RetrogeneDB ID:

retro_rnor_2559

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:8:32792126..32792622(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Akr1d1
Ensembl ID:ENSRNOG00000013004
Aliases:None
Description:3-oxo-5-beta-steroid 4-dehydrogenase [Source:RefSeq peptide;Acc:NP_620239]


Retrocopy-Parental alignment summary:






>retro_rnor_2559
ATTAACCTCAGTGCCGAGAACCACCAAATACCTCTAGAATGCTAGAAACAGCTTTCTAGTCATTGGGCGTGACACCTACT
CAGATCGTAAACCTATTCCTACAGAGGCCTTCTACCTCTGTGAAAGTGGTCATTGACACCAGGTATTGACACCCCAGTAG
GGATGGCTTCCACCACAATGAACATGAAGTTAGTGAGGACATCAGAGAGATGATAGGAGAAGGGAAGGTAAGGAGGGAAG
AGATTTTCTACTGAGTCGAGATGTGAGCTACAAATCATGTCCTGGAGATGGTCTGCCCATTCCTGCAGAGGATATTGGTG
ACCCTCAAGCTAGGTTATAGAGATGTTTACATCAGTGAGATACCCATGGCCTTTCAGCTAGGAAGAAATTTGATCTTGGA
GATGAAAATGACAAATGGTTACATCATGACTTGAATATGTGCAGTACTGACAAAGCCCTGGAAGATTGCAAAGATGTTGG
CTTGGTGAAACTCCTA

ORF - retro_rnor_2559 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.79 %
Parental protein coverage: 50.93 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMNLSTANHHIPL-NDGNSIPIIGLGTYSDPRPVPGKTFI-AVKTAIDEGYRHIDGAYVYRNEHEVGEAIR
.NLS..NH.IPL.N..NS...IG..TYSD..P.P...F...VK..ID..Y.H........NEHEV.E.IR
RetrocopyINLSAENHQIPL>NARNSFLVIGRDTYSDRKPIPTEAFY>SVKVVIDTRY*HPSRDGFHHNEHEVSEDIR
ParentalEKVAEGKVKREEIFYCGKLWSTDHDPEMVRPALERTLQTLKLDYIDLYIIEMPMAFKPG-EEFYPKDENG
E...EGKV.REEIFY......T.H..EMV.P.L.R.L.TLKL.Y.D.YI.E.PMAF..G...F...DEN.
RetrocopyEMIGEGKVRREEIFY*VEM*ATNHVLEMVCPFLQRILVTLKLGYRDVYISEIPMAFQLG<KKFDLGDEND
ParentalRVIYHKSNLCATWEALEACKDAGLVKSL
....H..N.C.T..ALE.CKD.GLVK.L
RetrocopyKWLHHDLNMCSTDKALEDCKDVGLVKLL

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 .00 RPM 0 .22 RPM
SRP017611_kidney 0 .00 RPM 0 .35 RPM
SRP017611_liver 0 .00 RPM 719 .17 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2559 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2559 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2559 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000128721 retrocopy
Homo sapiens ENSG000001227871 retrocopy
Gorilla gorilla ENSGGOG000000146841 retrocopy
Nomascus leucogenys ENSNLEG000000137101 retrocopy
Pongo abelii ENSPPYG000000180371 retrocopy
Pan troglodytes ENSPTRG000000197401 retrocopy
Rattus norvegicus ENSRNOG000000095131 retrocopy
Rattus norvegicus ENSRNOG000000097343 retrocopies
Rattus norvegicus ENSRNOG00000013004 1 retrocopy
retro_rnor_2559 ,
Rattus norvegicus ENSRNOG000000171651 retrocopy
Rattus norvegicus ENSRNOG000000383611 retrocopy



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