RetrogeneDB ID: retro_ocun_585

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:129224165..129224386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000009867
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit C, mitochondrial [Source:UniProtKB/TrEMBL;Acc:G1SY25]

Sequence

>retro_ocun_585
AGCGAGCAGCTCCGCGCGGTGGACACGGACAGGGTGGGGCCCATGGAGTCGCTCCTGGAGGACGGATGTCTACACTTGAC
ATTCGACAATGCAGGGGAAGGCACTGTGAGGAAGAACTCCTACAAAACTCCGGTCGTGGTGGGGAAGAGTATTTTGCACC
CCGCCCCCACCACGAGTATTCTCCCTTCGCCAAAGCTGGATAAACAGAGCGCTTCCCGCAC

Alignment

ORF - retro_ocun_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.67 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADRLRQVDTDGVEPMESVLEDRCLYLRSDNVVEG-NCAEELLQNSHRVVEEYFVAPPGN--IPLPKLDEQ
          ...LR.VDTD.V.PMES.LED.CL.L..DN..EG..C.EELLQNS.R..EEYF...P.....P..K....
Retrocopy SEQLRAVDTDRVGPMESLLEDGCLHLTFDNAGEG<HCEEELLQNSGRGGEEYFAPRPHHEYSPFAKAG*T

Parental  ESFPH
          E.FPH
Retrocopy ERFPH

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	8.44 RPM
SRP017611_kidney	0.00 RPM	9.73 RPM
SRP017611_liver	0.08 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_585 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_585 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585 , retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746,
Tarsius syrichta	ENSTSYG00000006845	1 retrocopy	retro_tsyr_1219,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,