Lag0007510 (gene) Sponge gourd (AG‐4) v1

Overview


Name	Lag0007510
Type	gene
Organism	Luffa acutangula (Sponge gourd (AG‐4) v1)
Description	Small nuclear ribonucleoprotein Sm D1
Location	chr9: 352111 .. 352524 (+)
RNA-Seq Expression	Lag0007510
Synteny	Lag0007510

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide

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

ATGCTTTTCTTGTATTACATAGGTGTGGATATTAGCATGAATACACATTTGAAGGCTGTGAAACTTACCCTAAAGGGGAAAAATCCAGTTACCATGGATCATTTAAGTGTGAGGGGTAACAACATCAGATATTATATTCTTCCTGACAGCTTGAATCTAGAAACTTTACTAGTTGAAGAGACACCTAGGGTCAAGCCCAAGAAACCAACTGCAGGTATGCGTTGTTCTTGTACTCTGGCCATTACTTTATGGTCATTTCGTGCAAATTGTTTTATATCGAATCATATGCAAATCTATTTCAGCATCTTATATGTTATGTCGCTTATGTATTTCTTCTCTGCTGCAACTGCAGGGAGGCCTTTGGGACGCGGGCGTGGACGGGGGCGGGGGCGTGGTCGCGGGCGTGGACGTTAG

mRNA sequence

ATGCTTTTCTTGTATTACATAGGTGTGGATATTAGCATGAATACACATTTGAAGGCTGTGAAACTTACCCTAAAGGGGAAAAATCCAGTTACCATGGATCATTTAAGTGTGAGGGGTAACAACATCAGATATTATATTCTTCCTGACAGCTTGAATCTAGAAACTTTACTAGTTGAAGAGACACCTAGGGTCAAGCCCAAGAAACCAACTGCAGGGAGGCCTTTGGGACGCGGGCGTGGACGGGGGCGGGGGCGTGGTCGCGGGCGTGGACGTTAG

Coding sequence (CDS)

ATGCTTTTCTTGTATTACATAGGTGTGGATATTAGCATGAATACACATTTGAAGGCTGTGAAACTTACCCTAAAGGGGAAAAATCCAGTTACCATGGATCATTTAAGTGTGAGGGGTAACAACATCAGATATTATATTCTTCCTGACAGCTTGAATCTAGAAACTTTACTAGTTGAAGAGACACCTAGGGTCAAGCCCAAGAAACCAACTGCAGGGAGGCCTTTGGGACGCGGGCGTGGACGGGGGCGGGGGCGTGGTCGCGGGCGTGGACGTTAG

Protein sequence

MLFLYYIGVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGRPLGRGRGRGRGRGRGRGR

Homology

[Close]

BLAST of Lag0007510 vs. NCBI nr
Match: RVW50139.1 (Small nuclear ribonucleoprotein SmD1b [Vitis vinifera] >RVX14832.1 Small nuclear ribonucleoprotein SmD1b [Vitis vinifera])

HSP 1 Score: 164.5 bits (415), Expect = 4.4e-37
Identity = 84/88 (95.45%), Postives = 86/88 (97.73%), Query Frame = 0


Query: 4  LYYIGVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPR 63
          LY IGVDISMNTHLK VKLTLKGKNPVTMDHLSVRGNNIRYYILPDS+NLETLLVEETPR
Sbjct: 12 LYVIGVDISMNTHLKTVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSINLETLLVEETPR 71

Query: 64 VKPKKPTAGRPLGRGRGRGRGRGRGRGR 92
          VKPKKPTAGRP+GRGRGRGRGRGRGRGR
Sbjct: 72 VKPKKPTAGRPMGRGRGRGRGRGRGRGR 99

[Close]

BLAST of Lag0007510 vs. NCBI nr
Match: PHT80497.1 (Small nuclear ribonucleoprotein Sm D1 [Capsicum annuum])

HSP 1 Score: 164.1 bits (414), Expect = 5.7e-37
Identity = 82/91 (90.11%), Postives = 90/91 (98.90%), Query Frame = 0


Query: 1  MLFLYYIGVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEE 60
          ++FL +IGVD+SMNTHLKAVK+TLKGKNPVT+DHLSVRGNNIRYYILPDSLNLETLLVE+
Sbjct: 6  VIFLIFIGVDVSMNTHLKAVKITLKGKNPVTLDHLSVRGNNIRYYILPDSLNLETLLVED 65

Query: 61 TPRVKPKKPTAGRPLGRGRGRGRGRGRGRGR 92
          TPRVKPKKPTAG+PLGRGRGRGRGRGRGRGR
Sbjct: 66 TPRVKPKKPTAGKPLGRGRGRGRGRGRGRGR 96

[Close]

BLAST of Lag0007510 vs. NCBI nr
Match: XP_038896756.1 (small nuclear ribonucleoprotein SmD1b isoform X2 [Benincasa hispida] >XP_038897024.1 small nuclear ribonucleoprotein SmD1b isoform X2 [Benincasa hispida])

