RetrogeneDB ID: retro_ocun_1625

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018721:76143..76718(+)
• Located in intron of: ENSOCUG00000000500

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSOCUG00000006602
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_ocun_1625
TGTGTTATTGCAGAATACGGAGAAATGAAGGAAGGCGATGATTGGGGAATCTTCCCCAAACCTGGCTCTGTGACAGTCAC
CCCGATTTCCCTGAGGATGCAGATACAGATTTGAAGGATGTCAATAAAATTCTATAGTAACAAAGACTTAGAAAACATTG
CAAATACTTTTTCAAATCTCAGACCTGGAAGATGGCCATTAAAAAATATACGAAAGCTTTAAGCTATATGGATGGTTCAA
AGGCTGGTACTGAGAAAGCAGGTAGATCCAGGCTGCGACCTATAGCTTGAAGCTGTGTACTGAATATTGGTGGTTATAAA
CTGAAGATGTCAAACTGGCAGGGAGCTATTTACAGTGGTTTTGAGACTCTGGTAACAGACCCGTCAAATACCAAGGCACT
GTTCTGCAGAGTTCAAGGATACCAAGGACTAAAAGAATAAGATCATAATTTGGCTGATCTTAAGAAAGCCCCCGAGATAG
CACCAGAAGACGAAGCTCTCCAGGAAGAACTGCTGAAAGTCAAACAAAAGATAAAGGCACAGAAAGACAAAGAGAAGGCC
ATATATGCCAAACTG

Alignment

ORF - retro_ocun_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.07 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CVIAECGELKEGDDWGIFPKDGSG-DSHPDFPEDADIDLKDVDKIL-LVTE-DLKNIGNNF-FKSQNWEM
          CVIAE.GE.KEGDDWGIFPK.GS..DSHPDFPEDAD.DLKDV.KIL..VT..DL.NI.N.F.FKSQ.W.M
Retrocopy CVIAEYGEMKEGDDWGIFPKPGSV<DSHPDFPEDADTDLKDVNKIL<IVTK<DLENIANTF<FKSQTWKM

Parental  AIKKYTKVLRYVESSRAVAEEADRLRLQPVALSCVLNTGACKLKLSDWQGAIDSCLEALEIDPLNTKALY
          AIKKYTK.L.Y...S.A..E.A.R.RL.P.A.SCVLN.G..KLK.S.WQGAI.S..E.L..DP.NTKAL.
Retrocopy AIKKYTKALSYMDGSKAGTEKAGRSRLRPIA*SCVLNIGGYKLKMSNWQGAIYSGFETLVTDPSNTKALF

Parental  RKAQGWQGLKEYDEALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEKAVYAKM
          ...QG.QGLKE.D..LADLKKA.EIAPED.A.Q.ELLKVKQKIKAQKDKEKA.YAK.
Retrocopy CRVQGYQGLKE*DHNLADLKKAPEIAPEDEALQEELLKVKQKIKAQKDKEKAIYAKL

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	0.11 RPM	57.34 RPM
SRP017611_kidney	0.00 RPM	49.26 RPM
SRP017611_liver	0.08 RPM	45.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1625 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1625 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625 ,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,