RetrogeneDB ID: retro_ocun_1373

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:115347137..115347798(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ocun_1373
CAGAATGAAAAAGGTCAGTGCGTACCTCCAGTTTGTGATATTCCCAGTGTGTGCTGATAAGGATGTGTTCCACGTGGTGG
TTGAAGTACCAGGCTGGTCCCACGCAAACATGGAGGTTGCTACAAAGCACGCTTTACATCCGAGTAAACAAGACGCAAAG
AAAGGAAAACTCTCTCCATGGCCAATTATTCCCTTACAAGGGACACATCTGGAACTATGGTGCCATCCCTCAGGCGTGGG
AAGACCTGGGACACAATGACAAACACACCAGCTGTTGTGGTGACAGTGACTCGGTTGAAACTGGAAAGCAAGAAAGTGGC
AGCAGGTTATATGCAAGAAGTGAAATCATCCGGGCGACAGTTCTGGGCATGTGTGCTGAGGTTCGCCAAGGGGAAACCGA
CTGGAAAGCCATTGCTGATAACGTGGCCGATCCCGACACAGCCAATTACAGTGATATTAGTGATGTCAAAAGGCTTTGGC
CTGGCCACCTAGAAGCTACTGTGGACTGGTTTAGAAGGTACAAGCTTCCCGATGGAAAACCAGAATTTGCTTTCAATGAA
GAATTTAAAGATAAGGGCTTTGCAGTTGATGTAATTAAAAGCACTCATGACTACTGGAAGCTGTACAGACTGAGAAGATG
GATGGGAAGGGAGCCAGCTGC

Alignment

ORF - retro_ocun_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.16 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ENEKGQYISPFHDIP-IYADKDVFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKG-KLRYVAN-LFPYK
          .NEKGQ...P..DIP...ADKDVFH.VVEVP.WS.A.ME.ATK..L.P.KQD.KKG.K....AN.LFPYK
Retrocopy QNEKGQCVPPVCDIP>VCADKDVFHVVVEVPGWSHANMEVATKHALHPSKQDAKKG<KTLSMAN<LFPYK

Parental  GYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVC--EIGSKVCARGEIIRVKVLGILAMIDEGETDWKV
          G.IWNYGAIPQ.WED.GHNDKHT.CCGD.D.......E.GS...AR.EIIR..VLG..A....GETDWK.
Retrocopy GHIWNYGAIPQAWEDLGHNDKHTSCCGDSDSVETGKQESGSRLYARSEIIRATVLGMCAEVRQGETDWKA

Parental  IAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEFKDKAFAVDIIKSTHDY
          IA.NV.DPD.ANY.DI.DVKRL.PG.LEATVDWFRRYK.PDGKP..EFAFN.EFKDK.FAVD.IKSTHDY
Retrocopy IADNVADPDTANYSDISDVKRLWPGHLEATVDWFRRYKLPDGKP--EFAFNEEFKDKGFAVDVIKSTHDY

Parental  WK-ALVTKKTDGKGISC
          WK.A..T.K.DGKG.SC
Retrocopy WK<AVQTEKMDGKGASC

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_1373 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1373 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,