RetrogeneDB ID: retro_ocun_1286

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:5129771..5130113(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SNX12
• Ensembl ID: ENSOCUG00000014919
• Aliases: None
• Description: sorting nexin 12 [Source:HGNC Symbol;Acc:14976]

Sequence

>retro_ocun_1286
ACTGCCCATGAAGTTCACGTGTGGACTGATCTACGTTGTCTTCAAGCTGAGGGGGGCCTGTGCGGGCGGCACCACAGTGA
CTCCGAGTGGCTGAAGAATGAGCTGGAGGGAGACAGCACGTTTGCAGTGCCACCTCCATGAGAGAAAGTCTTGAAGCAAC
AGCTCTCTTTAGAAGGAGAAGAAGGCTTTGAGGAGGCTTTCATTGGAGAAAGGAGGCAGGGCCTCGAACTGCTTACTGAT
AGAATTGCTGGGCATCCACAGGCTCAGACTGAACGCTGCCTACCTGTGTTCCTGCTGGAAGAAGCAATCCACAGGAACTC
GGCTCTGGCAAGGTGCGCCAGC

Alignment

ORF - retro_ocun_1286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 69.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTYEVRMRTNLP-IFKLKESCVR-RRYSDFEWLKNELERDSKIVVPPLPGKALKRQLPFRGDEGIFEESF
          T..EV...T.L...FKL...C...R..SD.EWLKNELE.DS...VPP...K.LK.QL...G.EG.FEE.F
Retrocopy TAHEVHVWTDLR>VFKLRGACAG<RHHSDSEWLKNELEGDSTFAVPPP*EKVLKQQLSLEGEEG-FEEAF

Parental  IEERRQGLEQFINKIAGHPLAQNERCLHMFLQEEAIDRNYVPGKLAA
          I.ERRQGLE.....IAGHP.AQ.ERCL..FL.EEAI.RN......A.
Retrocopy IGERRQGLELLTDRIAGHPQAQTERCLPVFLLEEAIHRNSALARCAS

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	23.95 RPM
SRP017611_kidney	0.00 RPM	17.03 RPM
SRP017611_liver	0.00 RPM	7.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1286 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1286 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9,
Oryctolagus cuniculus	ENSOCUG00000004744	1 retrocopy	retro_ocun_918,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286 ,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452,