RetrogeneDB ID: retro_ocun_1219

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:1186316..1186878(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000015651
• Aliases: None
• Description: Autophagy-related protein 3 [Source:UniProtKB/TrEMBL;Acc:G1T9W9]

Sequence

>retro_ocun_1219
GAAGCATGGCTACCAACATGCAAACAGTTTCTGGCAACCAAAAATGTGCCATGCTACAAACATATTGAATATTCAGATGA
ATTAGAAGTCATCACTAAAGATGATGATGGTGGTGGGAGATGGATAGATATGGACCACAACATGGTATTGCAGGAACAAC
AGAAGCAATTAAGGAGCTTATGACAAAAAGAAAAGACAACCCAAAGCTCCAGGATTACACAGCCTTATGTGATGAGGAAG
ATGTAGGCAAAGCTGCAAAGAAGGAAAAATATTTTTTAAAAAATGGATTATTGAAAAAGATGAAGACATTCCAGAAGCAA
GGAAAATAGTAGAAGCTTGTACATTAATAACTGATATTGGAGGTGAAGATGCTATTTCACAAATCAGAACAAGTGACCTT
TGCATCACTTAAAATAAACATCAGATGTCATGACCATGGTCACTTGACTATGACAAGCAATGTCAGCCTCTAACAGCTGA
CCACATGTGTGCAGACAGTAGTAGGGATCATCTGAAGAAAACAGTAGCTACTGAAAGTCACCGCCGTCTCCCATTACCTC
CC

Alignment

ORF - retro_ocun_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.33 %
• Parental protein coverage: 61.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KAYLPTGKQFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNT-GITGITEAVKEITLENKD
          .A.LPT.KQFL.TKNVPCY...K..EYSDELE.I...DDG.G.W.D..HN..GI.G.TEA.KE.....KD
Retrocopy EAWLPTCKQFLATKNVPCY---KHIEYSDELEVITKDDDGGGRWIDMDHNM<GIAGTTEAIKELMTKRKD

Parental  SIKLQDCSALCEEEEEEDEGEAADMEEYE-ESGLL-ETDEATLDTRKLVEACKAKADAGGEDAILQTRTY
          ..KLQD..ALC....EED.G.AA..E.Y....GLL.E.DE.....RK.VEAC....D.GGEDAI.Q.RT.
Retrocopy NPKLQDYTALCD---EEDVGKAAKKEKYFLKNGLL<EKDEDIPEARKIVEACTLITDIGGEDAISQIRTS

Parental  DLYITYDKYYQTPRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIENHPHLPPPP
          DL.IT..K..Q....W...YD.Q.QPLT..HM..D.S.DH.KKTV..E.H..LP.PP
Retrocopy DLCIT*NK-HQMS*PWSLDYDKQCQPLTADHMCADSSRDHLKKTVATESHRRLPLPP

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	33.61 RPM
SRP017611_kidney	0.00 RPM	31.22 RPM
SRP017611_liver	0.00 RPM	14.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1219 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1219 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2479
Pan troglodytes	retro_ptro_1434
Gorilla gorilla	retro_ggor_1544
Pongo abelii	retro_pabe_1827
Macaca mulatta	retro_mmul_594
Equus caballus	retro_ecab_594

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268, retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219 ,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,