RetrogeneDB ID: retro_ocun_1483

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:80421002..80421588(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000013041
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSOCUG00000029379
• Aliases: None
• Description: H1 histone family, member O, oocyte-specific [Source:HGNC Symbol;Acc:18463]

Sequence

>retro_ocun_1483
GAGAAGCTGAGGGAGGTAAGGCCGGGCCCTTCCAGCCAGGGCCAGGGGAAACAGGCACCCAAGAAGCCGGACAGGTTGGG
GAGGGCTCCTCCCAAACCAGGTGCAGCCAAGAAGGTCCCCAAGAAAGGCAGGAAGGCCAAGGCCAAGGATGCGGAGGCCA
AAATGGGCCAGGCCAGAAAGGCATCCAGGGAGGTTAGACAAGGCCACGCAGGCCTCTGCCAGTCCCAGTGTGTGCAAAGG
GAAGTCCAAGATCAAAGGTCACGTGCAAAGCCAAGGACATGCCAAAGCCCATGGGAGAACCAGCGCTGGCAGCAAGAGCT
CCAAACCCATTGCCAACAAGGTCAAGAATGGTGTCACCTCCCCAACTGGAACAAAGATCATGGCCAAGGCCCCTCTAGGA
GTGGTCCCCGGGATGGGGGCGGGGCCCAAAGCCAAGGCCACCACCCCCGCTAAGGGCAGTGGGTCCAAAGCGGGGCCTAC
ACCCCTATCTGGGAAGCCCGAGGGCCCCAGGAGCCCAAGAAAGGCTGGCTTGCCCTCTAAAGCCCTGGCATCCAAGGTGT
CGGGCAAGAAGGCCAAAGCCGAGGGT

Alignment

ORF - retro_ocun_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.67 %
• Parental protein coverage: 56.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKPREARPGPSSQGQGERAPKKPDGSGRAPPKPGAAKKVPKKGGKAKAKDAEAKVGQARKVS-GELDKAT
          EK.RE.RPGPSSQGQG..APKKPD..GRAPPKPGAAKKVPKKG.KAKAKDAEAK.GQARK.S.G.LDKAT
Retrocopy EKLREVRPGPSSQGQGKQAPKKPDRLGRAPPKPGAAKKVPKKGRKAKAKDAEAKMGQARKAS>GRLDKAT

Parental  QASASPSVRKGKSKVKGHGQSQGHAKAHGRTSAGSKSSKPTANKVKNGVASPSGKKTTAKAPRGVVPGVG
          QASASPSV.KGKSK.KGH.QSQGHAKAHGRTSAGSKSSKP.ANKVKNGV.SP.G.K..AKAP.GVVPG.G
Retrocopy QASASPSVCKGKSKIKGHVQSQGHAKAHGRTSAGSKSSKPIANKVKNGVTSPTGTKIMAKAPLGVVPGMG

Parental  AGPEAKAATPSKGRGSKAGPVPLSGKPEGPRSQRKPGLSSKAPASKASGKKAKAEG
          AGP.AKA.TP.KG.GSKAGP.PLSGKPEGPRS.RK.GL.SKA.ASK.SGKKAKAEG
Retrocopy AGPKAKATTPAKGSGSKAGPTPLSGKPEGPRSPRKAGLPSKALASKVSGKKAKAEG

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1483 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1483 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483 ,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,