RetrogeneDB ID: retro_ocun_1094

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:47943934..47944730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPM1B
• Ensembl ID: ENSOCUG00000005461
• Aliases: None
• Description: protein phosphatase, Mg2+/Mn2+ dependent, 1B [Source:HGNC Symbol;Acc:9276]

Sequence

>retro_ocun_1094
TTGAGACTTGATGGCTTTGTGACTAACTTTTCAGACCTCAGAAATGGGATGGACAGGAGTGGTTCTACTGCATGGGAGTT
ATGGTTTCACCTAAGCATGTCTGTTTTAACTGCGGTGATTCATGTGCCATTCTCTATAGAAACAGACATGTCTGTTTTCC
TACCCAGGATCACAAACCCTGCAATCCAAAGGAAAAGGAGCGAATTCAAAATGCAGGAGGCAGCGTCATGATACAAAGTG
TTAATGGTTCATTAGCAGTGTCTGGCGCTCTGGGGGACTGTGATTAAAAGTACGCTGAAGGCAAGGGCCCAACAGAACAA
CTTGTTGCTCCAAAGCTTGAGGTTTATGAAATTTTAAGGGCATAAGAAGATGAATTTATCATCTTGGCTTGTGATGGGAT
CTAGATTGTTATGAATAATGAGGAGCTCTGTGAATCTATGAAGTCTAGGCTTGAGGTATCTGACCACCTGGAAAACGTGT
CCAATTGAGTAGTGGACACTTGTTTACATGAGGGAAGTCTAGTACCATGAGTATTGTACTAGTTTGCTTTTCAAATGCCC
CCAAAGTCTCAGATGAAGCAATGAAGAAAGATTCAGAATTGGATAAACACCTGGAGTGAAGAAATTACGGAGAAATTTGG
TGAGGAAGGAAGGCCTGATCTTGCCCATGTCACAGCATCTTGCCTGCAAAAAATATCCCAAATTTGTCTGCTGGGGGAAG
TCTCGCTGGCAAGCACAATGTGATTGAACCTGTTTACAGTAGACTGAATCCACACAGAGAAAGCAATGGGGGTGCT

Alignment

ORF - retro_ocun_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.8 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKIDEYMRNFSDLRNGMDRSGSTA-VGVMISPKHVYFINCGDSRAVLYRNGQVCFSTQDHKPCNPREKER
          L..D....NFSDLRNGMDRSGSTA..GVM.SPKHV.F.NCGDS.A.LYRN..VCF.TQDHKPCNP.EKER
Retrocopy LRLDGFVTNFSDLRNGMDRSGSTA<MGVMVSPKHVCF-NCGDSCAILYRNRHVCFPTQDHKPCNPKEKER

Parental  IQNAGGSVMIQRVNGSLAVSRALGDYDYKCVDGKGPTEQLVSPEPEVYEILRAEEDEFIILACDGIWDVM
          IQNAGGSVMIQ.VNGSLAVS.ALGD.D.K...GKGPTEQLV.P..EVYEILRA.EDEFIILACDGI..VM
Retrocopy IQNAGGSVMIQSVNGSLAVSGALGDCD*KYAEGKGPTEQLVAPKLEVYEILRA*EDEFIILACDGI*IVM

Parental  SNEELCEFVKSRLEVSDDLENVCNWVVDTCLHKGS-RDNMSIVLVC-FSNAPKVSDEAVKKDLELDKHLE
          .NEELCE..KSRLEVSD.LENV.N.VVDTCLH.GS....MSIVLVC.F...PK......K..........
Retrocopy NNEELCESMKSRLEVSDHLENVSN*VVDTCLHEGS<SSTMSIVLVC>FQMPPK---SQMKQ*RKIQNWIN

Parental  SRVEEIMEKSGEEGMPDLAHVMR-ILSAENIPNLPPGGGLAGKRNVIEAVYSRLNPHRESDGAS
          ...EEI.EK.GEEG.PDLAHV...IL.A.NIPNL..GG.LAGK.NVIE.VYSRLNPHRES.G..
Retrocopy TWSEEITEKFGEEGRPDLAHVTA<ILPAKNIPNLSAGGSLAGKHNVIEPVYSRLNPHRESNGGA

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	68.32 RPM
SRP017611_kidney	0.00 RPM	32.84 RPM
SRP017611_liver	0.00 RPM	22.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1094 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1094 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
Mus musculus	ENSMUSG00000061130	1 retrocopy	retro_mmus_468,
Oryctolagus cuniculus	ENSOCUG00000005461	1 retrocopy	retro_ocun_1094 ,
Drosophila melanogaster	FBgn0035425	1 retrocopy	retro_dmel_64,
Drosophila melanogaster	FBgn0086361	1 retrocopy	retro_dmel_66,