HSP 1 Score: 163.3 bits (412), Expect = 9.8e-37
Identity = 84/84 (100.00%), Postives = 84/84 (100.00%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK
Sbjct: 24  GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 83

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           KPTAGRPLGRGRGRGRGRGRGRGR
Sbjct: 84  KPTAGRPLGRGRGRGRGRGRGRGR 107

[Close]

BLAST of Lag0007510 vs. NCBI nr
Match: XP_004150106.1 (small nuclear ribonucleoprotein SmD1b [Cucumis sativus] >XP_008454659.1 PREDICTED: small nuclear ribonucleoprotein Sm D1-like [Cucumis melo] >XP_022155676.1 small nuclear ribonucleoprotein SmD1b [Momordica charantia] >XP_022157762.1 small nuclear ribonucleoprotein SmD1b [Momordica charantia] >XP_022157763.1 small nuclear ribonucleoprotein SmD1b [Momordica charantia] >XP_038896755.1 small nuclear ribonucleoprotein SmD1b isoform X1 [Benincasa hispida] >XP_038897023.1 small nuclear ribonucleoprotein SmD1b isoform X1 [Benincasa hispida] >KGN59890.1 hypothetical protein Csa_002314 [Cucumis sativus])

HSP 1 Score: 163.3 bits (412), Expect = 9.8e-37
Identity = 84/84 (100.00%), Postives = 84/84 (100.00%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK
Sbjct: 31  GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           KPTAGRPLGRGRGRGRGRGRGRGR
Sbjct: 91  KPTAGRPLGRGRGRGRGRGRGRGR 114

[Close]

BLAST of Lag0007510 vs. NCBI nr
Match: XP_022931093.1 (small nuclear ribonucleoprotein SmD1b [Cucurbita moschata] >XP_022995872.1 small nuclear ribonucleoprotein SmD1b [Cucurbita maxima] >XP_023533992.1 small nuclear ribonucleoprotein SmD1b [Cucurbita pepo subsp. pepo] >KAG7036369.1 Small nuclear ribonucleoprotein SmD1b [Cucurbita argyrosperma subsp. argyrosperma])

HSP 1 Score: 162.2 bits (409), Expect = 2.2e-36
Identity = 83/84 (98.81%), Postives = 84/84 (100.00%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK
Sbjct: 31  GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           KPTAG+PLGRGRGRGRGRGRGRGR
Sbjct: 91  KPTAGKPLGRGRGRGRGRGRGRGR 114

[Close]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot
Match: Q9SY09 (Small nuclear ribonucleoprotein SmD1b OS=Arabidopsis thaliana OX=3702 GN=SMD1B PE=3 SV=1)

HSP 1 Score: 151.4 bits (381), Expect = 5.0e-36
Identity = 77/84 (91.67%), Postives = 82/84 (97.62%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVD+SMNTHLKAVKLTLKGKNPVT+DHLSVRGNNIRYYILPDSLNLETLLVE+TPR+KPK
Sbjct: 31  GVDVSMNTHLKAVKLTLKGKNPVTLDHLSVRGNNIRYYILPDSLNLETLLVEDTPRIKPK 90

Query: 68  KPTAGR-PLGRGRGRGRGRGRGRG 91
           KPTAG+ P GRGRGRGRGRGRGRG
Sbjct: 91  KPTAGKIPAGRGRGRGRGRGRGRG 114

[Close]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot
Match: Q9SSF1 (Small nuclear ribonucleoprotein SmD1a OS=Arabidopsis thaliana OX=3702 GN=SMD1A PE=3 SV=1)

HSP 1 Score: 148.3 bits (373), Expect = 4.3e-35
Identity = 73/84 (86.90%), Postives = 81/84 (96.43%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVD+SMNTHLK VK++LKGKNPVT+DHLS+RGNNIRYYILPDSLNLETLLVE+TPRVKPK
Sbjct: 31  GVDVSMNTHLKTVKMSLKGKNPVTLDHLSLRGNNIRYYILPDSLNLETLLVEDTPRVKPK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           KP AG+ +GRGRGRGRGRGRGRGR
Sbjct: 91  KPVAGKAVGRGRGRGRGRGRGRGR 114

[Close]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot
Match: Q3ZC10 (Small nuclear ribonucleoprotein Sm D1 OS=Bos taurus OX=9913 GN=SNRPD1 PE=3 SV=1)

HSP 1 Score: 113.6 bits (283), Expect = 1.2e-24
Identity = 60/84 (71.43%), Postives = 70/84 (83.33%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVD+SMNTHLKAVK+TLK + PV ++ LS+RGNNIRY+ILPDSL L+TLLV+  P+VK K
Sbjct: 31  GVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           K  A    GRGRGRGRGRGRGRGR
Sbjct: 91  KREAVAGRGRGRGRGRGRGRGRGR 114

[Close]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot
Match: P62314 (Small nuclear ribonucleoprotein Sm D1 OS=Homo sapiens OX=9606 GN=SNRPD1 PE=1 SV=1)

