RetrogeneDB ID: retro_ocun_1066

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:118146366..118146834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF6
• Ensembl ID: ENSOCUG00000006635
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:HGNC Symbol;Acc:28625]

Sequence

>retro_ocun_1066
GTCAAAAAACATAATCTGACTAAAAGATGGCTTATGAAAAGTATTGGTGAAAGGGAAAAAAATCCGGATGACAAAGTGTA
TGGTGGTATCCAGGCCCTGGAAAATGATGCTGCAAACACTCAGAGCGCTCTTCTTTATTTAACTTAGAAGCATTGGCTAG
GAAGGATCTTTTTGCAGATCACAGTGGAAAAGCCCAAGGCATTGTCGCTTGCTTGAGAGCAAGGTCCTATCCCAGCAGCA
GAAGAGAGCTGCTGCTTCCCGTGGATATTTGTATGCAGCGTGGTTTTCCCAAGAGGATGTCCTACAGAAGAGCCACGGTG
AAAACGGGAGAGGTGTGATATGTGGCAGTGCCCACCAGGCACACTCAGCCAGGTCCTTCCGCAGAAGTGAAGCCTTGCCT
GCTTTCTTCAGATGGTTTCTCCAGAGGACTACTTAAAGAAAACTCAGCAAATAGATTTTTTTTTTTTT

Alignment

ORF - retro_ocun_1066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKRHNLTKRWFMKIIDEREKNLDDKVYCNIQELENYAENTQSALLYLT-LETLGIKDLHADHAASHIGKA
          VK.HNLTKRW.MK.I.EREKN.DDKVY..IQ.LEN.A.NTQSALLYLT.LE.L..KDL.ADH.....GKA
Retrocopy VKKHNLTKRWLMKSIGEREKNPDDKVYGGIQALENDAANTQSALLYLT<LEALARKDLFADHS----GKA

Parental  QGIVTCLRATPYHGSRRKVFLPMDICMLHG-VSQEDVLRKSQDKKVRDVIYDIASQAHLHLKHARSFHKS
          QGIV.CLRA..Y..SRR...LP.DICM..G..SQEDVL.KS.....R.VI...A.QAH.....ARSF..S
Retrocopy QGIVACLRARSYPSSRRELLLPVDICMQRG<FSQEDVLQKSHGENGRGVICGSAHQAH----SARSFRRS

Parental  VPARAFPAF-LQTVSLEDYLKKIQQVDFDIF
          ....A.PAF.LQ.VS.EDYLKK.QQ.DF..F
Retrocopy ---EALPAF<LQMVSPEDYLKKTQQIDFFFF

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	10.21 RPM
SRP017611_kidney	0.00 RPM	19.66 RPM
SRP017611_liver	0.00 RPM	6.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1066 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1066 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007570	1 retrocopy	retro_btau_868,
Canis familiaris	ENSCAFG00000009419	1 retrocopy	retro_cfam_1423,
Equus caballus	ENSECAG00000019146	1 retrocopy	retro_ecab_141,
Oryctolagus cuniculus	ENSOCUG00000006635	1 retrocopy	retro_ocun_1066 ,