RetrogeneDB ID: retro_ocun_832

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:46682829..46683195(-)
• Located in intron of: ENSOCUG00000005671

Retrocopy information

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

Parental gene information

• Parental gene symbol: LEPROTL1
• Ensembl ID: ENSOCUG00000013931
• Aliases: None
• Description: leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555]

Sequence

>retro_ocun_832
GCTTTGATCAGTTTTCCTTTGGATGAACAACTGGGATGGTGTTTTTGATGCTTGGATGTGCCCTTCCAATATACAACCAA
TAGTTGCCCCATTGTTCTATTTTTCTGCATTGTTTCACTTATTCCATTATGTGTAGCAAGAAGTCTGGTGGATGACACAG
ATGCTATGAGTAATGCTTGCAAGGAACTAGTATTTCTTATAAGAGGCATTGTTGTCTCCGTTTTTGGAATTCTGATTATA
TTTTCCAGAGAACATGTGATTGAGTGGGGAGCCTGAGCACTTGTTCTCACAGGAAACATAGTTATCTTTGCATCTTCACT
AGACTTTTTATTAGTCTCTGGTAACAATGATAACTTCAGCTGGCAG

Alignment

ORF - retro_ocun_832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.46 %
• Parental protein coverage: 94.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALISL-SFGGAIGLMFLMLGCALPIYNQ-YWPLFVLFFYVLSPIPYCIARRLVDDTDAMSNACKELAIFL
          ALIS..SFG...G..FLMLGCALPIYNQ...P....F..V.S.IP.C.AR.LVDDTDAMSNACKEL..FL
Retrocopy ALISF<SFG*TTGMVFLMLGCALPIYNQ>SCPIVLFFCIV-SLIPLCVARSLVDDTDAMSNACKEL-VFL

Parental  TTGIVVSAFGLPIVFARAHLIEWGACALVLTGNTVIFATILGFFLVFGSNDDFSWQ
          ..GIVVS.FG..I.F.R.H.IEWGA.ALVLTGN.VIFA..L.F.LV.G.ND.FSWQ
Retrocopy IRGIVVSVFGILIIFSREHVIEWGA*ALVLTGNIVIFASSLDFLLVSGNNDNFSWQ

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	0.22 RPM	15.45 RPM
SRP017611_kidney	0.00 RPM	27.77 RPM
SRP017611_liver	0.00 RPM	5.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_832 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_832 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_832 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006530	1 retrocopy	retro_cfam_2171,
Choloepus hoffmanni	ENSCHOG00000012299	1 retrocopy	retro_chof_1305,
Dasypus novemcinctus	ENSDNOG00000014538	3 retrocopies	retro_dnov_1528, retro_dnov_2606, retro_dnov_876,
Erinaceus europaeus	ENSEEUG00000001360	1 retrocopy	retro_eeur_139,
Oryctolagus cuniculus	ENSOCUG00000013931	1 retrocopy	retro_ocun_832 ,