RetrogeneDB ID: retro_ocun_883

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:84397414..84397860(+)
• Located in intron of: ENSOCUG00000013453

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSOCUG00000016001
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_ocun_883
AACTATGGCCCATCCCTCAGACTCGGAAAGGCCCCAGACACAATGACAAACACACTGGCTGTTCTTAAGACAACGACAGG
ACTGATGAGTGTGAAACTCGAAGAAAGGTGTGTGCAAGAGTGAAAGTGCGCAAGGGTGAACGTTGTGGGCATATTGTGAC
TGACGAAGTGGAAACTGACTGGATGGTCAGGGCCTTTAATGTGCACGATCCTGATGAGGCCAATTATAATGACATTAATG
ACGTCAAAAGGCTGAAACCCAGTGACTTAGAAGGTCCTGGGGACTGCTTCAGAGGGTTCAAGTTTCCTGATAGAAAAACA
GAAAATGAACTTGCTTTCAGTGTAGAATTTAAGGATAAGGACTTTGCAGTCAAAATTATTAAAAGCACTTATGACCACTG
GAAAGCTTTAGTGACTAAGAAAATGGACAGAAAAGCAATCAGCTGT

Alignment

ORF - retro_ocun_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.58 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NYGA-IPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVKVLGILAMIDEGETDWKVIAINV
          NYG..IPQT...P.HNDKHTGC..DND..D.CE...KVCAR.........G.....DE.ETDW.V.A.NV
Retrocopy NYGP<IPQTRKGPRHNDKHTGCS*DNDRTDECETRRKVCARVKVRKGERCGHI-VTDEVETDWMVRAFNV

Parental  DDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDKAFAVDIIKSTHDYWKALV
          .DPD.ANYNDINDVKRLKP..LE...D.FR..K.PD.K.ENE.AF..EFKDK.FAV.IIKST.D.WKALV
Retrocopy HDPDEANYNDINDVKRLKPSDLEGPGDCFRGFKFPDRKTENELAFSVEFKDKDFAVKIIKSTYDHWKALV

Parental  TKKTDGKGISC
          TKK.D.K.ISC
Retrocopy TKKMDRKAISC

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	72.46 RPM
SRP017611_kidney	0.00 RPM	25.24 RPM
SRP017611_liver	0.00 RPM	22.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_883 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883 ,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,