HSP 1 Score: 113.6 bits (283), Expect = 1.2e-24
Identity = 60/84 (71.43%), Postives = 70/84 (83.33%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVD+SMNTHLKAVK+TLK + PV ++ LS+RGNNIRY+ILPDSL L+TLLV+  P+VK K
Sbjct: 31  GVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           K  A    GRGRGRGRGRGRGRGR
Sbjct: 91  KREAVAGRGRGRGRGRGRGRGRGR 114

[Close]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot
Match: Q4R5F6 (Small nuclear ribonucleoprotein Sm D1 OS=Macaca fascicularis OX=9541 GN=SNRPD1 PE=3 SV=1)

HSP 1 Score: 113.6 bits (283), Expect = 1.2e-24
Identity = 60/84 (71.43%), Postives = 70/84 (83.33%), Query Frame = 0


Query: 8   GVDISMNTHLKAVKLTLKGKNPVTMDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPK 67
           GVD+SMNTHLKAVK+TLK + PV ++ LS+RGNNIRY+ILPDSL L+TLLV+  P+VK K
Sbjct: 31  GVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSK 90

Query: 68  KPTAGRPLGRGRGRGRGRGRGRGR 92
           K  A    GRGRGRGRGRGRGRGR
Sbjct: 91  KREAVAGRGRGRGRGRGRGRGRGR 114

The following BLAST results are available for this feature:

BLAST of Lag0007510 vs. NCBI nr


Match Name	E-value	Identity	Description
RVW50139.1	4.4e-37	95.45	Small nuclear ribonucleoprotein SmD1b [Vitis vinifera] >RVX14832.1 Small nuclear...	[more]
PHT80497.1	5.7e-37	90.11	Small nuclear ribonucleoprotein Sm D1 [Capsicum annuum]	[more]
XP_038896756.1	9.8e-37	100.00	small nuclear ribonucleoprotein SmD1b isoform X2 [Benincasa hispida] >XP_0388970...	[more]
XP_004150106.1	9.8e-37	100.00	small nuclear ribonucleoprotein SmD1b [Cucumis sativus] >XP_008454659.1 PREDICTE...	[more]
XP_022931093.1	2.2e-36	98.81	small nuclear ribonucleoprotein SmD1b [Cucurbita moschata] >XP_022995872.1 small...	[more]

BLAST of Lag0007510 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q9SY09	5.0e-36	91.67	Small nuclear ribonucleoprotein SmD1b OS=Arabidopsis thaliana OX=3702 GN=SMD1B P...	[more]
Q9SSF1	4.3e-35	86.90	Small nuclear ribonucleoprotein SmD1a OS=Arabidopsis thaliana OX=3702 GN=SMD1A P...	[more]
Q3ZC10	1.2e-24	71.43	Small nuclear ribonucleoprotein Sm D1 OS=Bos taurus OX=9913 GN=SNRPD1 PE=3 SV=1	[more]
P62314	1.2e-24	71.43	Small nuclear ribonucleoprotein Sm D1 OS=Homo sapiens OX=9606 GN=SNRPD1 PE=1 SV=...	[more]
Q4R5F6	1.2e-24	71.43	Small nuclear ribonucleoprotein Sm D1 OS=Macaca fascicularis OX=9541 GN=SNRPD1 P...	[more]

InterPro

Analysis Name: InterPro Annotations of Sponge gourd (AG-4) v1
Date Performed: 2022-08-01


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	GENE3D	2.30.30.100		coord: 5..62 e-value: 1.0E-18 score: 68.6
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 70..91
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 61..91
None	No IPR available	PANTHER	PTHR23338:SF49	SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1	coord: 7..87
IPR001163	LSM domain, eukaryotic/archaea-type	PFAM	PF01423	LSM	coord: 8..46 e-value: 4.4E-7 score: 29.5
IPR027141	Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3	PANTHER	PTHR23338	SMALL NUCLEAR RIBONUCLEOPROTEIN SM	coord: 7..87
IPR010920	LSM domain superfamily	SUPERFAMILY	50182	Sm-like ribonucleoproteins	coord: 7..90

Relationships

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


Feature Name	Unique Name	Type
Lag0007510.1	Lag0007510.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0000387	spliceosomal snRNP assembly
biological_process	GO:0006396	RNA processing
cellular_component	GO:0071013	catalytic step 2 spliceosome
cellular_component	GO:0000243	commitment complex
cellular_component	GO:0034715	pICln-Sm protein complex
cellular_component	GO:0071011	precatalytic spliceosome
cellular_component	GO:0034719	SMN-Sm protein complex
cellular_component	GO:0097526	spliceosomal tri-snRNP complex
cellular_component	GO:0005689	U12-type spliceosomal complex
cellular_component	GO:0005685	U1 snRNP
cellular_component	GO:0005686	U2 snRNP
cellular_component	GO:0005687	U4 snRNP
cellular_component	GO:0005682	U5 snRNP
molecular_function	GO:0003723	RNA binding