Lag0037470 (gene) Sponge gourd (AG‐4) v1

Overview


Name	Lag0037470
Type	gene
Organism	Luffa acutangula (Sponge gourd (AG‐4) v1)
Description	Endoribonuclease YBEY, chloroplastic
Location	chr2: 6581041 .. 6581569 (-)
RNA-Seq Expression	Lag0037470
Synteny	Lag0037470

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: polypeptideexonCDS

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

ATGATTCTAAACACCCCACAGCTTCCTTGTGGTACGTGAACTTAGTTGAAGGTTTACTAATCCTATGAACTCCTGTTATGAATCTACTGAAGATCCAGATTGATACTTGACCATCTGTAAAAAAGGAATGTATGATTGCTTCTGAAACTAGAATCCATAATTTTGGTGCCGTTCATTTATCCTACATACAAATTTAGCATCATAATTGAAGGATCTTGTTGATTATTGGGTAGAAAAGTTCATTCAATACAGACATGATCTTGTGCTTAAACTGGTCTTGATTATGGTATTGGTTTTACAACACTGATCTTAAGTGGCTTAGACCTTTACCCTGACCCTGGGATTGTGCTTGATTATGTAGGTAATGGCTATTGGAGATGGGGAAAATGACATTGAGATGCTGGAGCTGGCATCTCTTGGGATTGCTTTGAGCAATGGATCAGAGAAAACAAAAGCTGTTGCTAACCTTATTGGTCCCAGCAATGATGAAGATGGTGTTGCAGATGTCATATACCGATACGCATTCTAG

mRNA sequence

ATGATTCTAAACACCCCACAGCTTCCTTGTGAAAAGTTCATTCAATACAGACATGATCTTGTGCTTAAACTGGTCTTGATTATGGTAATGGCTATTGGAGATGGGGAAAATGACATTGAGATGCTGGAGCTGGCATCTCTTGGGATTGCTTTGAGCAATGGATCAGAGAAAACAAAAGCTGTTGCTAACCTTATTGGTCCCAGCAATGATGAAGATGGTGTTGCAGATGTCATATACCGATACGCATTCTAG

Coding sequence (CDS)

ATGATTCTAAACACCCCACAGCTTCCTTGTGAAAAGTTCATTCAATACAGACATGATCTTGTGCTTAAACTGGTCTTGATTATGGTAATGGCTATTGGAGATGGGGAAAATGACATTGAGATGCTGGAGCTGGCATCTCTTGGGATTGCTTTGAGCAATGGATCAGAGAAAACAAAAGCTGTTGCTAACCTTATTGGTCCCAGCAATGATGAAGATGGTGTTGCAGATGTCATATACCGATACGCATTCTAG

Protein sequence

MILNTPQLPCEKFIQYRHDLVLKLVLIMVMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF

Homology

[Close]

BLAST of Lag0037470 vs. NCBI nr
Match: XP_038899849.1 (endoribonuclease YBEY, chloroplastic [Benincasa hispida])

HSP 1 Score: 108.2 bits (269), Expect = 3.4e-20
Identity = 55/55 (100.00%), Postives = 55/55 (100.00%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF
Sbjct: 537 VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 591

[Close]

BLAST of Lag0037470 vs. NCBI nr
Match: XP_022138817.1 (uncharacterized protein LOC111009890 [Momordica charantia])

HSP 1 Score: 107.1 bits (266), Expect = 7.6e-20
Identity = 53/55 (96.36%), Postives = 55/55 (100.00%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           VMAIGDGENDIEMLELASLGIALSNGSEKTKA+AN+IGPSNDEDGVADVIYRYAF
Sbjct: 536 VMAIGDGENDIEMLELASLGIALSNGSEKTKAIANIIGPSNDEDGVADVIYRYAF 590

[Close]

BLAST of Lag0037470 vs. NCBI nr
Match: XP_004136229.1 (endoribonuclease YBEY, chloroplastic [Cucumis sativus] >KGN60311.1 hypothetical protein Csa_001179 [Cucumis sativus])

HSP 1 Score: 106.7 bits (265), Expect = 9.9e-20
Identity = 54/55 (98.18%), Postives = 55/55 (100.00%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVA+VIYRYAF
Sbjct: 537 VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVAEVIYRYAF 591

[Close]

BLAST of Lag0037470 vs. NCBI nr
Match: XP_008466080.1 (PREDICTED: uncharacterized protein LOC103503611 [Cucumis melo])

HSP 1 Score: 106.7 bits (265), Expect = 9.9e-20
Identity = 54/55 (98.18%), Postives = 55/55 (100.00%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVA+VIYRYAF
Sbjct: 538 VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVAEVIYRYAF 592

[Close]

BLAST of Lag0037470 vs. NCBI nr
Match: XP_034683095.1 (endoribonuclease YBEY, chloroplastic [Vitis riparia])

HSP 1 Score: 105.5 bits (262), Expect = 2.2e-19
Identity = 53/55 (96.36%), Postives = 54/55 (98.18%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           VMAIGDGENDIEMLELASLGIALSNGSEKTKAVAN+IGPSNDEDGVAD IYRYAF
Sbjct: 539 VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANVIGPSNDEDGVADAIYRYAF 593

