RetrogeneDB ID: retro_ocun_1012

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:47167570..47168571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP46
• Ensembl ID: ENSOCUG00000017031
• Aliases: None
• Description: ubiquitin specific peptidase 46 [Source:HGNC Symbol;Acc:20075]

Sequence

>retro_ocun_1012
GGCACCAATGCCTTGGCATTCGAGAAAGAGAATGGCCCAGAACAGTTTCCCATCAACAAGCACTATTTTGAATTAGTCAA
TTTTGGGAATACCAACTACTATAATTCAGTTCTTCAAGAACTTTATTTCTGTTGTTCATTCCGGGAAGAAGTTCTAGCAT
ACAAGAGTCAGCTTAGAGAGGAGAGCTTTCTCAGGTACTTAGAGGACCTCGTCCATAGCATCACGACTCAAGAAAATGGT
AGGAGTTATCCCTTCAAAGTTCATAGCAATATTATGAAGGGGGGAAATGAGCTTTTTGACAACTACAAGTAACAAGATGC
CCATGAATTCTTAAATTGCCCACTAAATACAATTGCTGGTATTTTACAAGAAGAGAGAAAGCAGGATAAACAAAATGGTC
ACTTAATTGATGGAAATATTGACAGTGAAAATAACAACAGCACACCAGATCCAACAGAGGGTTAATGAGATTTTCAGGGA
ACATTAACTAATGAAACCAGATGTCTTACTCATATAAGCTAAGATGAAGATTTTTTAGAACTTTCTGTTGAGGTAGAACA
GAACACATTAATTACACGCTGCTTAAGGGGTTTTGGCAACACAGAAACCCTGTGCAGAAAATACATATAGTACTGTGAAG
AGTGTCACAGCAAGCAGGAAGCACACAAATGCATGAAAGTTAGAAAACTGCCCGTGATTCTAACTCTACACCTGAAGAGA
TTTAAATACATAGATCAAGTTCATCGATATGTAAAACTTTCTTATCAGGTAGTTTTTTCCTTTAGAACTTCATCTGTTTA
ACACATGAGGTTACGCAAACAATCTTGACAGGATATACGATCTTGTTGCTGTTATAGCTCACCCTGGAAGTGGTCCCAAT
CGAGGCCATTATGTTGCAATAGTCGAGTCATGATTTTTGGTTGATGATGACATTGTAGAAAAAAATAGATGTACAAGCTA
TTGAAGAATTCTATGGGTTGACATCAGATATCTCATAGAAC

Alignment

ORF - retro_ocun_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 80.81 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQALYFCRPFRENVLAYKAQQKKKENLLTCLAD
          GTNA.A.EK..GPEQFPIN.HYF.LVNFGNT.Y.NSVLQ.LYFC..FRE.VLAYK..Q...E..L..L.D
Retrocopy GTNALAFEKENGPEQFPINKHYFELVNFGNTNYYNSVLQELYFCCSFREEVLAYKS-QLREESFLRYLED

Parental  LFHSIATQKKKVGVIPPKKFISRLRK-ENDLFDNYMQQDAHEFLNYLLNTIADILQEEKKQEKQNGKLKN
          L.HSI.TQ....G...P.K..S...K..N.LFDNY..QDAHEFLN..LNTIA.ILQEE.KQ.KQNG.L..
Retrocopy LVHSITTQEN--GRSYPFKVHSNIMKGGNELFDNYK*QDAHEFLNCPLNTIAGILQEERKQDKQNGHLID

Parental  GNMNEPAENNKAELTWVHEIFQGTLTNETRCLNCETVSSKDEDFLDLSVDVEQNTSITHCLRDFSNTETL
          GN......N.....T.....FQGTLTNETRCL...T..S.DEDFL.LSV.VEQNT.IT.CLR.F.NTETL
Retrocopy GNIDSENNNSTPDPTEG**DFQGTLTNETRCL---THIS*DEDFLELSVEVEQNTLITRCLRGFGNTETL

Parental  CSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLKRFKYMEQLHRYTKLSYRVV-FPLELRLFNTSSDAV
          C.....YCE.C.SKQEA.K.M.V.KLP.IL.LHLKRFKY..Q.HRY.KLSY.VV.FPLEL.LFNT...A.
Retrocopy CRKYI*YCEECHSKQEAHKCMKVRKLPVILTLHLKRFKYIDQVHRYVKLSYQVV>FPLELHLFNT*GYAN

Parental  NLDRMYDLVAVVVHCGSGPNRGHYITIVKSHGFWLLFDDDIVE-KIDAQAIEEFYGLTSDISKN
          NLDR.YDLVAV..H.GSGPNRGHY..IV.S....L..DD.IVE.KID.QAIEEFYGLTSDIS.N
Retrocopy NLDRIYDLVAVIAHPGSGPNRGHYVAIVES--*FLVDDD-IVE>KIDVQAIEEFYGLTSDIS*N

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	182.51 RPM
SRP017611_kidney	0.00 RPM	55.95 RPM
SRP017611_liver	0.00 RPM	12.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1012 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1012 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
Mus musculus	ENSMUSG00000054814	1 retrocopy	retro_mmus_2479,
Oryctolagus cuniculus	ENSOCUG00000017031	1 retrocopy	retro_ocun_1012 ,