RetrogeneDB ID: retro_ocun_1276

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:7066603..7066904(+)
• Located in intron of: ENSOCUG00000014976

Retrocopy information

• Ensembl ID: ENSOCUG00000022153
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM1
• Ensembl ID: ENSOCUG00000015399
• Aliases: None
• Description: LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:20472]

Sequence

>retro_ocun_1276
CTGCTTCGAGTTTTAAGAAGCACTGATCAGTTTGCTAACTTACTACTATGTCGGACTGTGGAGCATACTCTTGTGGGCAA
AAAATACGGTGCTACTCCTCGAGGGACTTTTGTGGTCAGAGGAGAGAATGTGGTCCTCTAGGAGAAATAGACTGGAAAAG
GAGAGCGACACACCCCTGCAGCACGTGTCCATTGAAGCAGTCCTGGGAGAACGAAGGGTGGAACAACAGCCCAGGCTGGA
AGCAGAGGGGCTCCAAGTTCAGGCCCTGAAGGTTCGGGCTCTCTGCACTCCCTGGGCAGAC

Alignment

ORF - retro_ocun_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 75.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVL-LGEID-LEKESDTPLQQVSIEEI
          L...LRS.DQFANL.L..TVE...VGKKYG..PRG.FVVRGENVVL.LGEID.LEKESDTPLQ.VSIE..
Retrocopy LLRVLRSTDQFANLLLCRTVEHTLVGKKYGATPRGTFVVRGENVVL<LGEID<LEKESDTPLQHVSIEAV

Parental  LEEQRVEQQTKLEAEKLKVQALKDRGLSIPRAD
          L.E.RVEQQ..LEAE.L.VQALK.R.L..P.AD
Retrocopy LGERRVEQQPRLEAEGLQVQALKVRALCTPWAD

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	11.42 RPM
SRP017611_kidney	0.00 RPM	13.99 RPM
SRP017611_liver	0.08 RPM	2.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1276 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011141	1 retrocopy	retro_amel_263,
Myotis lucifugus	ENSMLUG00000003734	1 retrocopy	retro_mluc_723,
Mustela putorius furo	ENSMPUG00000009883	1 retrocopy	retro_mputfur_490,
Mus musculus	ENSMUSG00000037296	1 retrocopy	retro_mmus_3725,
Oryctolagus cuniculus	ENSOCUG00000015399	1 retrocopy	retro_ocun_1276 ,
Sarcophilus harrisii	ENSSHAG00000017260	1 retrocopy	retro_shar_532,