[Close]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot
Match: Q8L5Z4 (Endoribonuclease YBEY, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=YBEY PE=1 SV=1)

HSP 1 Score: 95.9 bits (237), Expect = 2.3e-19
Identity = 46/55 (83.64%), Postives = 53/55 (96.36%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRYAF 84
           +MAIGDGENDIEML+LASLG+ALSNG+EKTKAVA++IG SND+DGVAD IYRYAF
Sbjct: 530 IMAIGDGENDIEMLQLASLGVALSNGAEKTKAVADVIGVSNDQDGVADAIYRYAF 584

[Close]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot
Match: P0A8Y6 (Sugar phosphatase YidA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=yidA PE=3 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 2.0e-07
Identity = 28/53 (52.83%), Postives = 35/53 (66.04%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRY 82
           +MAIGD ENDI M+E A +G+A+ N     K VAN +  SN EDGVA  I +Y
Sbjct: 215 IMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKY 267

[Close]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot
Match: P0A8Y5 (Sugar phosphatase YidA OS=Escherichia coli (strain K12) OX=83333 GN=yidA PE=1 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 2.0e-07
Identity = 28/53 (52.83%), Postives = 35/53 (66.04%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRY 82
           +MAIGD ENDI M+E A +G+A+ N     K VAN +  SN EDGVA  I +Y
Sbjct: 215 IMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKY 267

[Close]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot
Match: P0A8Y7 (Sugar phosphatase YidA OS=Shigella flexneri OX=623 GN=yidA PE=3 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 2.0e-07
Identity = 28/53 (52.83%), Postives = 35/53 (66.04%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRY 82
           +MAIGD ENDI M+E A +G+A+ N     K VAN +  SN EDGVA  I +Y
Sbjct: 215 IMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKY 267

[Close]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot
Match: P70947 (5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YitU OS=Bacillus subtilis (strain 168) OX=224308 GN=yitU PE=1 SV=1)

HSP 1 Score: 53.9 bits (128), Expect = 1.0e-06
Identity = 24/53 (45.28%), Postives = 35/53 (66.04%), Query Frame = 0


Query: 29  VMAIGDGENDIEMLELASLGIALSNGSEKTKAVANLIGPSNDEDGVADVIYRY 82
           ++A GD +ND+EMLE A  G+A+ NG +  K +AN    +N+EDGVA  +  Y
Sbjct: 215 IIAFGDEDNDLEMLEFAGCGVAMGNGIDAVKQIANRTTATNEEDGVARFLKEY 267

The following BLAST results are available for this feature:

BLAST of Lag0037470 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_038899849.1	3.4e-20	100.00	endoribonuclease YBEY, chloroplastic [Benincasa hispida]	[more]
XP_022138817.1	7.6e-20	96.36	uncharacterized protein LOC111009890 [Momordica charantia]	[more]
XP_004136229.1	9.9e-20	98.18	endoribonuclease YBEY, chloroplastic [Cucumis sativus] >KGN60311.1 hypothetical ...	[more]
XP_008466080.1	9.9e-20	98.18	PREDICTED: uncharacterized protein LOC103503611 [Cucumis melo]	[more]
XP_034683095.1	2.2e-19	96.36	endoribonuclease YBEY, chloroplastic [Vitis riparia]	[more]

BLAST of Lag0037470 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q8L5Z4	2.3e-19	83.64	Endoribonuclease YBEY, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=YBEY PE=...	[more]
P0A8Y6	2.0e-07	52.83	Sugar phosphatase YidA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / ...	[more]
P0A8Y5	2.0e-07	52.83	Sugar phosphatase YidA OS=Escherichia coli (strain K12) OX=83333 GN=yidA PE=1 SV...	[more]
P0A8Y7	2.0e-07	52.83	Sugar phosphatase YidA OS=Shigella flexneri OX=623 GN=yidA PE=3 SV=1	[more]
P70947	1.0e-06	45.28	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YitU OS=Bacillus subtilis...	[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	PFAM	PF08282	Hydrolase_3	coord: 26..78 e-value: 2.3E-18 score: 66.9
None	No IPR available	PANTHER	PTHR46986:SF1	ENDORIBONUCLEASE YBEY, CHLOROPLASTIC	coord: 29..83
None	No IPR available	PROSITE	PS01229	COF_2	coord: 32..54
IPR023214	HAD superfamily	GENE3D	3.40.50.1000		coord: 29..78 e-value: 5.1E-18 score: 67.7
IPR002036	Endoribonuclease YbeY	PANTHER	PTHR46986	ENDORIBONUCLEASE YBEY, CHLOROPLASTIC	coord: 29..83
IPR036412	HAD-like superfamily	SUPERFAMILY	56784	HAD-like	coord: 29..81

Relationships

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


Feature Name	Unique Name	Type
Lag0037470.1	Lag0037470.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0009658	chloroplast organization
biological_process	GO:1901259	chloroplast rRNA processing
biological_process	GO:0006508	proteolysis
biological_process	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic
biological_process	GO:0006364	rRNA processing
cellular_component	GO:0009507	chloroplast
molecular_function	GO:0004521	endoribonuclease activity
molecular_function	GO:0046872	metal ion binding
molecular_function	GO:0004222	metalloendopeptidase activity