RetrogeneDB ID: retro_ocun_1230

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:42707344..42707552(+)
• Located in intron of: ENSOCUG00000009694

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSOCUG00000021484
• Aliases: None
• Description: ribosomal protein S28 [Source:HGNC Symbol;Acc:10418]

Sequence

>retro_ocun_1230
ATGAACACAAGCCTTGTGTAGCCCCTCAAGCTGGCCCGGGTCATCAATGTATTGGGCACAACTGGCTCTCAAGAACAGTG
CAGGAAGGTGTGGCTGGAACTTACAGATGGCATGAAGTCCTCTGTCATCAGGCAGTGTGAAAGGCGGAGAGCTTGAGAGT
GACTTCTTGACCGTGTTGGGGTCTGATGGAGAGGCGTGGAAACTGCGC

Alignment

ORF - retro_ocun_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIR-NVKGPVREGDVLTLLESEREARRLR
          M.TS.V.P.KLARV..VLG.TGSQ.QC..V..E..D....S.IR..VKG...E.D.LT.L.S..EA..LR
Retrocopy MNTSLV*PLKLARVINVLGTTGSQEQCRKVWLELTDGMKSSVIR>SVKGGELESDFLTVLGSDGEAWKLR

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	38.85 RPM
SRP017611_kidney	0.00 RPM	92.74 RPM
SRP017611_liver	0.00 RPM	18.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1230 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1230 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611, retro_fcat_752,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230 , retro_ocun_1799,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132, retro_sscr_191, retro_sscr_808,