RetrogeneDB ID: retro_ocun_933

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:16792572..16793222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSOCUG00000010086
• Aliases: None
• Description: enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]

Sequence

>retro_ocun_933
ATGTCTATCCTCAAGATCTGTGCCAGAAAAATGTTTGACGCTCGTGGGAATCCCACGGTTCAGGTTGACCTCTACACATC
AAAAGGTCTTTCTGGAGCTGCTGTGCCCAGTGGTGCTTCAGCTGGAATCGACGGAGCCCTGGAGCTGGGGGACAATGACA
AGCTTTGCCACGTGGGGAGGGTGTCTCAATGGCTGTTGAGCACATCAATGAAACTATCGCACCTGTGCTGGTTGGCAAGA
ACGTCCTGGAGCAGAGGAAGATTGACAAACTGATGGTTGAGATGGATGGGACAGAAAATAAATATAAGTTGGATGCAAAC
GCCATCCTGGGGGTGTCTCTTGATGTCTGCAAAGCTGGTGCCGTGGAGAAGGGGGTGCCCCTGTACCACCACATTGCTGA
CGTGGCTGGCAACTCTGAAGTCATCCTACCAGTCCCCACATTCAGCGTCATCAACAGCGGCTCTCGCACCAGCAACTAAC
TCTCCACGCAGGAGTTCATGATCCTGCCCATCAGAGCAGCCAACTTCTGGGAAGTCATGCACATTGGAGCTGAGGCTTAC
CACAACCTGAAGAATGTCATCAAGGAGAATTACGGAAAAGATGCCACCAGTGTGGGGGATGAAGGTGAGTTTGCGCCCAA
CATCCTGGAA

Alignment

ORF - retro_ocun_933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 50.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVLKVHAREIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGK-GVSKAVEHI
          MS.LK..AR..FD.RGNPTV.VDLYTSKGL..AAVPSGAS.GI..ALEL.DNDK....G..GVS.AVEHI
Retrocopy MSILKICARKMFDARGNPTVQVDLYTSKGLSGAAVPSGASAGIDGALELGDNDKLCHVGR<GVSMAVEHI

Parental  NKTIAPALVSKKLNVVEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAG
          N.TIAP.LV.K..NV.EQ.KIDKLM.EMDGTENK.K..ANAILGVSL.VCKAGAVEKGVPLY.HIAD.AG
Retrocopy NETIAPVLVGK--NVLEQRKIDKLMVEMDGTENKYKLDANAILGVSLDVCKAGAVEKGVPLYHHIADVAG

Parental  NSEVILPVPAFNVINGGSHAGNKLAMQEFMILPIGAASFREAMRIGAEVYHNLKNVIKEKYGKDATNVGD
          NSEVILPVP.F.VIN.GS...N.L..QEFMILPI.AA.F.E.M.IGAE.YHNLKNVIKE.YGKDAT.VGD
Retrocopy NSEVILPVPTFSVINSGSRTSN*LSTQEFMILPIRAANFWEVMHIGAEAYHNLKNVIKENYGKDATSVGD

Parental  EGGFAPNILE
          EG.FAPNILE
Retrocopy EGEFAPNILE

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	532.79 RPM
SRP017611_kidney	0.00 RPM	449.52 RPM
SRP017611_liver	0.00 RPM	335.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_933 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_933 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933 ,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,