RetrogeneDB ID: retro_ocun_1372

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:106226122..106226487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACYP2
• Ensembl ID: ENSOCUG00000015408
• Aliases: None
• Description: Acylphosphatase-2 [Source:UniProtKB/Swiss-Prot;Acc:P00820]

Sequence

>retro_ocun_1372
CTCTCTCTCTCCGCCACTGCAGTCGCCACGCGCCGAACCCCGCTCGGGCTTCTCGGCAGAGGGCTTGCCCCACCGTGTCT
ACCGCCGGCCACTGAAATCTGTCCTACGAAATGTTCAGGAGAGTGCAGGGTGTTTGCTTCAGAATGTATACGGAGGGTGA
AGCTAAGAAAATAGGACTGGTTGGCTGGGTGAATACCAGCAAAGGCATTGTGACAGTTCAAGTTCAAGACCCTGAAGACA
AAGCCAATTCTATGAAATCCTGGCTGAGCAAGGTTGAGAATCCTGGTTCTCGCATTGACTGCACAAACTTTTCTAATGAA
AAAAGCATTTGCAAACTTGAATACTCCAACTTTAGAATTCGATAT

Alignment

ORF - retro_ocun_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 97.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSLAAATVAARRTPLRLLGRGLAA-AMSTAGPLKSVDYEVFGRVQGVCFRMYTEGEAKKIGVVGWVKNTS
          LSL.A..VA.RRTPL.LLGRGLA....STAG......YE.F.RVQGVCFRMYTEGEAKKIG.VGWV.NTS
Retrocopy LSLSATAVATRRTPLGLLGRGLAP<TVSTAGH*-NLSYEMFRRVQGVCFRMYTEGEAKKIGLVGWV-NTS

Parental  KGTVTGQVQGPEDKVNSMKSWLSKVGSPSSRIDRTNFSNEKTISKLEYSNFSIRY
          KG.VT.QVQ.PEDK.NSMKSWLSKV..P.SRID.TNFSNEK.I.KLEYSNF.IRY
Retrocopy KGIVTVQVQDPEDKANSMKSWLSKVENPGSRIDCTNFSNEKSICKLEYSNFRIRY

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	38.08 RPM
SRP017611_kidney	0.00 RPM	5.07 RPM
SRP017611_liver	0.00 RPM	4.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1372 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023070	1 retrocopy	retro_cfam_57,
Echinops telfairi	ENSETEG00000017888	1 retrocopy	retro_etel_1505,
Oryctolagus cuniculus	ENSOCUG00000015408	1 retrocopy	retro_ocun_1372 ,
Tupaia belangeri	ENSTBEG00000013671	1 retrocopy	retro_tbel_935,