RetrogeneDB ID: retro_ocun_266

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:50321370..50322000(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001077
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000014201
• Aliases: None
• Description: None

Sequence

>retro_ocun_266
ATGGAGGCGGGGGACGGCCCTGCCACTGCCGCCGCCGCCTGCTACCAGCCAGCCGGCCCTCCGCGGGATGCCTGTGTCTA
CAGCAGCTGCTACTGTGAAGAAAATATTTGGAAGCTCTGTGAACACATCAAGAACCATGACCAGTACCCTTTGGAAGAGT
GTTATGCTGTCTTCATATCTAAAGAGAGAAAGATGATACCTATTTGGAAACAACAGGCAAGATGCGGGAACGGACCTGTG
ATCTGGGATTACCACGTTGTTTTGCTCCATGTTTCAAGTGGAGGACAGAGCTTCATCTATGATCTGGATACTGTCTTGCC
CTCTCCCTGTCCCTCTGACACTTACGTAGAAGATGCCTTTAAGTCTGATGACGACATTCACCCACAGTTCAGGAGGAAAT
TTAGAGTGATCCGTGCAGATTCATATCTGAAGAACTTTGCTTCCAACCGATCGCACATGAAAGACTCCAGTGGGAACTGG
AGGGAGCCGTCCCCGCCTTATCCCTGCATTGAGACTGGAGATTCCAAAATGAACCTGAATGATTTTATCAGTATGGACCC
TAAGTTGGGATGGGGCACTGTCTACACACTATCTGAATTTGCACATCGGTTTGGCAGTAAAAGCTACTGA

Alignment

ORF - retro_ocun_266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAGDRSAAAAAACYQPAGPPRDACVYSSCYCEENIWKLCEHIKNHDQYPLEECYAVFISNERKMIPIWK
          MEAGD..A.AAAACYQPAGPPRDACVYSSCYCEENIWKLCEHIKNHDQYPLEECYAVFIS.ERKMIPIWK
Retrocopy MEAGDGPATAAAACYQPAGPPRDACVYSSCYCEENIWKLCEHIKNHDQYPLEECYAVFISKERKMIPIWK

Parental  QQARPGNGPVIWDYHVVLLHVSSGGQSFIYDLDTVLPFPCPFDTYVEDAFKSDDDIHPQFRRKFRVIRAD
          QQAR.GNGPVIWDYHVVLLHVSSGGQSFIYDLDTVLP.PCP.DTYVEDAFKSDDDIHPQFRRKFRVIRAD
Retrocopy QQARCGNGPVIWDYHVVLLHVSSGGQSFIYDLDTVLPSPCPSDTYVEDAFKSDDDIHPQFRRKFRVIRAD

Parental  SYLKNFASDRSHMKDSSGNWREPPPPYPCIETGDSKMNLNDFISMDPKVGWGAVYTLSEFAHRFGSKS
          SYLKNFAS.RSHMKDSSGNWREP.PPYPCIETGDSKMNLNDFISMDPK.GWG.VYTLSEFAHRFGSKS
Retrocopy SYLKNFASNRSHMKDSSGNWREPSPPYPCIETGDSKMNLNDFISMDPKLGWGTVYTLSEFAHRFGSKS

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	0.06 RPM	23.07 RPM
SRP017611_kidney	0.00 RPM	22.70 RPM
SRP017611_liver	0.00 RPM	18.34 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_266 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_266 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000865	1 retrocopy	retro_cjac_4210,
Macropus eugenii	ENSMEUG00000008130	3 retrocopies	retro_meug_1679, retro_meug_491, retro_meug_565,
Oryctolagus cuniculus	ENSOCUG00000014201	1 retrocopy	retro_ocun_266 ,