RetrogeneDB ID: retro_olat_38

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 5:2356316..2357230(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000016889
• Aliases: None
• Description: None

Sequence

>retro_olat_38
GAGGTGGCTGACACCTTCAATGTGTCTCAGCGTCAAGTACAAAGAATAAGAAAAAGATTTGAAGAGACTGGAGATGTTTT
TGACAAGCCCAGGTCCGGCAGACCCTGCAAGACAACTGCTCGGGAGGACCGTTTGTTGGTTCCAAAATCCAAGGCCAGCC
TCTTTTCCACTGCAGCAGAGCTCCACCAGGCCTGGTCAACTCAAGTCCCTGTGTCAACCAGAACAGTTTGTAGAATTCTG
TCTCAAAATGGCCTCCATGGTCGAATCAGTGCCCAGAAACCAGCACTAAACAAAAGGCAATTGAAAAAACGTGTGGCATT
TGCCAAGGCCCACAGCTGCTAAAAGGATGGACGCTGGAAAAGTGGCAGAAGGTGGATTTCTCAGATGAGTCTTCAGTTGA
ATTACATCACAGGAGACCAACTGGAGGCCGCATGGACCCAAGACTCACCCAGAAAACCGTTAAGTTTGGTGGCGGAAAAA
TCATGGTCTGGGGTTACATCCAGTATGGGGGTGTGCGAAACATTTGCAGGGTGGAAGGCAATATCAATAGCCTAAAATAT
CAAGAAGTATTAGCTACCTCTTACATTCCCATCCATAAAAGGGATCAACTTCTGCAGCAGAATGGTGTTCCATCGCATAC
TTCCATCTCTACATCAAAGTTCCTCAAGGCGAAGAAGATCAAGGTGCTCCAGGACTGGCCAGCCCAGTCACACGACATGA
ACATCATTGAGCATGTCTGGGGTAGAATGAAAGAGGAAGCATGGAGGACGAAACCAAAGAATCTTGATGAACTCTGGGAG
GCATGTAAGACTGCTTTCTTTGCTATTCCCGATGACTTCATCGATAAATTGTATGAATCATTGTCAAACCGCATGGATAC
TGTCCTTCAAGCTCATGGAAGTCATACAAGATAT

Alignment

ORF - retro_olat_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMSSLLNIPQSAVSSIRTTWKSLGTTATQPPSGRPGNLMERSQRMLKLRVQRETLLNLEDSLSRRVGAGE
          E.....N..Q..V..IR......G.....P.SGRP.....R..R.L........L......L........
Retrocopy EVADTFNVSQRQVQRIRKRFEETGDVFDKPRSGRPCKTTAREDRLLVPK-SKASLFSTAAELHQAWSTQV

Parental  HLNGRTVCRVLSENGLHGPSSAQKPALNKRQLKK-TCGICQGPEPAK--RMDAGKVADGGDESSVELHHR
          ....RTVCR.LS.NGLHG..SAQKPALNKRQLKK.TCGICQGP...K..........D..DESSVELHHR
Retrocopy PVSTRTVCRILSQNGLHGRISAQKPALNKRQLKK<TCGICQGPQLLKGWTLEKWQKVDFSDESSVELHHR

Parental  KPTGARMDSRFTQKTFKFGGRKIMVRGYILYGGVRNICRVEGNINSLKYQEVLATSSIPNHKRGQILQQD
          .PTG.RMD.R.TQKT.KFGG.KIMV.GYI.YGGVRNICRVEGNINSLKYQEVLATS.IP.HKR.Q.LQQ.
Retrocopy RPTGGRMDPRLTQKTVKFGGGKIMVWGYIQYGGVRNICRVEGNINSLKYQEVLATSYIPIHKRDQLLQQN

Parental  GAPSHTSISTSKFLKAKKMKVLQDRPAQSPDMNIIEHVWGRMKEGAWKTKPKNLDELWEAWKTAFFAIPD
          G.PSHTSISTSKFLKAKK.KVLQD.PAQS.DMNIIEHVWGRMKE.AW.TKPKNLDELWEA.KTAFFAIPD
Retrocopy GVPSHTSISTSKFLKAKKIKVLQDWPAQSHDMNIIEHVWGRMKEEAWRTKPKNLDELWEACKTAFFAIPD

Parental  DFIHKLYESLSNRMDAVLQAPGSHTRY
          DFI.KLYESLSNRMD.VLQA.GSHTRY
Retrocopy DFIDKLYESLSNRMDTVLQAHGSHTRY

Legend:

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

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_38 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_38 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_38 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000016889	2 retrocopies	retro_olat_20, retro_olat_38 ,