RetrogeneDB ID: retro_ocun_694

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:45736879..45737515(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027334
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A46
• Ensembl ID: ENSOCUG00000012366
• Aliases: None
• Description: solute carrier family 25, member 46 [Source:HGNC Symbol;Acc:25198]

Sequence

>retro_ocun_694
ATGGATTCGAGGCACCCGGATGGATTCGGTGGCTTGGGCTACTGCGCAGGGCCCGGGAGGAGTAGGGCTTTAGCGGGCAC
TTTGCCTTCAAGGTCTTTCAGCTCCAGCCCGGACCTGGGCCACTGGGTGATGCTTGCCCCAGACAGCCGGGCAGCCAGCC
TGCACTGGGACGAGAAGGGTCCGCGGCTCGCTGTGCCCTCCTCCTCCACACCGCACAAAGGCCCCGCAAGGAGCCTTTTC
CTGGCAGGGGCGGCGGTGGCTTTAGGGGCAGAGCAGTTGAATGCACTCGCTGGATTTGGTATTGGACTTGCAAGTCTTTT
TACAGACAATGCATTGGCCCTTCCTTGCAATGTCCTACGCCATCAATGTCAGGTTTATTACCATGACCGGCCTTATCATT
TCATTCCATTTACAGGCATCAGTATTATGTACAGCTTCAACAAAACTCAGGGACCAAGAGCCCTGTGGAAAGTAATGGGG
AGTACGTTTATTGTCCAAGGAGTCACACTTGGGGCAGAAGGCATAATTAGTGAATTCACATCTTTGCGAAGGGAGGTTTC
ACACAAATGGAATCCTGGACAAATAGAACACCGTCTATTGAAATCCCTAACTAATTTAGTAGTGATACCTTTTTAT

Alignment

ORF - retro_ocun_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 51.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MHPRRPDGFDGLGYRGG-ARDEQGFGGAF-PARSFSSGSDLGHWVTTPPDIPGSRNLHWGEKSPPFGVPS
          M..R.PDGF.GLGY..G.AR.E.GF.G.F.P.RSFSS..DLGHWV...PD......LHW.EK.P...VPS
Retrocopy MDSRHPDGFGGLGYCAG<AREE*GFSGHF>PSRSFSSSPDLGHWVMLAPDSRAA-SLHWDEKGPRLAVPS

Parental  ASTPHEVPAEEPFPGTGGGGVQGQSSEQLNRFAGFGIGLASLFTENVLAHPCIVLRRQCQVNYHARHYHL
          .STPH..PA...F.....G.......EQLN..AGFGIGLASLFT.N.LA.PC.VLR.QCQV.YH.R.YH.
Retrocopy SSTPHKGPARSLFLA---GAAVALGAEQLNALAGFGIGLASLFTDNALALPCNVLRHQCQVYYHDRPYHF

Parental  TPFTVINIMYSFNKTQGPRALWKGMGSTFIVQGVTLGAEGIISEFTPLPREVSHKWSPKQIGEHLLLKSL
          .PFT.I.IMYSFNKTQGPRALWK.MGSTFIVQGVTLGAEGIISEFT.L.REVSHKW.P.QI.EH.LLKSL
Retrocopy IPFTGISIMYSFNKTQGPRALWKVMGSTFIVQGVTLGAEGIISEFTSLRREVSHKWNPGQI-EHRLLKSL

Parental  TYIIAMPFY
          T.....PFY
Retrocopy TNLVVIPFY

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	120.64 RPM
SRP017611_kidney	0.00 RPM	48.55 RPM
SRP017611_liver	0.00 RPM	34.99 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_694 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012366	1 retrocopy	retro_ocun_694 ,
Sorex araneus	ENSSARG00000001814	1 retrocopy	retro_sara_341,