RetrogeneDB ID: retro_olat_40

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 7:7527706..7528290(+)
• Located in intron of: ENSORLG00000003806

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000019689
• Aliases: None
• Description: None

Sequence

>retro_olat_40
ATGCGGTTAAAGGAGCTCTCCATGCAGGTGAAAGGAGCCATCATTAAGCTGAGAAAACAGTAAAAAAAAAAACATGCGAG
TTATTTCTACAATATTAGGAGTGGCAAAATCAACAGTGTGGTACATCCTGAGAAAGAAAGAAAGCACTGGTGAACTCAGC
AACACAAAAGACCTGGACGTCCATGGAAGACAACAGTGGTGGATGAGGGCAGAATCATTTCCATGGTGAAGAGGAACCCG
TTCACAACAGCCAACTAAGTGAACAACACTCTCCAGGAGGTAGACGTATCAATATCCAAGTCTACCATAAAAAGAAGACT
GCATGAAAGTAGAAACAGAAGGTACACTGCAAGATGCAAGCCACTCATGAGCCTCATGAATAGGAAGGCTGGATTGGACT
TTGCTAAAAAGCATCTAAAAAAGCCAGAACAGTTCTGGAAAAACATTCTTTGGACAGATGAAACCAAATCAACCTCTACC
AGAATGATGGCAAGAGAAAAGTATGGAAAAGGCGTGGAGAAGCTCATGATCCAAAGCACACTACATCATCAGTAAAACAC
TGTGGATGCAGTGTGATGGGCTGG

Alignment

ORF - retro_olat_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKTKELSKYTRNQTVDLHQ-AGRAGLNSVHALLGVATSTVWSILRKKESTGEISNTK-RPGRPQKTTVVD
          ...KELS.........L...............LGVA.STVW.ILRKKESTGE.SNTK.RPGRP.KTTVVD
Retrocopy MRLKELSMQVKGAIIKLRK>SXXXXMRVISTILGVAKSTVWYILRKKESTGELSNTK<RPGRPWKTTVVD

Parental  DGRIISRVKRNPFTTANQVNNTLQEVGGSISKSTMKRRLHESRSRGYTARCKPLISLKNRKARLDFAKKH
          .GRIIS.VKRNPFTTAN.VNNTLQEV..SISKST.KRRLHESR.R.YTARCKPL.SL.NRKA.LDFAKKH
Retrocopy EGRIISMVKRNPFTTAN*VNNTLQEVDVSISKSTIKRRLHESRNRRYTARCKPLMSLMNRKAGLDFAKKH

Parental  LKKPAQFWKNILWTDETK-INLYQNDGKRKVWRRRGEAPDPKHTTSSVKHGGGSVMVW
          LKKP.QFWKNILWTDETK.INLYQNDGKRKVW.RRGEA.DPKHTTSSVKH.G.SVM.W
Retrocopy LKKPEQFWKNILWTDETK<INLYQNDGKRKVWKRRGEAHDPKHTTSSVKHCGCSVMGW

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_40 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_40 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000010891	1 retrocopy	retro_olat_22,
Oryzias latipes	ENSORLG00000013353	2 retrocopies	retro_olat_32, retro_olat_53,
Oryzias latipes	ENSORLG00000014457	2 retrocopies	retro_olat_35, retro_olat_43,
Oryzias latipes	ENSORLG00000018922	1 retrocopy	retro_olat_31,
Oryzias latipes	ENSORLG00000019689	1 retrocopy	retro_olat_40 ,
Oryzias latipes	ENSORLG00000019879	1 retrocopy	retro_olat_28,
Oryzias latipes	ENSORLG00000020726	1 retrocopy	retro_olat_26,