RetrogeneDB ID: retro_ocun_372

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:68232305..68232614(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023951
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL53
• Ensembl ID: ENSOCUG00000015342
• Aliases: None
• Description: mitochondrial ribosomal protein L53 [Source:HGNC Symbol;Acc:16684]

Sequence

>retro_ocun_372
ATGGCGGCGGCCTGGGCTCGGCTCGGGCTCTGTGCGGTGAAGGAGGTCCGTGTTCAGTTCTGCCCCTTCGAGCAGAACGT
GGAGTCGACGAGGACCTTCCTCCAGGCGGTGAGCAGCGAGAAGGTGCACTCCACCAATCTCATCTGCTCGGTGGTTGCGG
ACGTGAGGCATGATGGCTCCGAGCCCTGCGTGGACGTGCTGTTCCGAGACGGGCATCGCCTGATCATGCGCGGCGCCCAC
CTCACCGCTCAGGAGATGCTCACTGCCTTCGCTTCCCACATCCAGGCCAGGTGCGGCGGGGGGCGGGGA

Alignment

ORF - retro_ocun_372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 91.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAALARLGLRAVKEVRVQFCPFEQNVESTRTFLQAVSSEKVRSTNLNCSVVVDVRHDGSEPCVDVLFGD
          MAAA.ARLGL.AVKEVRVQFCPFEQNVESTRTFLQAVSSEKV.STNL.CSVV.DVRHDGSEPCVDVLF.D
Retrocopy MAAAWARLGLCAVKEVRVQFCPFEQNVESTRTFLQAVSSEKVHSTNLICSVVADVRHDGSEPCVDVLFRD

Parental  GHRLIMRGAHLTAQEMLTAFASHIQARGAAGVG
          GHRLIMRGAHLTAQEMLTAFASHIQAR...G.G
Retrocopy GHRLIMRGAHLTAQEMLTAFASHIQARCGGGRG

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	17.16 RPM
SRP017611_kidney	0.00 RPM	16.22 RPM
SRP017611_liver	0.00 RPM	6.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_372 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016599	3 retrocopies	retro_btau_1132, retro_btau_1528, retro_btau_799,
Nomascus leucogenys	ENSNLEG00000000672	1 retrocopy	retro_nleu_44,
Oryctolagus cuniculus	ENSOCUG00000015342	1 retrocopy	retro_ocun_372 ,
Pan troglodytes	ENSPTRG00000033835	1 retrocopy	retro_ptro_90,
Tarsius syrichta	ENSTSYG00000002278	2 retrocopies	retro_tsyr_1300, retro_tsyr_1840,