RetrogeneDB ID: retro_ocun_1482

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:73067875..73068591(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000015213
• Aliases: None
• Description: None

Sequence

>retro_ocun_1482
ACTTCTAATGCTGAAAGAAAGGAAGACTTAGGTGAAGGTCAAGAGGAGAGCCAGAAGCCAGAAGGTGAAGGGGTTAAACC
AATATCTAAAAGACAAATGAAGACGCTAATAAAACAGAAACAGTGGGAGGAACAACGAGAACTCCACAAACAAAAACAGA
AAGAAAAACGCAAGAGAAAAAAATTAGAGCAACAATGTCAACTGGACTCAAACTCAGATGGAAATGACAGAAAACGTGTG
CAAAGACATGCTGTTCACAGCACACTCTGCCTTGTCATTGACTGCAGTTTTGATGACTTGATGGTATTAAAGGATATTAA
AGAACTTCATAAGCAGATTCAATGATGTTATGCAGAAAACCGATGTGCACTGCATCCTGTGCAGTTTTACTTGACAAGCC
ATGGAGGCCAGCTGAAAAAGAATATGGATGAAAGTGACAAAGGATGGGTCAACTGGAAGGATATCAACATCAAACCAGAG
CACTATACTGAACTCATTAAAAAAGACTTGATTTATCTGACATCAGATTCACCTAATGTACTGGAGGAATTAGATGAATC
AAAGGTTTATGTGATTGGAGGATTAGTAGATCACAACCATCACAAGGAATCACATATAAATAAGAATCATATTATGGAAT
TGACCACACACAGCTCCCCCTTGGAAATTTTGTGAAGATGAATAGCGGAAAAGTTTTGGCTGTTAATCATGTGTTT

Alignment

ORF - retro_ocun_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.7 %
• Parental protein coverage: 71.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSNVERKEDLGEGQEESQKPEGEGVEPISKRQMKKLIKQKQWEEQRELRKQKRKEKRKRKKLERQCQLDS
          TSN.ERKEDLGEGQEESQKPEGEGV.PISKRQMK.LIKQKQWEEQREL.KQK.KEKRKRKKLE.QCQLDS
Retrocopy TSNAERKEDLGEGQEESQKPEGEGVKPISKRQMKTLIKQKQWEEQRELHKQKQKEKRKRKKLEQQCQLDS

Parental  NSDGNDRKRVRRHAVHSTLRLVIDCSFDDLMVLKDIKKLHKQIQRCYAENRRALHPVQFYLTSHGGQLKK
          NSDGNDRKRV.RHAVHSTL.LVIDCSFDDLMVLKDIK.LHKQIQ.CYAENR.ALHPVQFYLTSHGGQLKK
Retrocopy NSDGNDRKRVQRHAVHSTLCLVIDCSFDDLMVLKDIKELHKQIQ*CYAENRCALHPVQFYLTSHGGQLKK

Parental  NMDESDKGWVNWKDINIKSEHYTELIKKEDLIYLTSDSPNVLEELDESKAYVIGGLVDHNHHK-GITYKQ
          NMDESDKGWVNWKDINIK.EHYTELIKK.DLIYLTSDSPNVLEELDESK.YVIGGLVDHNHHK.GITYK.
Retrocopy NMDESDKGWVNWKDINIKPEHYTELIKK-DLIYLTSDSPNVLEELDESKVYVIGGLVDHNHHK<GITYK*

Parental  ASDYGIDHAQLPLGNFVKMNSRKVLAVNHVF
          .S.YGIDH.QLPLGNFVKMNS.KVLAVNHVF
Retrocopy ESYYGIDHTQLPLGNFVKMNSGKVLAVNHVF

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	1.21 RPM
SRP017611_kidney	0.00 RPM	2.23 RPM
SRP017611_liver	0.00 RPM	0.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1482 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1482 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001076	1 retrocopy	retro_amel_1868,
Macaca mulatta	ENSMMUG00000009090	1 retrocopy	retro_mmul_2024,
Mus musculus	ENSMUSG00000004127	3 retrocopies	retro_mmus_3007, retro_mmus_3008, retro_mmus_3368,
Oryctolagus cuniculus	ENSOCUG00000010994	1 retrocopy	retro_ocun_671,
Oryctolagus cuniculus	ENSOCUG00000015213	1 retrocopy	retro_ocun_1482 ,
Otolemur garnettii	ENSOGAG00000005330	2 retrocopies	retro_ogar_2061, retro_ogar_3335,
Ictidomys tridecemlineatus	ENSSTOG00000005064	1 retrocopy	retro_itri_1131,