RetrogeneDB ID: retro_ocun_365

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:56185905..56186461(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023642
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016174
• Aliases: None
• Description: None

Sequence

>retro_ocun_365
CCTAGGCCTGGCTCAGGAGCCCCTGGAAGCCAGGAGGAAGAGGAGCCATGACTGGGTGATGGTGACCTGGGGGACAGTGC
CATTGAGGACCAGGAGCCAGAAGTGCTCAAAGCCGGAATCAGAGGGATGGAGGAGGAAGTTGAGAAACTGAAGGAGCTAC
AGAACAAGGTAGAGGAGCAGATGAATATGAGTCCCCTGGCAGGCAGCGCTGGCCCAGTGATCACGTCTGCTGAGGAGAAG
TTGGAGGCTGGCGCCTGTTACGTCTATGCTACCAATATGGACGGGGTTGCAACAGAAGAGCTAGAAGCTCGCTTTGATGG
CTGTGATTCAGTCAACCAGGTAACTATAATTGTGACAAGTTCAGTGGCCATCCCAAAGGGTTTGCATATACAGAGTTCTC
AGACACAGACAGTGAGGACTTCCCTGGCCTTACACGAGTCCCTATTTAGTGGAAGACAAATCAAGGTGATTCCAAAATGA
ACCAACAGACCAGGCATCATGATACACAACAGACAGGGGTTTCCTGTGTGCCCGCTCCCAGGCCAGGACCACCAAC

Alignment

ORF - retro_ocun_365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 62.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGPGSGAPGNQEEEEEPGLVEGDPGDSAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGN
          P.PGSGAPG.QEEEE.P.L..GD.GDSAIED.E.E..KA..R.MEEE.EKLKELQN.VE.QMNMSP..G.
Retrocopy PRPGSGAPGSQEEEE-P*LGDGDLGDSAIEDQEPEVLKAGIRGMEEEVEKLKELQNKVEEQMNMSPLAGS

Parental  AGPVIMSIEERMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTIL-CDKFSGHP-KGFAYIEFSDK
          AGPVI.S.EE..EA.A...Y..N.D.G...EELEA.F.GC.SVN.VTI..CDKFSGHP.KG...I..S..
Retrocopy AGPVITSAEEKLEAGACYVYATNMD-GVATEELEARFDGCDSVNQVTII<CDKFSGHP>KGL-HIQSSQT

Parental  ESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDR-GFP-RARYRARTTN
          ..VRTSLAL.ESLF.GRQIKVIPK.TNRPGI....R.GFP..AR..ARTTN
Retrocopy QTVRTSLALHESLFSGRQIKVIPK*TNRPGIMIHNRQGFP>CARSQARTTN

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	0.06 RPM	94.37 RPM
SRP017611_kidney	0.00 RPM	57.77 RPM
SRP017611_liver	0.00 RPM	42.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_365 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_365 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Oryctolagus cuniculus	ENSOCUG00000016174	4 retrocopies	retro_ocun_1185, retro_ocun_1741, retro_ocun_1930, retro_ocun_365 ,