RetrogeneDB ID: retro_ocun_1897

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:69413400..69414011(+)
• Located in intron of: ENSOCUG00000007579

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCE1
• Ensembl ID: ENSOCUG00000009821
• Aliases: None
• Description: RCE1 homolog, prenyl protein protease (S. cerevisiae) [Source:HGNC Symbol;Acc:13721]

Sequence

>retro_ocun_1897
ATCCTTTTCTTGGGTCCACTGATGCAGCTCTCTATGGATTGCCCCTGTGACCTAAGAGATGGGCTGACAGTTGTCCTGGC
TTCTTGCTCCTGGGCCTACTGTCTCATAAATGTGCAGTGGTTGCAGAACCAAGTAATCGCGCCCCTGACTGAGGACCTGG
TGTTCCGGGCCTGCATGCTGACCATGTTAGTGCCCTGTACTGGCCTGGGCCCTGCAGTGTTCACCTGCCCACTCTTCTTT
GAAGATGCCCATTTCCACCACATCATTGAGCAGCTGCGTTTCCACTAGAGCAGTGTGGGGAGCATCTTCCTGTTTGCAGC
GTTCCAGTTCTACACAGCTGTCTTCGGTGCCTACACTGCTTTCTCTTCATCCACACAGGACACCTGATCAGGTCAGTTCT
CTGTCACTCTTTTTGTAATTACATGGGCTTCCCTATCGTGTGTGCAGCCCAGGAGCACCTGCAGAGGTGGCCCCTGCTGG
CAGGCTATGCCCAGGATGTGGGCCTCTTCCTGCTTCTGCTCCAACCCCTAATGGATCCCAAATTCTACAGCAGCCTTCCC
CTTTGTGTGATTTTGGAGTGTGCTGGGAACTCAGAGATCTCCCTGTGCTCC

Alignment

ORF - retro_ocun_1897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 76.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILFLGPLMQLSMDCPCDLTDGLKVVLAPRSWARCLTDMRWLRNQVIAPLTEELVFRACMLPMLAPCTGLG
          ILFLGPLMQLSMDCPCDL.DGL.VVLA..SWA.CL....WL.NQVIAPLTE.LVFRACML.ML.PCTGLG
Retrocopy ILFLGPLMQLSMDCPCDLRDGLTVVLASCSWAYCLINVQWLQNQVIAPLTEDLVFRACMLTMLVPCTGLG

Parental  PAVFTCPLFFGVAHFHHIIEQLRFRQSSVGSIFLSAAFQFSYTAVFGAYTA-FLFIRTGHLIGPVLCHSF
          PAVFTCPLFF..AHFHHIIEQLRF..SSVGSIFL.AAFQF.YTAVFGAYTA.FLFI.TGHLI..VLCHSF
Retrocopy PAVFTCPLFFEDAHFHHIIEQLRFH*SSVGSIFLFAAFQF-YTAVFGAYTA<FLFIHTGHLIRSVLCHSF

Parental  CNYMGFPAVCAALEHPQRRPLLAGYALGVGLFLLLLQPLTDPKLYGSLPLCVLLQRAGNSEIPLCA
          CNYMGFP.VCAA.EH.QR.PLLAGYA..VGLFLLLLQPL.DPK.Y.SLPLCV.L..AGNSEI.LC.
Retrocopy CNYMGFPIVCAAQEHLQRWPLLAGYAQDVGLFLLLLQPLMDPKFYSSLPLCVILECAGNSEISLCS

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	24.61 RPM
SRP017611_kidney	0.00 RPM	35.88 RPM
SRP017611_liver	0.00 RPM	17.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1897 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004274	2 retrocopies	retro_dnov_106, retro_dnov_1957,
Oryctolagus cuniculus	ENSOCUG00000009821	1 retrocopy	retro_ocun_1897 ,