RetrogeneDB ID: retro_ocun_809

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:78240683..78241425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSOCUG00000010746
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_ocun_809
TGGTTGTGGTAGGTGGGACCACAGTCAAGGGGAGCAGAGGAGGTGGCCAACTTTGCTGCTTATGCATTTGCACCAGCCAT
GCTAGTGACTCTGCTAGGAGCTCTCAGCACCCTCGTAAGTGCCATTCTTTCTTCATACTTTCTAAATGAAAGACTTAATC
TTCATGGGAACATTGGATGTTTGCGAAGTGCTTTGAGATCTACAGTAAATGGCCTTTCATGCTCCAAATGAAGAGGAGAT
TGAGACCTTAAATGAAATGTCTCAGAAACTAGATGATTCAGGTTTTATGGTCTTGGCCACACTTGTGGTCATTGGGTCCT
TGACAGTCATCTTCGTGGTAGGCCCTCGCCATGGGCAAACCTTCTGGTGCACATAACAATCTGTTCCATCACTGAGCATT
TTCAGTGTCCTGTGTGAAGGGCCTGGGCACTGCTATCAAAGAGCTGTTTGCAAGAAAGGTCATGCTGTGGCTTCCTCTGA
CCTGGATCTTTCTGGAGAGCCTGATTGTCTATGTGAGCACACAGATTTATTATCTAAACAAGGCCCTGGACATATCATTA
CTGCAATCGTAACTCCAATATATTATGTATTCTTTACAAACTCCATCTTAACATGTTCGGCTATTCTTTTTAAGGAATGG
CAAGATATGCCTACTGCTGGTGTCATTGGTACTCCGAGTGGCTTCTTTACAGTCATTGTGGGGATCTTCCTGTTGCATGC
CTTTAAAGACCTCAACTTTAGC

Alignment

ORF - retro_ocun_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 69.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WLWWAGLLSMGAGEVANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTV-
          WLW..G..S.GA.EVANFAAYAFAPA.LVT.LGALS.LVSAILSSYFLNERLNLHG.IGCL.S.L.STV.
Retrocopy WLW*VGPQSRGAEEVANFAAYAFAPAMLVTLLGALSTLVSAILSSYFLNERLNLHGNIGCLRSALRSTV>

Parental  MVIHAPKEEEIETLNEMSHKLGDPGFVVFATLVVIVSLIFIFVV-GPRHGQTNILVYITICSVIG-AFSV
          M..HAP.EEEIETLNEMS.KL.D.GF.V.ATL.V.........V.G......N.LV.ITICS....AFSV
Retrocopy MAFHAPNEEEIETLNEMSQKLDDSGFMVLATL-VVIGSLTVIFV<GRPSPWANLLVHITICSITE<AFSV

Parental  SCVKGLGIAIKELFAGKPVLRHPLAWILLLSLVVCVSTQINYLNRALDI-FNTSIVTPIYYVFFTTSVLT
          SCVKGLG.AIKELFA.K..L..PL.WI.L.SL.V.VSTQI.YLN.ALDI...T.IVTPIYYVFFT.S.LT
Retrocopy SCVKGLGTAIKELFARKVMLWLPLTWIFLESLIVYVSTQIYYLNKALDI<IITAIVTPIYYVFFTNSILT

Parental  CSAILFKEWQDMPVDDVIGTLSGFFTIIVGIFLLHAFKDVSFS
          CSAILFKEWQDMP...VIGT.SGFFT.IVGIFLLHAFKD..FS
Retrocopy CSAILFKEWQDMPTAGVIGTPSGFFTVIVGIFLLHAFKDLNFS

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	30.96 RPM
SRP017611_kidney	0.00 RPM	48.25 RPM
SRP017611_liver	0.00 RPM	15.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_809 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809 ,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,