RetrogeneDB ID: retro_ocun_414

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:179664477..179664937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSOCUG00000003901
• Aliases: None
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:HGNC Symbol;Acc:14264]

Sequence

>retro_ocun_414
CTGTCATTTCTGGACCGAGGTCCTGGAGGCTTTAATCGGTGGTTGGAGGTGGCGGCTTCAGTTGTGGGGGTGGGGGACAC
CAGCAACAACCACTTCCACGGTGGAGGCAGCAGCAATTTCAGGGCGGGTAGAGGAAGATTTGGAAGTGGAAGTGGCCACC
AGGACTTTAGCAAAAGCCAAACCGTTCCTCCAGAAGGCACAGTCCTATGAGGAGATTCCGAGCATCCTTGTGAACATGTC
ATAGTTTGTAAATATACCGCAGATGAAAGTGAAGTGCCCTGTTTTGATACTCCTATTTATTTAGAAAGCTAAGAACACAT
TGGAAAAGTGGATGCAACATTTTGACAACTTGGGTTTTTTTAATTTTTCAGTTAAATTGTTAGAAATCCTGAAGGTATTT
TCCTTTAAAAAATATATGGAGGTTTTATATAGACCTTGTAAGCTACTGCCACTGCAGAGG

Alignment

ORF - retro_ocun_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 71.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSFRGGGRGGFNRG-GGGGGFNRGGSSN-NSHFRGGGG--NFRGGGRGGFGRGGGRGGFNKGQDQGPPER
          .SF...G.GGFNR...GGGGF..GG..........GGG..NFR..GRG.FG.G.G...F.K.Q...PPE.
Retrocopy LSFLDRGPGGFNRW<VGGGGFSCGGGGH>SNNHFHGGGSSNFR-AGRGRFGSGSGHQDFSKSQTV-PPEG

Parental  VVILGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQ-LRDFYFSVKLSENMKASSF
          .V..G...HPCE..IVCK.T.DE..VP.F..P.YLE..E.IGKVD..F.Q.L..F.FSVKL.E..K..SF
Retrocopy TVL*GDSEHPCEHVIVCKYTADESEVPCFDTPIYLES*EHIGKVDATF*Q>LGFFNFSVKLLEILKVFSF

Parental  KKLQKFYIDPYKLLPLQR
          KK.......P.KLLPLQR
Retrocopy KKYMEVLYRPCKLLPLQR

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	5.68 RPM
SRP017611_kidney	0.00 RPM	8.51 RPM
SRP017611_liver	0.00 RPM	3.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_414 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414 ,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,