RetrogeneDB ID: retro_ocun_1280

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:10448211..10448902(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000001832
• Aliases: None
• Description: None

Sequence

>retro_ocun_1280
ATGGCTCCCAGCGTGCCAGCAGGCGAACCCGAGTACCCTAAAGGCATCCGGGCCGTGCTGCTGGGGCCGCCCGGGGCTGG
CAAAGGTACCCAGGCACCCAGATTGGCTGAAAATTTCTGTGTCTGCCATTTGGCCACTGGGGACATGCTGGGGGCCATGG
TAGCTTCTGGCTCAGAGCTGGGAAAAAAGCTAAAGGCAACTATGGATGCTGGGAAACTGGTGAGTGACGAAATGGTCGTG
GAGCTTATTGAGAAGAACCCAGAGACCCCTTCGTGCAAGAATGGTTTTCTTCTGGATGGCTTCCCTCGCACTGGAGGCAG
GCAGAAATGCTTGACAACCTCATGGAGAAGCAGAAAGAGAAGCCTGATTCTATGATTGAATTCAGTATCCCAGATTCCCT
GCTGATCCGGAGAATCACAGGAAGGCTGATTCACCCACAAGTGGACGTTCCTACCACGAGGAGTTCAATCCCCCAAAGGA
ACCCATGAAAGATGACATCACTGGAGAACCCTTGATCCATCGATCAGATGATAACGAGAAGGCCTTGAAGATCCGCCTGG
AGGCCTGCCACACTCAGACCACCCCGCTTGTGGAGTACTACAGGAAACGGGACATCCACGCTGCCGTCGATGCGTCCCAG
ACCCCGGATGTCGTGTTTGCGTGCATCCTCGCAGCCTTCTCCAAAGCCACA

Alignment

ORF - retro_ocun_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 96.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPSVPAGEPEHPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLRAMVASGSELGKKLKATMDA
          MAPSVPAGEPE.PKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDML.AMVASGSELGKKLKATMDA
Retrocopy MAPSVPAGEPEYPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLGAMVASGSELGKKLKATMDA

Parental  GKLVSDEMVVELIEKNLETPSCKNGFLLDGFPRT-VRQAEMLDNLMEKRKEKLDSVIEFSIPDSLLIRRI
          GKLVSDEMVVELIEKN.ETPSCKNGFLLDGFPRT..RQAEMLDNLMEK.KEK.DS.IEFSIPDSLLIRRI
Retrocopy GKLVSDEMVVELIEKNPETPSCKNGFLLDGFPRT<WRQAEMLDNLMEKQKEKPDSMIEFSIPDSLLIRRI

Parental  TGRLIH-PTSGRSYHEEFNPPKEPMKDDITGEPLIRRSDDNEKALKIRLEAYHTQTTPLVEYYRKRGIHA
          TGRLIH.PTSGRSYHEEFNPPKEPMKDDITGEPLI.RSDDNEKALKIRLEA.HTQTTPLVEYYRKR.IHA
Retrocopy TGRLIH<PTSGRSYHEEFNPPKEPMKDDITGEPLIHRSDDNEKALKIRLEACHTQTTPLVEYYRKRDIHA

Parental  AVDASQTPDVVFACILAAFSKAT
          AVDASQTPDVVFACILAAFSKAT
Retrocopy AVDASQTPDVVFACILAAFSKAT

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	0.17 RPM	6.29 RPM
SRP017611_kidney	1.93 RPM	68.31 RPM
SRP017611_liver	4.24 RPM	92.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1280 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1280 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017605	2 retrocopies	retro_btau_1146, retro_btau_1168,
Canis familiaris	ENSCAFG00000010390	1 retrocopy	retro_cfam_1622,
Callithrix jacchus	ENSCJAG00000001105	1 retrocopy	retro_cjac_509,
Dasypus novemcinctus	ENSDNOG00000014113	4 retrocopies	retro_dnov_1077, retro_dnov_2052, retro_dnov_2690, retro_dnov_588,
Echinops telfairi	ENSETEG00000002333	2 retrocopies	retro_etel_1466, retro_etel_309,
Homo sapiens	ENSG00000004455	1 retrocopy	retro_hsap_395,
Gorilla gorilla	ENSGGOG00000000069	1 retrocopy	retro_ggor_395,
Myotis lucifugus	ENSMLUG00000000793	1 retrocopy	retro_mluc_1463,
Macaca mulatta	ENSMMUG00000006284	1 retrocopy	retro_mmul_1326,
Monodelphis domestica	ENSMODG00000017363	1 retrocopy	retro_mdom_1792,
Nomascus leucogenys	ENSNLEG00000003152	1 retrocopy	retro_nleu_1313,
Oryctolagus cuniculus	ENSOCUG00000001832	2 retrocopies	retro_ocun_1280 , retro_ocun_445,
Otolemur garnettii	ENSOGAG00000000818	1 retrocopy	retro_ogar_2760,
Ochotona princeps	ENSOPRG00000005023	1 retrocopy	retro_opri_822,
Pongo abelii	ENSPPYG00000001579	1 retrocopy	retro_pabe_1965,
Pan troglodytes	ENSPTRG00000000499	1 retrocopy	retro_ptro_1587,
Rattus norvegicus	ENSRNOG00000000122	3 retrocopies	retro_rnor_1965, retro_rnor_2315, retro_rnor_974,
Sorex araneus	ENSSARG00000000202	1 retrocopy	retro_sara_556,
Sus scrofa	ENSSSCG00000024355	1 retrocopy	retro_sscr_714,
Ictidomys tridecemlineatus	ENSSTOG00000016042	1 retrocopy	retro_itri_595,
Tursiops truncatus	ENSTTRG00000008979	2 retrocopies	retro_ttru_1579, retro_ttru_978,