RetrogeneDB ID: retro_ocun_665

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:106351425..106352006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSOCUG00000009275
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_ocun_665
CAGATGAAATATCCCAGGACTTTTTTTCTTCTCAAATGAAAGAGTTAATGTGCCAGCATCAATAGGATTTATGGATGTAA
AAAGATAACAGTATTAAACCTGGGACACTTTTACAGACTGTTTTAACTATTGAAGGATAGCAGCCATTGTGGAGGAGAAA
AATCTGCCGTCATGGAAGTTTATCGGCAGCTCTTCAATCTATGTAGTATATTATACAAACTATGCAACCAACTGATGTTG
GTCTTTTTGTGATCGTTTGCGGTCTGACCCACATAAAGATGTCTTAGGCTGGGGTGAAAATGACAGAGTGTCCTTCACAT
TGGGTGCAGAAGTGGTTGCAAAGTTTCTCGGTAAGCATGATTTGACTCTTGTATGTAGAGGTCATCAGGTGGTTAATGAT
GGATATGAGTTTTTTCAAAGAGGCAGTGGGTCACTCTGTTCTCTGCACCAAACTATTGCAGATATTTTGACAATGCAAGT
GCCATGATTAGTGTGGAAGAAACACTAATGTGTTCCTTTCGATTTTAAAATCTTCAGAGAAAAACAAGACCAATGTCACA
AAACCTATAACTCCTCAGAGG

Alignment

ORF - retro_ocun_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.72 %
• Parental protein coverage: 60.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KIKYPEN-FFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDE-KIFCCHGGLSP
          ..KYP...FF......E........GF.D.....Y....W.TFTDCFN...IAAIV.E.KI.C.HG.LS.
Retrocopy QMKYPRT>FFF---SNERVNVPASIGFMDVKR*QY*T--WDTFTDCFNY*RIAAIVEE>KI-CRHGSLSA

Parental  DLQSMEQIRRIMRPTDVPDQGLL-CDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRA
          .LQSM..I...M.PT...D.GL..CD.L.SDP.KDVLGWGENDR.VSFT.GAEVVAKFL.KHDL.L.CR.
Retrocopy ALQSM*YIIQTMQPT---DVGLF<CDRLRSDPHKDVLGWGENDR-VSFTLGAEVVAKFLGKHDLTLVCRG

Parental  HQVVEDGYEF-FAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQ-ILKPAEKKKPNATRPVTPPR
          HQVV.DGYEF.F.KRQ.VTLFSAPNYC..FDNA.AM.SV.ETLMCSF..ILK..EK.K.N.T.P.TP.R
Retrocopy HQVVNDGYEF<FSKRQWVTLFSAPNYCRYFDNASAMISVEETLMCSFR<ILKSSEKNKTNVTKPITPQR

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	119.92 RPM
SRP017611_kidney	0.00 RPM	70.85 RPM
SRP017611_liver	0.00 RPM	48.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_665 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232, retro_ocun_665 ,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,