RetrogeneDB ID: retro_ocun_621

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:98583607..98583963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSOCUG00000008972
• Aliases: None
• Description: mitochondrial assembly of ribosomal large subunit 1 [Source:HGNC Symbol;Acc:21721]

Sequence

>retro_ocun_621
CTTCCCTCTGGACCAGCACCTGGCCAGGCCTGCTTGACCCAGGTGTTGTGTGCAGCTTGCACTGTGGCCCTGGGCTACAG
AAAAGGATGGGGGAGGGGGGTCCAGCTGATGAGGGACGCCCAGAGTCAGGCCCAGCAGTTTATATGGGTCCCAAGTTTGA
CATCAATGTGCTGGTTTCACTTCTGAGGCAAGAAAATGCAAGATACACTGATGTCATCAAGTTTGCTCCAGAAATAAAAT
ACACAGATTATCTTGTGATTAGTGTTGGAACTTCCACCCTGCACTTAGATCCCATGACCTACTACACTGTGAAAATGTAC
AAAAACCTGAAATGTGAAAGCAAGCCTCCTGTTAAA

Alignment

ORF - retro_ocun_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 54.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPSAPAPGPACLAA-SPVRGLRVGPRLEKGT-EAGAADEGRPESGSADHTGPKFDVDLLVSLLRQENARD
          LPS.PAPG.ACL.....V..L..GP.L.K...E.G.ADEGRPESG.A...GPKFD...LVSLLRQENAR.
Retrocopy LPSGPAPGQACLTQ<GVVCSLHCGPGLQKRMGEGGPADEGRPESGPAVYMGPKFDINVLVSLLRQENARY

Parental  ICVIQVPPEMKYTDYFVIASGTSTRHLHAMACYLVKMYKYLKCRSEPHVK
          ..VI...PE.KYTDY.VI..GTST.HL..M..Y.VKMYK.LKC.S.P.VK
Retrocopy TDVIKFAPEIKYTDYLVISVGTSTLHLDPMTYYTVKMYKNLKCESKPPVK

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	19.48 RPM
SRP017611_kidney	0.00 RPM	12.87 RPM
SRP017611_liver	0.00 RPM	5.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_621 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_621 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621 ,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,