RetrogeneDB ID: retro_ocun_1128

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:167778957..167779267(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA6
• Ensembl ID: ENSOCUG00000015446
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa [Source:HGNC Symbol;Acc:7690]

Sequence

>retro_ocun_1128
TCATCTTCAGCTGGGACAGCCAAGCAGAGAATGAGTGAGCTCCACTCTGCCTGGTGCTGGGAGGTGCTGAACACGGTGCA
CTTATTCCAGCTGATGTCACCATGAAACAGAGACAGGAGAAAGAGAAATGATTATAAAGAGTGCATGTTACAGACCCCAG
GGTGGTTGATATTCTGGTCATTAAGGGAAACACAGAAGTGGAGGAAACAATTAAAACATGGAAGCAGCAGACACAGGCGT
TGTGATTCTTCCATGAAACAGAAACACCAAGGCCAAAGGTTTCCTGTCCAGGTTCTATGTCAGCCATAAC

Alignment

ORF - retro_ocun_1128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRDMNEAKRRVRELYRAWYREVPNTVHLFQL-DITVKQGRDKVREMFMKNAHVTDPRVVDLLVIKGKMEL
          S.....AK.R..EL..AW..EV.NTVHLFQL.D.T.KQ...K..E......HVTDPRVVD.LVIKG..E.
Retrocopy SSSAGTAKQRMSELHSAWCWEVLNTVHLFQL<DVTMKQRQEK--EK*L*RVHVTDPRVVDILVIKGNTEV

Parental  EETIKVWKQRTHVMRVFHETETPRPK-DFLSKFYVGHD
          EETIK.WKQ.T.....FHETETPRPK..FLS.FYV.H.
Retrocopy EETIKTWKQQTQAL*FFHETETPRPK<GFLSRFYVSHN

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	44.43 RPM
SRP017611_kidney	0.00 RPM	93.05 RPM
SRP017611_liver	0.00 RPM	18.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1128 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1128 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128 ,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,