RetrogeneDB ID: retro_olat_20

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 11:8080774..8081689(+)
• 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_20
GAGGTGGCTGACACCTTCAATATGTCTCAGCGTCAAGTACAAAGAATAAGAAAAAGATTTGAAGAGACTGAAGATGTTTT
TGACAAGCCCAGGTCCGGCAGACCCCGCAAGACAACTGCCCGGGAGGACCGTTTGTTGGTTCCAAAATCCAAGGCCAGCC
TCTTTTCCACTGCAGCAGAGCTCCACCAGGCCTGGTCAACTCAAGTCCCTGTGTCAACCAGAACAGTTTGTAGAATTCTG
TCTCAAAATGGCCTCCATGGTCGAATCAGTGCCCAGAAACCAGCACTAAACAAAAGGCAATTGAAAAAACGTGTGGCATT
TGCCAAGGCCCACAGCTGCTAAAAGGATGGACGCTGGAAAAGTGGCAGAAGGTGGATTTTTCAGATGAGTCTTCAGTTAA
ATTACATCACAGGAGACCAACTGGAGCCCACATGGACCCAAGATTCACCCAGAAAACAGTTAAGTTTGGTGGCGGAAAAA
TCATGGTCTGGGGTTACATCCAGTATGGGGGTGTGCGAAACATTTGCAGGGTGGAAGGCAATATCAATAGCCTAAAATAT
CAAGAAGTATTAGCTACCTCTTACATTCCCAACCATAAAAGGGGTCAAATTCTGCAGCAGAATGGTGCTCCATCGCACAC
TTCCATCTCTACATCAAAGTTCCTCAAGGCGAAGGAGATCAAGGTGCTCCAGGACTTGGCCAGCCCAGTCACCAGACATG
AACATCATTGAGCATGTCTGGGGTAGAATGAAAGAGGAAGCGTGGAAGACGAAATCAAAGAATCTTGATGAACTCTGGGA
GGCATGTAAAACTGCTTTCTTTGCTATTCCTGATGACTTCATCGATAAATTATATGAGTCATTGTCAAACCGCATGGATG
CTGTCCTTCAAGCTCATGGAAGTCATACAAGATAT

Alignment

ORF - retro_olat_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

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

Parental  HLNGRTVCRVLSENGLHGPSSAQKPALNKRQLKK-TCGICQGPEPAK--RMDAGKVADGGDESSVELHHR
          ....RTVCR.LS.NGLHG..SAQKPALNKRQLKK.TCGICQGP...K..........D..DESSV.LHHR
Retrocopy PVSTRTVCRILSQNGLHGRISAQKPALNKRQLKK<TCGICQGPQLLKGWTLEKWQKVDFSDESSVKLHHR

Parental  KPTGARMDSRFTQKTFKFGGRKIMVRGYILYGGVRNICRVEGNINSLKYQEVLATSSIPNHKRGQILQQD
          .PTGA.MD.RFTQKT.KFGG.KIMV.GYI.YGGVRNICRVEGNINSLKYQEVLATS.IPNHKRGQILQQ.
Retrocopy RPTGAHMDPRFTQKTVKFGGGKIMVWGYIQYGGVRNICRVEGNINSLKYQEVLATSYIPNHKRGQILQQN

Parental  GAPSHTSISTSKFLKAKKMKVLQDR-PAQSPDMNIIEHVWGRMKEGAWKTKPKNLDELWEAWKTAFFAIP
          GAPSHTSISTSKFLKAK..KVLQD..PAQSPDMNIIEHVWGRMKE.AWKTK.KNLDELWEA.KTAFFAIP
Retrocopy GAPSHTSISTSKFLKAKEIKVLQDL>PAQSPDMNIIEHVWGRMKEEAWKTKSKNLDELWEACKTAFFAIP

Parental  DDFIHKLYESLSNRMDAVLQAPGSHTRY
          DDFI.KLYESLSNRMDAVLQA.GSHTRY
Retrocopy DDFIDKLYESLSNRMDAVLQAHGSHTRY

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_20 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_20 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,