RetrogeneDB ID:

retro_ptro_1555

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2A:95088749..95089135(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS24
Ensembl ID:ENSPTRG00000002666
Aliases:None
Description:ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]


Retrocopy-Parental alignment summary:






>retro_ptro_1555
CTAACTATCCACGCTAGAAAGTTCACGACCAACAGACTACTTCCGAGGAAACAAATGCTCACTGATGTCCTTCACCTCGG
GAAGGCAACAGTGCCTAAGACAGAAATTCGGGAAAAACTAGCCAAAATGTACAAGACCACACCAGATGTCATCTCTGTAT
TTGGATTCAGAACTAATTTTGGTGGTAGCAAGACAACTGGCTTTGGCAGGATTTACAATTCTCTGGATTATGCAAAGAAA
AACGAACCCAAACACAGACTTGCAAGACATAGCCTCTATGAGAAGAAAAAAACCTCAAGAAGGCAATAAAAGGGAACACC
AAGAACAGAATGAAGAAAGTCAGGAGAACTGCAAAGGCTAGTGTTGGTGCTGGCAAAAAGCTGAAG

ORF - retro_ptro_1555 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 96.97 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGM
.TI..RKF.TNRLL.RKQM..DVLH.GKATVPKTEIREKLAKMYKTTPDVI.VFGFRT.FGG.KTTGFG.
RetrocopyLTIHARKFTTNRLLPRKQMLTDVLHLGKATVPKTEIREKLAKMYKTTPDVISVFGFRTNFGGSKTTGFGR
ParentalIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQ-RKERKNR-MKKVRGTAKANVGAGKKQK
IY.SLDYAKKNEPKHRLARH.LYEKKKTSR.Q...E.....MKKVR.TAKA.VGAGKK.K
RetrocopyIYNSLDYAKKNEPKHRLARHSLYEKKKTSRRQ>KREHQEQ>MKKVRRTAKASVGAGKKLK

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 165 .41 RPM
SRP007412_cerebellum 0 .00 RPM 121 .81 RPM
SRP007412_heart 0 .06 RPM 107 .14 RPM
SRP007412_kidney 0 .00 RPM 169 .33 RPM
SRP007412_liver 0 .07 RPM 135 .09 RPM
SRP007412_testis 0 .00 RPM 76 .82 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1555 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1555 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1555 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000132649 retrocopies
Felis catus ENSFCAG000000008493 retrocopies
Homo sapiens ENSG000001383263 retrocopies
Gadus morhua ENSGMOG000000125951 retrocopy
Loxodonta africana ENSLAFG0000002787810 retrocopies
Myotis lucifugus ENSMLUG000000241021 retrocopy
Mustela putorius furoENSMPUG000000037781 retrocopy
Oryctolagus cuniculus ENSOCUG000000124721 retrocopy
Otolemur garnettii ENSOGAG000000110053 retrocopies
Pan troglodytes ENSPTRG00000002666 10 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000130004 retrocopies



Copyright © RetrogeneDB 2014-2017