RetrogeneDB ID: retro_ocun_1891

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:62860125..62860620(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000027456
• Aliases: None
• Description: None

Sequence

>retro_ocun_1891
ATGGCCTCAGGAGTACAAGTTGCTGATGAAGTATGTCGCATATTTTATGACATGAAAGTTCGGAAATGCTCCACACCAGA
AGAAATCAAGAAGAGAAAGAAGGCTGTCATTTTTTGTCTCAGTGCAGACAAAAAGTGCATCACTGTAGAAGAAGGCAAGG
AGATCTTGGTTGGAGATGTTGGTGTGACCATAACGGATCCTTTCAAGCATTTTGTAGGAATGCTTCCTGAAAAAGATTGT
CGCTATACTTTGTATGATGCCAGCTTTGAAACCAAGGAATCCAGAAAAGAAGAGTTGATGTTTTTTTTGTGGGCACCAGA
ACTAGCACCTCTGAAAAGTAAAATGATCTATGCAAGCTCCAAGGATGCAATCAAAAAGAAGTTCCAAGGGATAAAACATG
AATGTCAAGCAAATGGGCCAGAAGACCTCAATCGGGCTTGCATTGCAGAGAAGCTAGGTGGATCCTTAATTGTAGCTTTT
GAAGGATGCCCTGTG

Alignment

ORF - retro_ocun_1891 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIFCLSADKKCIIVEEGKEILVGDVGVTITDPFKH
          MASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIFCLSADKKCI.VEEGKEILVGDVGVTITDPFKH
Retrocopy MASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIFCLSADKKCITVEEGKEILVGDVGVTITDPFKH

Parental  FVGMLPEKDCRYALYDASFETKESRKEELMFFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQANGP
          FVGMLPEKDCRY.L................FFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQANGP
Retrocopy FVGMLPEKDCRYTLXXXXXXXXXXXXXXXXFFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQANGP

Parental  EDLNRACIAEKLGGSLIVAFEGCPV
          EDLNRACIAEKLGGSLIVAFEGCPV
Retrocopy EDLNRACIAEKLGGSLIVAFEGCPV

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	25.83 RPM	84.82 RPM
SRP017611_kidney	52.30 RPM	144.84 RPM
SRP017611_liver	20.27 RPM	62.20 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1891 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000009383	1 retrocopy	retro_ocun_1397,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891 ,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,