RetrogeneDB ID: retro_olat_8

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 11:26656745..26657066(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000013988
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: inip (2 of 2)
• Ensembl ID: ENSORLG00000011577
• Aliases: None
• Description: ints3 and nabp interacting protein [Source:ZFIN;Acc:ZDB-GENE-040426-961]

Sequence

>retro_olat_8
ATGGCTACTCCTGCTAACCCGCCAGTTCCGGGCTTCCAGAACAAAACCCGGGTGGCCATCCTCGCGGAGCTGGACAAGGA
GAAGAGGCGCCTGCTGCAGAGCCAGTCCATGAACAGCCCCGGGGCCACCATCCCGCTGGCCTCGTCCAGGCCCAGCCTGA
AGGAGGCGCGGGACAGCGCGGAGCAGCAGCACATCGCCGCGCAGCAGAAGGCCGCGCTGCAGCACGCGCACGGACACTCG
TCGGGCTTCTTCATCACGCAGGACTCCTCGTTCGGGAACCTGATCCTGCCGGTGCTGCCCCGGCTGGAGCCCGAGCTCTG
A

Alignment

ORF - retro_olat_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.0 %
• Parental protein coverage: 96.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANPPGQAVPNNARVAILAELERERRRLIQSQSMNTPGASISL--SRPSVKDFRDNAEQQHIAAQQKAALQ
          ANPP.....N..RVAILAEL..E.RRL.QSQSMN.PGA.I.L..SRPS.K..RD.AEQQHIAAQQKAALQ
Retrocopy ANPPVPGFQNKTRVAILAELDKEKRRLLQSQSMNSPGATIPLASSRPSLKEARDSAEQQHIAAQQKAALQ

Parental  HAHAHSSGFFITQDSSFGNLILPVIPRLVP
          HAH.HSSGFFITQDSSFGNLILPV.PRL.P
Retrocopy HAHGHSSGFFITQDSSFGNLILPVLPRLEP

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_8 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_8 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006841	1 retrocopy	retro_amel_1661,
Equus caballus	ENSECAG00000008524	1 retrocopy	retro_ecab_187,
Homo sapiens	ENSG00000148153	1 retrocopy	retro_hsap_2980,
Microcebus murinus	ENSMICG00000001130	1 retrocopy	retro_mmur_92,
Nomascus leucogenys	ENSNLEG00000016554	1 retrocopy	retro_nleu_1508,
Oryctolagus cuniculus	ENSOCUG00000016717	1 retrocopy	retro_ocun_335,
Oryzias latipes	ENSORLG00000011577	1 retrocopy	retro_olat_8 ,
Pan troglodytes	ENSPTRG00000023472	1 retrocopy	retro_ptro_2015,
Sorex araneus	ENSSARG00000003661	1 retrocopy	retro_sara_104,
Xiphophorus maculatus	ENSXMAG00000002259	1 retrocopy	retro_xmac_8,