RetrogeneDB ID:

retro_ocun_1017

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:19:16589446..16589842(-)
Located in intron of:ENSOCUG00000000075
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PBDC1
Ensembl ID:ENSOCUG00000001088
Aliases:None
Description:polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]


Retrocopy-Parental alignment summary:






>retro_ocun_1017
AAAAAATTTGAGAAACTCAAGGTAGAAGTATTGGACCCAGAACAACTCAAGTCAGAACCGGCAGAAGAGAAGTAGAGACC
ATTCTCCTTGAAGTTGGAAGGGATTGTGGAAGACTTGACTATGGTCCTTTGCTGCAACTAGATCGTTCTCAGGGTTACAC
TGAGGAAAACACCATGTTTGCCCCCAGAATAGTTTTTGGCTACTGAAGTCGCTCAGAACCAGGAAGGTTGTAACAAGGAA
GTTTAGTTGGTGTTCAGCACAGAGAATGAGAGAAAGCAGGGGTCAGTGGAGGACAGCAAGAGAAAGCCGAGAGACAAAGG
AGAGAAAGGAGCCAACAGTGGAGGAGAAGTGGAGGGAGCTGCTGGAGAAGGAGAAAGAGAAAGAAGCGACAAAGAA

ORF - retro_ocun_1017 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.31 %
Parental protein coverage: 60.63 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalKIFEKLKIDVLDPEELKSESAKETWRPFCLKFEGIVED-FNYGTLLRLDCSQGYTEENTIFAPRI-QFLA
K.FEKLK..VLDPE.LKSE.A.E..RPF.LK.EGIVED...YG.LL.LD.SQGYTEENT.FAPRI..F..
RetrocopyKKFEKLKVEVLDPEQLKSEPAEEK*RPFSLKLEGIVED<LDYGPLLQLDRSQGYTEENTMFAPRI<SFWL
ParentalIEIARNRE-GYNKAV-YVGAQHKEGERAGVSGAEQE-KPEKKEEEGANSGGKKEEGVAGEGEKEEKAKE
....R.R..G.NK.V..VG.QH.E.E.AGVSG..QE.KP..K.E.GANSGG...EG.AGEGE.E...KE
RetrocopyLKSLRTRK<GCNKEV<LVGVQHRE*EKAGVSGGQQE>KPRDKGEKGANSGG-EVEGAAGEGERERSDKE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .77 RPM 6 .46 RPM
SRP017611_kidney 0 .30 RPM 4 .16 RPM
SRP017611_liver 0 .31 RPM 2 .24 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1017 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1017 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1017 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000172282 retrocopies
Callithrix jacchus ENSCJAG000000185711 retrocopy
Equus caballus ENSECAG000000098821 retrocopy
Erinaceus europaeus ENSEEUG000000011161 retrocopy
Monodelphis domestica ENSMODG000000096852 retrocopies
Mus musculus ENSMUSG000000312261 retrocopy
Oryctolagus cuniculus ENSOCUG00000001088 3 retrocopies
retro_ocun_1017 , retro_ocun_1402, retro_ocun_595,
Otolemur garnettii ENSOGAG000000152051 retrocopy
Rattus norvegicus ENSRNOG000000026623 retrocopies
Sarcophilus harrisii ENSSHAG000000178721 retrocopy
Tupaia belangeri ENSTBEG000000034113 retrocopies



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