RetrogeneDB ID: retro_ocun_116

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:46197816..46198422(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023919
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011970
• Aliases: None
• Description: None

Sequence

>retro_ocun_116
ATGGCCAACAAGGGTCCTTCCTACGGCATGAGCCGCGAGGTGCAATCCAAAATTGAGAAGAAGTACGATGAGGAGCTGGA
GGAGCGGCTGGTGGAGTGGATCATCGTGCAGTGCGGCCCTGACGTGGGCCGCCCGGACCGTGGGCGCCTGGGCTTCCAGG
TCTGGCTGAAGAACGGCGTGATCCTGAGCAAGCTGGTGAACAGCCTGTACCCAGAGAGTTCCAAGCCAGTCAAGGTGCCC
GAGAACCCGCCCTCCATGGTCTTCAAGCAGATGGAGCAGGTGGCTCAGTTCCTGAAGGCAGCTGAGGACTACGGGGTCAC
CAAGACCGACATGTTCCAGACTGTTGACCTCTTTGAAGGCAAAGACATGGCTGCAGTGCAGAGGACCCTGATGGCTTTGG
GCAGCCTGGCAGTGACCAAGAATGATGGGCACTACCGCGGAGATCCCAACTGGTTTATGAAGAAAGCCCAGGAGCACAAG
CGGGAGTTCACAGAGAGCCAGCTGCAGGAGGGCAAGCATGTCATCGGCCTTCAGATGGGCAGCAACAGAGGGTCCTCGCA
GGCGGGCATGACGGGCTACGGACGACCTCGGCAGATCATCAGCTAG

Alignment

ORF - retro_ocun_116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.5 %
• Parental protein coverage: 93.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGVILSKLVNSLY
          MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGVILSKLVNSLY
Retrocopy MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGVILSKLVNSLY

Parental  PESSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDMAAVQRTLMALGSLAVTK
          PESSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDMAAVQRTLMALGSLAVTK
Retrocopy PESSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDMAAVQRTLMALGSLAVTK

Parental  NDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGASQAGMTGYGRPRQII
          NDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRG.SQAGMTGYGRPRQII
Retrocopy NDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGSSQAGMTGYGRPRQII

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	2.70 RPM	2.98 RPM
SRP017611_kidney	4.56 RPM	6.69 RPM
SRP017611_liver	0.54 RPM	1.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_116 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723, retro_cjac_778,
Microcebus murinus	ENSMICG00000002371	1 retrocopy	retro_mmur_666,
Oryctolagus cuniculus	ENSOCUG00000011970	1 retrocopy	retro_ocun_116 ,