RetrogeneDB ID: retro_ocun_1582

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018702:2421562..2422129(-)
• Located in intron of: ENSOCUG00000000751

Retrocopy information

• Ensembl ID: ENSOCUG00000024637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THAP1
• Ensembl ID: ENSOCUG00000001391
• Aliases: None
• Description: THAP domain containing, apoptosis associated protein 1 [Source:HGNC Symbol;Acc:20856]

Sequence

>retro_ocun_1582
ATGGTGCAGTCCCGTTCTGCTTAACTGCTGCGAGAACCAGTACGACAAGGACAAGGCAGTGTCTTCCCATAAGCTTCCAC
TTACTCGACCCATTCTTTGTAGAAAATGGGAGGTGGCTGTCAGAAGAAAAAACGTGATGCCGGTCAAGCACAGAAGCATC
GGTTCAGAGCACTTTACTCCAGATAGCTTTAAGAGGAAGTGCAACAACAAGTCACTGAGGGAGCATGCTCTTCCCACAAT
ATTTCTTTGTATCGAACTGCATGACAAGAAGGAAGATCTTCTTGGGTCACAGGAGCAGCTGCCTCCAGCTCCTTTAACAC
CTCCCAGGATGGATGCTGCTGTTGGATTGCTAGTGCCTCCTCTACAGCCCCCGCCAACCCCTCCGTCTCCTGTGATCACA
GCTACACCGTGGAGGAGCCCATGCACTACAGGAAAAGGATTCAGCAACTGGAACAGCAGGTTGAGAAACTCAGGAAGAAG
CTTAAGACAGCACAGCAGCGGTGCAGAAGACAGGAACAGCAGCCTGAAAAGTTGAGAGAGGTCCTACGTTTCCAAAAAGG
GAGAGAG

Alignment

ORF - retro_ocun_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.17 %
• Parental protein coverage: 89.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVQSCSA-YGCKNRYDKDKPVSFHKFPLTRPSLCKKWEAAVRRKNFKPTKYSSICSEHFTPDCFKRECNN
          MVQS.SA...C.N.YDKDK.VS.HK.PLTRP.LC.KWE.AVRRKN..P.K..SI.SEHFTPD.FKR.CNN
Retrocopy MVQSRSA>NCCENQYDKDKAVSSHKLPLTRPILCRKWEVAVRRKNVMPVKHRSIGSEHFTPDSFKRKCNN

Parental  KLLKENAVPTIFLCIEPHDKKEDVLGSQEQLPPAPLTPPISQMDAAIGLLMPPLQ-TPDNLSVFCDHNYT
          K.L.E.A.PTIFLCIE.HDKKED.LGSQEQLPPAPLTPP...MDAA.GLL.PPLQ..P.N.SV.CDH.YT
Retrocopy KSLREHALPTIFLCIELHDKKEDLLGSQEQLPPAPLTPP--RMDAAVGLLVPPLQ<APANPSVSCDHSYT

Parental  VEDTMHQRKRIQQLEQQVEKLRKKLKTAQQRCRRQERQLEKLREVVHFQKERD
          VE..MH.RKRIQQLEQQVEKLRKKLKTAQQRCRRQE.Q.EKLREV..FQK.R.
Retrocopy VEEPMHYRKRIQQLEQQVEKLRKKLKTAQQRCRRQEQQPEKLREVLRFQKGRE

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	17.72 RPM
SRP017611_kidney	0.00 RPM	11.86 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1582 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1582 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003332	2 retrocopies	retro_eeur_131, retro_eeur_172,
Myotis lucifugus	ENSMLUG00000003837	1 retrocopy	retro_mluc_1607,
Oryctolagus cuniculus	ENSOCUG00000001391	1 retrocopy	retro_ocun_1582 ,