [Cucurbita moschata] >XP_022981642.1 sm-like pro...	[more]

BLAST of Spg017782 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
F4K4E3	9.7e-21	97.78	Sm-like protein LSM4 OS=Arabidopsis thaliana OX=3702 GN=LSM4 PE=1 SV=1	[more]
Q9LGE6	9.7e-21	97.78	Probable U6 snRNA-associated Sm-like protein LSm4 OS=Oryza sativa subsp. japonic...	[more]
Q43582	9.7e-21	97.78	Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum OX=4097 P...	[more]
Q9ZRU9	3.7e-20	95.56	Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica OX=28930 GN...	[more]
Q3ZBK6	1.0e-17	86.67	U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus OX=9913 GN=LSM4 PE=2 SV=1	[more]

BLAST of Spg017782 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A2G9IAA6	3.6e-18	97.78	U6 snRNA-associated Sm-like protein LSm4 OS=Handroanthus impetiginosus OX=429701...	[more]
A0A5D2E990	3.6e-18	97.78	U6 snRNA-associated Sm-like protein LSm4 OS=Gossypium darwinii OX=34276 GN=LSM4 ...	[more]
A0A059A9J1	3.6e-18	97.78	U6 snRNA-associated Sm-like protein LSm4 OS=Eucalyptus grandis OX=71139 GN=LSM4 ...	[more]
A0A1U7WYS5	3.6e-18	97.78	U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana sylvestris OX=4096 GN=LOC1...	[more]
A0A1U8KMG3	3.6e-18	97.78	U6 snRNA-associated Sm-like protein LSm4 OS=Gossypium hirsutum OX=3635 GN=LOC107...	[more]

BLAST of Spg017782 vs. TAIR 10


Match Name	E-value	Identity	Description
AT5G27720.1	6.9e-22	97.78	Small nuclear ribonucleoprotein family protein	[more]
AT1G20580.1	2.6e-05	43.18	Small nuclear ribonucleoprotein family protein	[more]
AT1G76300.1	2.2e-04	38.64	snRNP core protein SMD3	[more]

InterPro

Analysis Name: InterPro Annotations of Sponge gourd (cylindrica) v1
Date Performed: 2022-08-01


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR001163	LSM domain, eukaryotic/archaea-type	SMART	SM00651	Sm3	coord: 3..48 e-value: 0.0011 score: 28.3
IPR001163	LSM domain, eukaryotic/archaea-type	PFAM	PF01423	LSM	coord: 4..47 e-value: 2.9E-12 score: 46.1
None	No IPR available	GENE3D	2.30.30.100		coord: 1..51 e-value: 1.0E-19 score: 71.8
None	No IPR available	PANTHER	PTHR23338:SF42	SM-LIKE PROTEIN LSM4	coord: 3..47
IPR027141	Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3	PANTHER	PTHR23338	SMALL NUCLEAR RIBONUCLEOPROTEIN SM	coord: 3..47
IPR034101	Sm-like protein Lsm4	CDD	cd01723	LSm4	coord: 3..47 e-value: 5.1935E-32 score: 103.039
IPR010920	LSM domain superfamily	SUPERFAMILY	50182	Sm-like ribonucleoproteins	coord: 3..47

Relationships

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


Feature Name	Unique Name	Type
Spg017782.1	Spg017782.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006298	mismatch repair
biological_process	GO:0000956	nuclear-transcribed mRNA catabolic process
biological_process	GO:0033962	P-body assembly
biological_process	GO:0000387	spliceosomal snRNP assembly
biological_process	GO:0000398	mRNA splicing, via spliceosome
biological_process	GO:0006396	RNA processing
cellular_component	GO:0120115	Lsm2-8 complex
cellular_component	GO:0032300	mismatch repair complex
cellular_component	GO:0000932	P-body
cellular_component	GO:0005681	spliceosomal complex
cellular_component	GO:0097526	spliceosomal tri-snRNP complex
cellular_component	GO:0005688	U6 snRNP
molecular_function	GO:0005524	ATP binding
molecular_function	GO:0016887	ATP hydrolysis activity
molecular_function	GO:0030983	mismatched DNA binding
molecular_function	GO:0017070	U6 snRNA binding