RetrogeneDB ID: retro_ocun_235

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018935:126565..127291(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028156
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000027511
• Aliases: None
• Description: None

Sequence

>retro_ocun_235
ATGACAATCCAGTGGGTGGCGGTCGCAACTTTCCTTTACGCTGAAATAGGACTCATTTTAATCTTCTGTCTGCCTTTCAT
TCCTCCTCAGAGATGGCAGAAGATTTTTTCATTTAGTGTCTGGGGAAAAATTGCAACTTTTTGGAACAAGGCTTTCCTTA
CTATTATAATCCTATTGATTGTTTTATTTCTAGATGCTGTGAGAGAAGTACGCAAATACTCCTCTGCTCATGCCGTTGAG
AAGGGCTCAACCGTCAAACCTGGGGGCTTTGAACATACACAGATGAAACTTTTTAGGTCTCAAAGAAATCTCTACATTTC
TGGATTTTCATTATTTTTTTGGCTTGTGTTGAGACGTCTGGTTACGCTTATAACTCAGCTGGCAAAGGAACTGTCAAACA
AAGGAGTACTTAAAAGTCAAGCAGAAAATACTAACAAGGCTGCCAAAAAATTCATGGAAGAGAATGAGAAACTAAAATGG
ATCTTGAAAACCCAGGGCAAGGATGACGAAAACATGTTGGAAGCAGAAAATAAAAAACTAGTGGAAGACCAGGAAAAGCT
GAAAACTGAATTAAAGAAGACTTCAGAAGCCCTTTTCAAGGCACAAAATGATGTGATTGCAATGAAGATGCAATCAGAGA
GACTTTCGAAAGAATATGATCGACTCCTGAAAGAACACTCTGAACTTCAGAATCGTTCAGAAAAAGTCAATAAGAAAGGC
CTGTGA

Alignment

ORF - retro_ocun_235 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTIQWVAVATFLYAEIGLILIFCLPFIPPQRWQKIFSFSVWGKIATFWNKAFLTIIILLIVLFLVDAVRE
          MTIQWVAVATFLYAEIGLILIFCLPFIPPQRWQKIFSFSVWGKIATFWNKAFLTIIILLIVLFL.DAVRE
Retrocopy MTIQWVAVATFLYAEIGLILIFCLPFIPPQRWQKIFSFSVWGKIATFWNKAFLTIIILLIVLFL-DAVRE

Parental  VRKYSSAHAVEKGSTVKPGGFEHTQMKLFRSQRNLYISGFSLFFWLVLRRLVTLITQLAKELSNKGVLKS
          VRKYSSAHAVEKGSTVKPGGFEHTQMKLFRSQRNLYISGFSLFFWLVLRRLVTLITQLAKELSNKGVLKS
Retrocopy VRKYSSAHAVEKGSTVKPGGFEHTQMKLFRSQRNLYISGFSLFFWLVLRRLVTLITQLAKELSNKGVLKS

Parental  QAENTNKAAKKFMEENEKLKWILKTQGKDDENMLEAENKKLVEDQEKLKTELKKTSE
          QAENTNKAAKKFMEENEKLKWILKTQGKDDENMLEAENKKLVEDQEKLKTELKKTSE
Retrocopy QAENTNKAAKKFMEENEKLKWILKTQGKDDENMLEAENKKLVEDQEKLKTELKKTSE

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	6.29 RPM	1.66 RPM
SRP017611_kidney	2.43 RPM	0.81 RPM
SRP017611_liver	2.24 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_235 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016329	1 retrocopy	retro_cjac_2669,
Echinops telfairi	ENSETEG00000008025	1 retrocopy	retro_etel_194,
Oryctolagus cuniculus	ENSOCUG00000027511	1 retrocopy	retro_ocun_235 ,
Otolemur garnettii	ENSOGAG00000013116	1 retrocopy	retro_ogar_2169,