RetrogeneDB ID: retro_ocun_578

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:105770760..105771381(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000013444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CRIP3
• Ensembl ID: ENSOCUG00000005795
• Aliases: None
• Description: cysteine-rich protein 3 [Source:HGNC Symbol;Acc:17751]

Sequence

>retro_ocun_578
ATGGCTTCCAAGTGCCCCAAGTGCGACAAGACGGTGTACTTCGCTGAGAAGGTGAGCTCCCTGGGCAAGGACTGGCACAA
GTTCTGTCTCAAGTGCGAGCGCTGCAACAAGACGCTGACGCCAGGCGGCCACGCCGAGCGTGACAGGAAGCCCTTCTGCC
ACAAGCCCTGCTACCCATGTTGTTCGGACCCAAAGGCGTGAACATCGGCGGTGCCGGCTCCTACATCTACATCTACGAGA
AACCCCGGCCGAGGGGCCTGCAGTCACCGGCCCCATCGAGGTCCCCGCCGCCCGACCTGAAGAGCGGTGGCGAGTGGCCC
CCTGAAGGGGCCCAGCAAAGCCTCCAGCGTCACCACCTTCACCGGGGAGCCCAAGTGTGCCCTCGCTGCAACAAGCGAGT
GTATTTCGCCAAGAAGGTGACGTCACTGGGCAAGGATTGGCACCGGCCATGCCTGCGATGCAAGCGCTGTGGGAAGACGC
TGACGCCGAGCGGGCACGCGGAGCACGATGGCCAGCCCTTACTGCCACAAGCCCTGCTATGGAATACTCTTCGGACCCAA
GGGAGTGAACAGCGGAGCAGTGGGCAGCTACATCTACGACGCCCCTGAAGGCACCAGCCAG

Alignment

ORF - retro_ocun_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSWTCPRCQQPVFFAEKVSSLGKNWHRFCLKCERCHSILSPGGHAEHNGRPYCHKPCYGA-LFGPRGVNI
          M...CP.C...V.FAEKVSSLGK.WH.FCLKCERC...L.PGGHAE....P.CHKPCY...LFGP.GVNI
Retrocopy MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCNKTLTPGGHAERDRKPFCHKPCYPC<LFGPKGVNI

Parental  GGVGSYLYNPPAPTPVSATPLSPSSFSPPRPRTG---LPQGKKSPPHMKTFTGETSLCPGCGEPVYFAEK
          GG.GSY.Y....P.P.......PS...PP....G....P.G................CP.C...VYFA.K
Retrocopy GGAGSYIYIYEKPRPRGLQSPAPSRSPPPDLKSGGEWPPEGAQQSLQRHHLHRGAQVCPRCNKRVYFAKK

Parental  VMSLGRNWHRPCLRCQRCRKTLTAGSHAEHDG-VPYCHIPCYGYLFGPKGVNIGDVGCYVYDPVDVKSE
          V.SLG..WHRPCLRC.RC.KTLT...HAEHDG..PYCH.PCYG.LFGPKGVN.G.VG.Y.YD.....S.
Retrocopy VTSLGKDWHRPCLRCKRCGKTLTPSGHAEHDG>SPYCHKPCYGILFGPKGVNSGAVGSYIYDAPEGTSQ

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	39.46 RPM	1.49 RPM
SRP017611_kidney	18.85 RPM	0.41 RPM
SRP017611_liver	3.93 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_578 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_578 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005795	1 retrocopy	retro_ocun_578 ,
Oryctolagus cuniculus	ENSOCUG00000008330	2 retrocopies	retro_ocun_1165, retro_ocun_649,