RetrogeneDB ID: retro_ocun_725

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:135346004..135346615(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSOCUG00000001383
• Aliases: None
• Description: mitochondrial ribosomal protein L9 [Source:HGNC Symbol;Acc:14277]

Sequence

>retro_ocun_725
CCGCTGGCCGGCGAAGGCCGGAAGCCGCGCCTGCACCGGCGGCTCCGTGATACAAGCTGGTGGAGGACACGAAGCAGCGG
CCCAAGGAGGACCTGGAGCTCATCCTCACGCAGGCTGTGGAGGACCTTGGAGTCCGGGGCGATCTGATCTCCGTGAAGAA
ATCTGTGGGCCGCAACCGACTCCTCCCTCAGGGACTGGCTGTGGATGCCTCTCCTGAAAACGAGAAACTGTTTGAAGGGG
AGAAATGGCTAAGACAGGAAGGAAAATTAGAGAAGATCCAGACCAAGGCAGGTGAGGCGACAGTGAAGTTCCCGAGGAGC
TGTCACCTGGAGGTGGGGATGAAGAACAACGTCAAACGGGAGCTGAACTCGGAAATAGCTGCCCGCCACTTCCTGAAGAA
CCTTGGTGTTGTGATCGCCCCACATGCAGTAAAGTTACCCAAAGAACCTATCACACGGTGGGGCGAGTACTGGTGTGAGG
TGACGGTAAATGGGCTTGACACTGTGAGAGTGCCTATGTCTGTGGTGAACTTTGAGAAGCCCAAGACCAAAAGATATAAG
TACTGGTGAGCCCAGCAAGCTGCCAAGAGGCTGGCCCCCACCAGCAACCAG

Alignment

ORF - retro_ocun_725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.68 %
• Parental protein coverage: 76.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLAGEGRKPRLHRRHRV-YKLVEDTKHRPKEDLELILTQSVEDLGVRGDLISVKKSVGRNRLLPQGLAVY
          PLAGEGRKPRLHRR.R..YKLVEDTK.RPKEDLELILTQ.VEDLGVRGDLISVKKSVGRNRLLPQGLAV.
Retrocopy PLAGEGRKPRLHRRLRD<YKLVEDTKQRPKEDLELILTQAVEDLGVRGDLISVKKSVGRNRLLPQGLAVD

Parental  ASPENKKLFEGEKLLRQEGKLEKIQTKAGEATVKFLRSCHLEVGMKNNVKWELNSEIVARHFLKNLGVVV
          ASPEN.KLFEGEK.LRQEGKLEKIQTKAGEATVKF.RSCHLEVGMKNNVK.ELNSEI.ARHFLKNLGVV.
Retrocopy ASPENEKLFEGEKWLRQEGKLEKIQTKAGEATVKFPRSCHLEVGMKNNVKRELNSEIAARHFLKNLGVVI

Parental  APHAVKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKSLAPTSNQ
          APHAVKLP.EPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYW.AQQAAK.LAPTSNQ
Retrocopy APHAVKLPKEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYW*AQQAAKRLAPTSNQ

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	22.24 RPM
SRP017611_kidney	0.00 RPM	37.60 RPM
SRP017611_liver	0.00 RPM	19.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_725 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_725 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725 ,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,