RetrogeneDB ID: retro_oind_37

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 1:22673187..22674282(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA001452
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA004758
• Aliases: None
• Description: None

Sequence

>retro_oind_37
ATGGGCGCCTCCTGCTCCTCCCCCTTCCCCCCTCCTCCTCCACCTGCCGAATCCAACGCCCCTTCCGCCTCCGCGATGCA
CCACCCGCCTCACCCCGCGGCCGGAGGAGGAGGACCCGTCATGCCGTACGCCGACGCCGACCGCACCCTCCGCGCGCTGG
CCGGCGCGGCGGAGGGCTTCGGCCGCCGCGCCATCGGCGGGCTCCACGGCCCGCTCTACCGCGTCACCTCCCTCGACGAC
GACGGCCACGGCACCCTCCGCCAGGCGTGCCGCGCCCACGGCCCGCTCTGGATCGTCTTCGACGTCTCCGGCGACATCCA
CCTCCGCACCTACCTCCGCGTCACCTCCCACAAGACCATCGACGGGCGCGGCCAGCGCGTGCGCCTCCTGGGCAAGGGGC
TCCAGCTCAAGGAGTGCCGCCACGTGATCGTCTGCAACCTCCAGATCGAGGGCGGGCGCGGCCACGACGTGGACGCCATC
CAGATCAAGCCCTCCTCCGCCGACATCTGGATCGACCGCTGCAGCCTCGCCGACTGCGACGACGGCCTCGTGGACATCAC
CCGCGGGAGCACCGACGTCACCGTCTCCCGGTGCCGCTTCTCCCGCCACGACAAGACCATGCTGGTGGGCGCCGACCCGT
CCCACACCGGCGACCGCGGCATCCGCGTCACCGTCCACCACTGCTTCTTCGACGGCACGCGGCAGCGCCACCCGCGGGTG
CGGTTCGGGAGGGCGCACCTGTACAACAACTACACGAGGGGGTGGGGCATCTACGCGGTGGCCGCCGGGGTGGAGGCGCA
GGTGGCGTCGCAGTGCAACGTGTACGAGGCCGGGGCGGAGAGGAAGGCGGTGTTCAGGTACGTGCCGGAGAGGGCGGCGG
ACCGGGAGGAGGCGGAGGCCGGGTGGGTGAGGTCGGAGGGGGACGCCTTCCTCAACGGGGCGCGGCCGTGCCTGGTGGAC
GGCGGCGACGCGGCGGTGTTCAGGCCGGAGGAGTACTACGAGAGGTGGACCATGGAGGCGGCGTCGCCGGCGCTCAAGGA
GGTGGTGCAGCTGTGCGCCGGGTGGCAGCCCGTGCCGAGGCCACCGGGCGAGTGA

Alignment

ORF - retro_oind_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.55 %
• Parental protein coverage: 80.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDDGDGSLREGCRRREPLWIVFDVSGTIHLSTGLRVSSYKTIDGRGQRVTLSGKGLQLRECEHVIVCNL
          ..DDG.G.LR..CR...PLWIVFDVSG.IHL.T.LRV.S.KTIDGRGQRV.L.GKGLQL.EC.HVIVCNL
Retrocopy LDDDGHGTLRQACRAHGPLWIVFDVSGDIHLRTYLRVTSHKTIDGRGQRVRLLGKGLQLKECRHVIVCNL

Parental  EVEGCRGHDADAVAVKPGSRHVWIDRCGLRGCGDGLLDVTRGSTDVTVSRCRFSAHDKAVLIGGSAGHVE
          ..EG.RGHD.DA...KP.S...WIDRC.L..C.DGL.D.TRGSTDVTVSRCRFS.HDK..L.G....H..
Retrocopy QIEGGRGHDVDAIQIKPSSADIWIDRCSLADCDDGLVDITRGSTDVTVSRCRFSRHDKTMLVGADPSHTG

Parental  DRAIRVTIHHCLFDGTRQRHPRVRFGRVHLYNNYTRGWGIYAVCASVESQIVSQCNIYEAG-EKKKVFKY
          DR.IRVT.HHC.FDGTRQRHPRVRFGR.HLYNNYTRGWGIYAV.A.VE.Q..SQCN.YEAG.E.K.VF.Y
Retrocopy DRGIRVTVHHCFFDGTRQRHPRVRFGRAHLYNNYTRGWGIYAVAAGVEAQVASQCNVYEAGAERKAVFRY

Parental  MIEQAADRDQSSTGFIRSEGDLFLNGAEECTAQDSEAA
          ..E.AADR.....G..RSEGD.FLNGA..C......AA
Retrocopy VPERAADREEAEAGWVRSEGDAFLNGARPCLVDGGDAA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_37 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004758	1 retrocopy	retro_oind_37 ,
Leersia perrieri	LPERR01G31380	1 retrocopy	retro_lper_4,
Oryza meridionalis	OMERI01G33590	1 retrocopy	retro_omer_1,
Oryza nivara	ONIVA01G41460	1 retrocopy	retro_oniv_25,
Oryza punctata	OPUNC01G35260	1 retrocopy	retro_opun_9,
Oryza glaberrima	ORGLA01G0303100	1 retrocopy	retro_ogla_4,
Oryza sativa japonica	OS01G0837100	1 retrocopy	retro_osat_37,