RetrogeneDB ID: retro_ocun_704

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:67833934..67834354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000015837
• Aliases: None
• Description: None

Sequence

>retro_ocun_704
AAGCCTGACCCTGTCGTCATTCCCTGGAATGTGACCATCAGTACTGAGGGCAAGCCCCGTGTGCCCCTCGATTCTCCCCT
GAAGGTGGCATTAACTGTGGACAGGGAAGTGGCAGGTTTCTGGATCCAGGTCCCCTGAATGGAACAGCTCTGCAGCTGCA
CCTGCGAAGGTGTCTGGGATGTGCTGGATGTGCTCATTCCCCCTGGGGAGTCCTGCCCAGAGCCCCTGCACACCCATGGG
CTTCCCTGCCACTGCCCCTTCGAAGAAGACACCTACTCACTGCCCAAAAGCTAGTTCACTGTGCCTGTTTTGGAGCTGCC
CAGCTGGCTCAGCTTTGGCAACTACCACACTGAGGGTGTCCTAGTCAGAGGCCAGGAGCAGCTGGCCTGCCTCAAGATCA
CTACCTCCCTGAAGGGCAAA

Alignment

ORF - retro_ocun_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 72.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPDPVVIPGNVTISTEGKTGVRLDTPLKVILTVEKEVAGFWIKVPCVEQLGSCTYDDVCNMLATLIPPGE
          .PDPVVIP.NVTISTEGK..V.LD.PLKV.LTV..EVAGFWI.VP..EQL.SCT...V...L..LIPPGE
Retrocopy KPDPVVIPWNVTISTEGKPRVPLDSPLKVALTVDREVAGFWIQVP*MEQLCSCTCEGVWDVLDVLIPPGE

Parental  SCPEPLHTYGLPCHCPFKEGTYSLPKSEFTIPDLELPSWLSTGNYRVEGVLARGQERLACVKIAASLKGK
          SCPEPLHT.GLPCHCPF.E.TYSLPKS.FT.P.LELPSWLS.GNY..EGVL.RGQE.LAC.KI..SLKGK
Retrocopy SCPEPLHTHGLPCHCPFEEDTYSLPKS*FTVPVLELPSWLSFGNYHTEGVLVRGQEQLACLKITTSLKGK

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	87.31 RPM
SRP017611_kidney	0.00 RPM	58.38 RPM
SRP017611_liver	0.00 RPM	37.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_704 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000020587	1 retrocopy	retro_ecab_510,
Homo sapiens	ENSG00000196743	2 retrocopies	retro_hsap_264, retro_hsap_2715,
Gorilla gorilla	ENSGGOG00000015302	2 retrocopies	retro_ggor_1891, retro_ggor_313,
Macropus eugenii	ENSMEUG00000010421	1 retrocopy	retro_meug_1818,
Microcebus murinus	ENSMICG00000000690	1 retrocopy	retro_mmur_518,
Myotis lucifugus	ENSMLUG00000003215	1 retrocopy	retro_mluc_920,
Macaca mulatta	ENSMMUG00000022869	1 retrocopy	retro_mmul_454,
Nomascus leucogenys	ENSNLEG00000010966	1 retrocopy	retro_nleu_866,
Oryctolagus cuniculus	ENSOCUG00000015837	1 retrocopy	retro_ocun_704 ,
Ochotona princeps	ENSOPRG00000006171	1 retrocopy	retro_opri_1169,
Pongo abelii	ENSPPYG00000015962	1 retrocopy	retro_pabe_403,
Pan troglodytes	ENSPTRG00000017431	2 retrocopies	retro_ptro_1834, retro_ptro_221,
Ictidomys tridecemlineatus	ENSSTOG00000028500	1 retrocopy	retro_itri_759,
Tursiops truncatus	ENSTTRG00000000503	1 retrocopy	retro_ttru_488,