RetrogeneDB ID: retro_ocun_1180

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:142171982..142172342(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016194
• Aliases: None
• Description: None

Sequence

>retro_ocun_1180
AGAACCCGAGCCCAGCACATTGTACCCTCTACTATATCCCAGCTGCTTTCTGCCACTCTGGTTGATGAAGTGTTCAAGAT
TGGGAATGTTGAGATTTCACAGGTCACCATTGTGGGGATAATCAGACATACAGAGAAGGCACCAACCAACATTGTTTACA
AAATAGATGACATGACAGCTGCACCCATGGACGTTCGTCAGTGGGTCAACACAGATGACGCCAGTGGTGAGAACAATGTG
GTTCTGCCAGAAACATACGTGAAGGTGGCTGGTCACCTGAGGTCTTTCCAGAACAAGAAGAGCCTGGTAGCCTTTAAAAT
CATGCCCCTGGAGGACGTGAACGAGTCCACCGCTCACATT

Alignment

ORF - retro_ocun_1180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RARAQHIVPCTISQLLSATLADEVFKIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVD
          R.RAQHIVP.TISQLLSATL.DEVFKIGNVEISQVTIVGIIRH.EKAPTNIVYKIDDMTAAPMDVRQWV.
Retrocopy RTRAQHIVPSTISQLLSATLVDEVFKIGNVEISQVTIVGIIRHTEKAPTNIVYKIDDMTAAPMDVRQWVN

Parental  TDDASGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTAHI
          TDDASGEN.VV.PETYVKVAGHLRSFQNKKSLVAFKIMPLED.NE.TAHI
Retrocopy TDDASGENNVVLPETYVKVAGHLRSFQNKKSLVAFKIMPLEDVNESTAHI

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	0.06 RPM	11.92 RPM
SRP017611_kidney	0.10 RPM	14.39 RPM
SRP017611_liver	0.00 RPM	4.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1180 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1180 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180 ,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,