RetrogeneDB ID: retro_ocun_793

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:30724346..30724954(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010837
• Aliases: None
• Description: None

Sequence

>retro_ocun_793
ATGGAGAGGTGTGTGTCTAACCTAATGGTTTGCAACCTGACCTACAGCAGGAAGCTGGAGGATCTGAGGGAGACCATCCT
GCCAATAAATCCCTGGCTACCAGAACTGACCAGGACGGCAGAACCGCATTGCATTGGGCATGCTCAGCTGGACATAAAGA
AATTGTTGAATTCTTGCTGCAACTTGGAGTGTCAGTGATTGATAAAGACGATGCAGGTTGGTCTCCTCTTCACATCGCTG
CTTCTGCTGGCCGAGATGAAATTCCGAAAGCCCTTCTGGGGAAGGGTGCTCAAGTGAACGCTGTCAATCAAAATGGCTAC
GCTCCCCTACATTAGGCAGCTTCCGAAAATAGGCAAGAGATTGCTGTCATGCTACTGGAAGGCAGTGCTAATCCAGATGC
TAAGGACCATTACACGGCTACATCAATGCACCAGGCAGCAGCCAAGGGTAACTTGAAGATGATTCATATCCTTCTGTACT
ACAAAGTATCCACAAGCATCCAAGACACTGAGGGTAACTCTTCTCTACACTTAGCCTATGATGAGGAGAGAGTGGAAGAG
GCAAAACTTCTGGTGTCCCAAGGAGCAAGTATTTACATAGAAGAAAGA

Alignment

ORF - retro_ocun_793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.76 %
• Parental protein coverage: 89.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSGKLEELRESIL-ADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDK
          ME.CVSNLMVCNL.YS.KLE.LRE.IL.A.KSLATRTDQD.RTALHWACSAGH.EIVEFLLQLGV.V.DK
Retrocopy MERCVSNLMVCNLTYSRKLEDLRETIL<ANKSLATRTDQDGRTALHWACSAGHKEIVEFLLQLGVSVIDK

Parental  DDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYE
          DDAGWSPLHIAASAGRDEI.KALLGKGAQVNAVNQNG..PLH.AAS.NR.EIAVMLLEG.ANPDAKDHY.
Retrocopy DDAGWSPLHIAASAGRDEIPKALLGKGAQVNAVNQNGYAPLH*AASENRQEIAVMLLEGSANPDAKDHYT

Parental  ATSMHRAAAKGNLKMIHILLYYKASTNIQDTEGNTPLHLACDEERVEEAKLLVSQGASIYIENK
          ATSMH.AAAKGNLKMIHILLYYK.ST.IQDTEGN..LHLA.DEERVEEAKLLVSQGASIYIE..
Retrocopy ATSMHQAAAKGNLKMIHILLYYKVSTSIQDTEGNSSLHLAYDEERVEEAKLLVSQGASIYIEER

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	13.69 RPM
SRP017611_kidney	0.00 RPM	14.29 RPM
SRP017611_liver	0.00 RPM	4.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_793 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_793 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Microcebus murinus	ENSMICG00000002059	1 retrocopy	retro_mmur_550,
Myotis lucifugus	ENSMLUG00000014534	1 retrocopy	retro_mluc_2008,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793 ,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,