RetrogeneDB ID:

retro_rnor_1856

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:179707010..179707560(+)
Located in intron of:ENSRNOG00000028708
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl17
Ensembl ID:ENSRNOG00000018680
Aliases:Rpl17, ASI, rpL23
Description:60S ribosomal protein L17 [Source:UniProtKB/Swiss-Prot;Acc:P24049]


Retrocopy-Parental alignment summary:






>retro_rnor_1856
ATGGTTTGCTACCCTCTTGGCCCAGAAAACCCCACAAAACCATGCAAGTCAAGAAGTTCAAACCTTTGTGTTCACTTGAA
GAACACCCAGGAAACTGCCCAGGCCGTTAAGGGCATGCATATCCGCAAAGCCACCAAGTATCTGAAGGATGTCATTTTAA
AGAAGCAATATATGCATTCTGGCGGCATAATGGTGGTGTTGGTAGGTGTACCCGGGCCAAACAGTGGGGCTGGACACAGG
AACGGTGGCCAAAAAAGAGTGCTGAATTTTTGCTACACATGCTTAAAAATGCAGAGAGTAATGCTGAACTTAAGTGTTTA
GACGTAGATTTTCCAGTTATTGAACACATCCAGGTGAACCAGGTACCTAAGAGGCACCGACGAACCTACAGAGCTTGTGG
CCAGATTAACCCATCCATGAGCTTCCCCTGATCATTGAGATGATCCTCACTGAGAAGGAACAGATTGTTCCAAAGCCAGA
AGAAGAGGTTGCACAGAAGAAAAAGATATCCCAGAAGAAACTGAAGATACAAAAACTCATGGCAGGGGAA

ORF - retro_rnor_1856 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCV-PFRRYNGGVGR
MV.Y.L.PENPTK.CKSR.SNL.VH.KNT.ETAQA.KGMHIRKATKYLKDV.LKKQ....F.R.NGGVGR
RetrocopyMVCYPLGPENPTKPCKSRSSNLCVHLKNTQETAQAVKGMHIRKATKYLKDVILKKQYM<AFWRHNGGVGR
ParentalCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPY
C..AKQWGWTQ.RWPKKSAEFLLHMLKNAESNAELK.LDVD..VIEHIQVN..PK..RRTYRA.G.INP.
RetrocopyCTRAKQWGWTQERWPKKSAEFLLHMLKNAESNAELKCLDVDFPVIEHIQVNQVPKRHRRTYRACGQINPS
ParentalMS-SPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
MS..P..IEMILTEKEQIVPKPEEEVAQKKKISQKKLK.QKLMA.E
RetrocopyMS<LPLIIEMILTEKEQIVPKPEEEVAQKKKISQKKLKIQKLMAGE

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 93 .82 RPM
SRP017611_kidney 0 .00 RPM 127 .21 RPM
SRP017611_liver 0 .00 RPM 76 .72 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1856 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1856 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1856 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 443 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000229025 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Monodelphis domestica ENSMODG0000000353411 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Rattus norvegicus ENSRNOG00000018680 48 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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