RetrogeneDB ID: retro_ocun_928

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:82934287..82934917(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005878
• Aliases: None
• Description: None

Sequence

>retro_ocun_928
CTCCTGTCACCACCACCACTGCTTCCTCATTCATTCATGTGCACCCTCCAGTGTGGAGAGAGATGTGGGACACCTCTGTA
TGACCGTCCTTTTGGCCAAAGATTTCCAGAGAACTGTGCAAGAAGGGAACGTTTGAACGCCTGTCTCTGCAAACAGATGA
AGGTGAACACAGTATTGAAATGCATTTGATTATACAGCTAAAGCCATGGAAGCTGTAAGGATGAATTTACCAATTATTCC
TGTACTGGTTGGCGCTCTGAGTCAAAAGAACAGGAATTCGGAAAACTTCAGTAACGATCTGGCGGATCCTAGTTATCTCT
TTGCGGTTTCTTGTGATTTCTCCCATTGGGGTCAAGGTTCCATTACAGTTACTATGATGAACCCCAGGGGGAGACTTATA
GATCCATAGAACATCTAGATAAAATGGGTGTGAGTATTATAGAGCAATTAGACCCTGTACCTTTTAGCAATTACTTGAGG
AAACACCATAATACTATATATGGAAGACATCCCACTGGGGTGTAATTAAATGCTATCACTGAGCTCCAGAAAAATGGAAT
GAAAGGGAGCTTTTCCTTTTTAAATTACGCCCAGGGAAGCCAGTGCAGAAACCAGCAGGACAGTTCAGTT

Alignment

ORF - retro_ocun_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.18 %
• Parental protein coverage: 76.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ILGPSHHVPLS-RCALSSVDIYRTPLYDLRIDQ-KIYGELWKTGMFERMSLQTDEDEHSIEMHL-PYTAK
          .L.P....P.S..C.L.......TPLYD....Q.KI..EL.K.G.FER.SLQTDE.EHSIEMHL..YTAK
Retrocopy LLSPPPLLPHSFMCTLQCGERCGTPLYDRPFGQ<KISRELCKKGTFERLSLQTDEGEHSIEMHL<DYTAK

Parental  AME-SHKDEFT-IIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQ-RFRYSYYDESQGEI
          AME.S.KDEFT.IIPVLVGALS..........FS..LADPS.LF.VS.DF.HWGQ.RF.YSYYDE.QGE.
Retrocopy AME<SCKDEFT>IIPVLVGALSQKNRNS--ENFSNDLADPSYLFAVSCDFSHWGQ<RFHYSYYDEPQGET

Parental  YRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNGMNMSFSFLNYAQSSQC
          YRSIEHLDKMG.SIIEQLDPV.FSNYL.K.HNTI.GRHP.GV.LNAITELQKNGM..SFSFLNYAQ.SQC
Retrocopy YRSIEHLDKMGVSIIEQLDPVPFSNYLRKHHNTIYGRHPTGV*LNAITELQKNGMKGSFSFLNYAQGSQC

Parental  RNWQDSSV
          RN.QDSSV
Retrocopy RNQQDSSV

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	8.77 RPM
SRP017611_kidney	0.00 RPM	10.95 RPM
SRP017611_liver	0.00 RPM	4.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_928 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_928 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Choloepus hoffmanni	ENSCHOG00000012339	2 retrocopies	retro_chof_2257, retro_chof_2552,
Cavia porcellus	ENSCPOG00000012278	1 retrocopy	retro_cpor_1159,
Dasypus novemcinctus	ENSDNOG00000001254	1 retrocopy	retro_dnov_253,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Macropus eugenii	ENSMEUG00000010461	2 retrocopies	retro_meug_1496, retro_meug_1697,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mustela putorius furo	ENSMPUG00000005208	1 retrocopy	retro_mputfur_679,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928 ,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,
Pteropus vampyrus	ENSPVAG00000011427	1 retrocopy	retro_pvam_184,
Ictidomys tridecemlineatus	ENSSTOG00000002828	2 retrocopies	retro_itri_1321, retro_itri_537,