RetrogeneDB ID: retro_ocun_666

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:110618516..110619102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023216
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSOCUG00000008444
• Aliases: None
• Description: ubiquitin family domain containing 1 [Source:HGNC Symbol;Acc:30565]

Sequence

>retro_ocun_666
GGGACTCCTGCACCGGCCCCAGCCCAGGCCCCCTGAGGACCCTACAGCCCAGGCTTCAGTCAGCAATGGCGAGGACACAG
GCTGCGGCTTGGGCAAGGAGCTGGAGGACCTGTGGATCATCTGGAACAAGATGGAGCAAGATGTGAAGTTCCCACTGGAC
AGCGTAGGCTCTGAGCTGGAACAGAAGATCCACTTGAATCCAGGTCTCCCACCTACCATGCAGAAAGTCATGCATACGGG
GGTTGTTCCTAAGGATGAGACATTGAGAGAAATAAAAGTGACCAGTGGAGCCAAGATCATGGTGATCTGTTCCCGATAAA
GGATGTTTTAACGGGAAACACACCCAAAGACGCTGTGCAGCAAGACGGAGAACAAAAGGAGCCTCTGTGTAGGCTCAATC
AATACAGGAAAGTCTTGGATAAAGGAAATCCCAAAGATATGACCCATCTGTTAGGGGTGCTCGGGAGCTCCTGCCACAGT
CCCTTTGTCCAGCTTGTACAGTAAGTCCCCAGGAAAACTGAGACTCGCCTATAAGCTGGACCAAGGCCAGCTACAGATCA
GCAGCAGAGAGCGGACTGAGAAATTG

Alignment

ORF - retro_ocun_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 64.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSLQPAPAQ-PPGDPAAQASVSNGEDAGGGAGQELVDLKIIWNKTKHDVKFPLDSTGSELKQKIHSITGL
          G...PAPAQ.PP.DP.AQASVSNGED.G.G.G.EL.DL.IIWNK...DVKFPLDS.GSEL.QKIH...GL
Retrocopy GTPAPAPAQ>PPEDPTAQASVSNGEDTGCGLGKELEDLWIIWNKMEQDVKFPLDSVGSELEQKIHLNPGL

Parental  PPAMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGS-TINDVLAVNTPKDAAQQDAKAEENKKEPLCRQKQ
          PP.MQKVM..G.VP.D.TLREIKVTSGAKIMV..S..I.DVL..NTPKDA.QQD.......KEPLCR..Q
Retrocopy PPTMQKVMHTGVVPKDETLREIKVTSGAKIMVICS<PIKDVLTGNTPKDAVQQDGE----QKEPLCRLNQ

Parental  HRKVLDKGKPEDVM-PSVKGAQERLP-TVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKL
          .RKVLDKG.P.D...PSV.GA.E.LP.TVPLS..Y.KS.GK.RL..KL.Q.QL.I...ERTEKL
Retrocopy YRKVLDKGNPKDMT<PSVRGARELLP<TVPLSSLYSKSPGKLRLAYKLDQGQLQISSRERTEKL

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	50.06 RPM
SRP017611_kidney	0.00 RPM	44.19 RPM
SRP017611_liver	0.00 RPM	24.66 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_666 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_666 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,
Oryctolagus cuniculus	ENSOCUG00000008444	1 retrocopy	retro_ocun_666 ,