RetrogeneDB ID: retro_ocun_812

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:83342503..83343025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRA1
• Ensembl ID: ENSOCUG00000021569
• Aliases: None
• Description: steroid receptor RNA activator 1 [Source:HGNC Symbol;Acc:11281]

Sequence

>retro_ocun_812
AGAGTCCCCACATCAGAGCTATCTCCTGAGCATCCCCCAATTGGGCCTCCAACTCCAAGTAAGTCTCCCAGGCCTCCATC
TGTGGAGAGCTGTCCTTCCTCTTGTGTGGTGTCAAGTTCCCCAGCCACTGAGCCTGAGGCTCTGTTGGAGGATGTGTTGA
GACCTTTGGACCAGGCACTGAAGGACTGTTGTGGCCACACAAGGCAGCAGCTATGTGATGACATCAGCCGACATCTGGCA
CTGCGGCGGGAACAGTGGGCTGGAGGGAAGCTCTCAGTGCCTGTAAACAAGAGGATGGTTCTGCTGGCGCAAGAGCTTTC
AAGCCTCCAGTGGGATGCAGCAGATGACATCCGCCGCTCACTTGTGGTTGACCATGTGACTGAAGTCAGTCAGTGGATGG
TGGGAGTTAAAAGATTAATTGCAGAAAAAAAAAAAAGCCTACCTTCAGAGGAGGCAGCCAATGAAGAAAAATCGGCAGCT
GCAGCTGAGAATGAGACCATGTCAGGCCTTCAACAAGCTCCA

Alignment

ORF - retro_ocun_812 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 74.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVPTSELSPGHPPVGPPPPSKAPGPPPVESCPSSCVVPTSSPVIEPEALLEDVLRPLEQALKDCHGHTRK
          RVPTSELSP.HPP.GPP.PSK.P.PP.VESCPSSCVV..SSP..EPEALLEDVLRPL.QALKDC.GHTR.
Retrocopy RVPTSELSPEHPPIGPPTPSKSPRPPSVESCPSSCVV-SSSPATEPEALLEDVLRPLDQALKDCCGHTRQ

Parental  QLCDDISRRLVLLREQWAGGKLSVPVKKRMALLVQELSSRQWDAADDIHRSLMVDHVTEVSQWMVGVKRL
          QLCDDISR.L.L.REQWAGGKLSVPV.KRM.LL.QELSS.QWDAADDI.RSL.VDHVTEVSQWMVGVKRL
Retrocopy QLCDDISRHLALRREQWAGGKLSVPVNKRMVLLAQELSSLQWDAADDIRRSLVVDHVTEVSQWMVGVKRL

Parental  IAEK-RSLSSEEAAKEEKSAAATENETMSGLQQAP
          IAEK..SL.SEEAA.EEKSAAA.ENETMSGLQQAP
Retrocopy IAEKKKSLPSEEAANEEKSAAAAENETMSGLQQAP

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	22.08 RPM
SRP017611_kidney	0.00 RPM	26.15 RPM
SRP017611_liver	0.00 RPM	10.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_812 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_812 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016613	1 retrocopy	retro_cjac_490,
Oryctolagus cuniculus	ENSOCUG00000021569	1 retrocopy	retro_ocun_812 ,