RetrogeneDB ID:

retro_rnor_1915

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:121225812..121226677(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Tra2b
Ensembl ID:ENSRNOG00000001783
Aliases:Tra2b, Sfrs10, Srsf10
Description:Transformer-2 protein homolog beta [Source:UniProtKB/Swiss-Prot;Acc:P62997]


Retrocopy-Parental alignment summary:






>retro_rnor_1915
ATGAGCGACAGCGGCGAGCAGAACTACGGCGAGCGGGAATCCCGTTCTGCTTCCCGAAGTGGAAGTGCCCATGGATCGGG
GAAATCTGCATGGCACACACCTGCAAGGTCTCGCTCCAAGGAAGATTCAAGACGTTCTAGATCAAAGTCAAGATCCAGAT
CTGAATCTAGGGCTAGATCCAGAAGAAGTTCTAGAAGGCATTATACAAGGTCACGATCATGATCTCACTCTCATAGACGA
TCCCGGAGCAAGTCTTACAGCCGAGACTATCGCAGACGCCACAGCCACAGCCATTCTCCCATGTCTACTCGAAGGCGTCA
TGTTGGGAACCGGGCAAATCCTGACCCCAACTGTTGTCTTGGAATGTTTGGATTGAGCTTGTACACCACAGAAAGAGATC
TGAAGAGAAGTGTTCTCTAAGTATGGCCCCATTGCTGATGTGTCTATTGTGTATGACCAGCAGTCTAGACGGTCAAGAGG
ATTTGCCTTTGTATATTTTGAAAATGTAGATGATGCCAAGGAAGCTAAAGAACGTGCCAATGGAATGGAGCTTGATGGAC
GTCGTATTAGGGTCGATTTCTCTATAACAAAAAGGCCCCATACCCCAACACCAGGAATTTATATGGGGAGACCCACTTAT
GGCAGTTCACGACGCCGGGACTATTTTGACCGAGGATATGATCGGGGTTATGATGACCGGGACTATTACAGCAGATCATA
CAGAGGAGGAAGAGGAGGGGGAGGTGGATGGAGAGCAGCTCAAGATAAAGATCAGATTTACAGAAGGCGGTCACCTTCTC
CTTACTACAGTTGTGGAGGATACAGGTCTCATTCTCGATCAAGATCCTACTCACCTCGTCGCTAT

ORF - retro_rnor_1915 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTR
MSDSGEQNYGERESRSASRSGSAHGSGKSA.HTPARSRSKEDSRRSRSKSRSRSESR.RSRRSSRRHYTR
RetrocopyMSDSGEQNYGERESRSASRSGSAHGSGKSAWHTPARSRSKEDSRRSRSKSRSRSESRARSRRSSRRHYTR
ParentalSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDL-REVFS
SRS.S.SHRRSRS.SYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLG.FGLSLYTTERDL.REVFS
RetrocopySRS*SHSHRRSRSKSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGMFGLSLYTTERDL>REVFS
ParentalKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG
KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG
RetrocopyKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG
ParentalRPTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSPSPYYSRGGYRSRSR
RPTYGSSRRRDY.DRGYDRGYDDRDYYSRSYRGG.GGGGGWRAAQD.DQIYRRRSPSPYYS.GGYRS.SR
RetrocopyRPTYGSSRRRDYFDRGYDRGYDDRDYYSRSYRGGRGGGGGWRAAQDKDQIYRRRSPSPYYSCGGYRSHSR
ParentalSRSYSPRRY
SRSYSPRRY
RetrocopySRSYSPRRY

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 .14 RPM 40 .55 RPM
SRP017611_kidney 0 .14 RPM 47 .24 RPM
SRP017611_liver 0 .00 RPM 34 .02 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1915 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1915 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1915 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000016972 retrocopies
Canis familiaris ENSCAFG000000133452 retrocopies
Cavia porcellus ENSCPOG000000063131 retrocopy
Microcebus murinus ENSMICG000000106113 retrocopies
Myotis lucifugus ENSMLUG000000057812 retrocopies
Mustela putorius furoENSMPUG000000031571 retrocopy
Mus musculus ENSMUSG000000228586 retrocopies
Ochotona princeps ENSOPRG000000079902 retrocopies
Rattus norvegicus ENSRNOG000000008661 retrocopy
Rattus norvegicus ENSRNOG00000001783 4 retrocopies
Sarcophilus harrisii ENSSHAG000000024372 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000067202 retrocopies
Tupaia belangeri ENSTBEG000000159271 retrocopy
Tarsius syrichta ENSTSYG000000003881 retrocopy



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