RetrogeneDB ID: retro_ocun_1117

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:123075435..123075993(-)
• Located in intron of: ENSOCUG00000006156

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKRA
• Ensembl ID: ENSOCUG00000005489
• Aliases: None
• Description: protein kinase, interferon-inducible double stranded RNA dependent activator [Source:HGNC Symbol;Acc:9438]

Sequence

>retro_ocun_1117
GAACCTTCTAAGCAACAATAGCACCAGTTTAATCCCATTGGTCATTACCAGAATTGGCCATTCATCAAGTATGGAGACTT
CCTGAATATACCCTTTTCCAGGAGGCAGAACCTGCTCATAAGAAATAATATACCACAACTAGCAGGCTAGAGTCATTTAT
GGAAACTGGAAAGAAGATGTCAAAAAGCAAGCCAAAAGAAATGCTGCTGAGAAATTTCTTGCCAAATATTTCTTCAGAGA
AGCACATTTCTTTAACAAATCTGTGATAGGATATTCTTTAGGATGTACTTGGCACTCCTTGAGGAATTCTCCTGGGGAAA
AGATCAACTTATTGAAAAGAAGTCTCTTTAGTATTTCAAATACAGATTACATCCAGCTGCTTAGTGAAACTGCCAGCAAA
CAAGGTTTCAGTATAACATATTTGGATATAAAAGAAATAAGTGCCAATGAACATTATCAATGTGTCACTGAACTGTCAGC
CAGTTCCATCACAGTCTGTCATGGCTCAGGTGCCTCTATAGCCATGTACAAAGTAAGGCAGTCCATAATACTTTGCAG

Alignment

ORF - retro_ocun_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.31 %
• Parental protein coverage: 60.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DPSKQPKNQLNPIG-SLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASK-KQAKRN
          .PSKQ...Q.NPIG.SL.ELAIH..WRLPEYTL.QE..PAHK..YTT..RLESFMETGK..SK.KQAKRN
Retrocopy EPSKQQ*HQFNPIG<SLPELAIHQVWRLPEYTLFQEAEPAHKK*YTTTSRLESFMETGKKMSK<KQAKRN

Parental  AAEKFLAKFSNISPENHISLTNVVGHSLGCTWHSLRNSPGEKINLLKRSLLSLPNTDYIQLLSDIAKEQG
          AAEKFLAK......E.H.....V.G.SLGCTWHSLRNSPGEKINLLKRSL.S..NTDYIQLLS..A..QG
Retrocopy AAEKFLAKY--FFREAHFFNKSVIGYSLGCTWHSLRNSPGEKINLLKRSLFSISNTDYIQLLSETASKQG

Parental  FNITYLDIEELSANGHYQCLAELSTSPITVCHGSGISC-GNAQSDAAHNALQ
          F.ITYLDI.E.SAN.HYQC..ELS.S.ITVCHGSG.S.....QS.A.HN.LQ
Retrocopy FSITYLDIKEISANEHYQCVTELSASSITVCHGSGASI<SHVQSKAVHNTLQ

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	30.52 RPM
SRP017611_kidney	0.00 RPM	21.69 RPM
SRP017611_liver	0.00 RPM	2.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1117 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002185	1 retrocopy	retro_mmul_809,
Oryctolagus cuniculus	ENSOCUG00000005489	1 retrocopy	retro_ocun_1117 ,
Sorex araneus	ENSSARG00000003080	1 retrocopy	retro_sara_381,
Tursiops truncatus	ENSTTRG00000009700	1 retrocopy	retro_ttru_1852,