RetrogeneDB ID:

retro_ptro_3018

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:GL391828.1:2638..3220(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSU72
Ensembl ID:ENSPTRG00000000034
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_3018
ATGCTCTCCTCCACACTCAGGGTGGCTGTGGTGTGCGTGAGCAATGTCAACAGGAGCATGGAGGCCCACAGCATCCTCAG
GAGAAAAGGGCTAAGTGTCCGGTCTTTTGGAACTGAATCTCATGTGAGGCTACCAGGACCAAGACCCGATCGTCCTGTAG
TTTATGATTTTGCAACAACATATAAGGAGATGTACAATGACCTCCTCAGGAATGATAGAGAATGCTACACCCGCAACGGA
ATCTTACACATCTTGGGAAGAAATGAGAGAATCAAGCCCGGTCCAGAAAGGTTTCAGGACTGCACTGATTTCTTTGATGT
CATCTTCACCTGTGAGGAGAGGGTCTATGACACAGTGGTGGAAGATCTGTGTTCCAGAGAACAGCAGACCTTTCAGCCTG
TGCACGTGATCAACATGGACATCCAAGATACCCTGGAAGATGCCACCCTGGGAGCTTTCCTCATCTCTGAGATTTGCCAG
TGCCTGCAGCAGTCAGACGACATGGAAGACAATCTGGAGGAGCTGCTGTTGCAAATGGAGGAGAAGGCAGGAAAAAGCTT
TCTTCACACCGTCTGCTTCTAC

ORF - retro_ptro_3018 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.13 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPSSPLRVAVVCSSNQNRSMEAHNILSKRGFSVRSFGTGTHVKLPGPAPDKPNVYDFKTTYDQMYNDLLR
M.SS.LRVAVVC.SN.NRSMEAH.IL...G.SVRSFGT..HV.LPGP.PD.P.VYDF.TTY..MYNDLLR
RetrocopyMLSSTLRVAVVCVSNVNRSMEAHSILRRKGLSVRSFGTESHVRLPGPRPDRPVVYDFATTYKEMYNDLLR
ParentalKDKELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVVNVD
.D.E.YT.NGILH.L.RN.RIKP.PERFQ.C.D.FD.I.TCEERVYD.VVEDL.SREQ.T.QPVHV.N.D
RetrocopyNDRECYTRNGILHILGRNERIKPGPERFQDCTDFFDVIFTCEERVYDTVVEDLCSREQQTFQPVHVINMD
ParentalIQDNHEEATLGAFLICELCQCIQHTEDMENEIDELLQEFEEKSGRTFLHTVCFY
IQD..E.ATLGAFLI.E.CQC.Q...DME....ELL...EEK.G..FLHTVCFY
RetrocopyIQDTLEDATLGAFLISEICQCLQQSDDMEDNLEELLLQMEEKAGKSFLHTVCFY

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 79 .99 RPM
SRP007412_cerebellum 0 .00 RPM 89 .69 RPM
SRP007412_heart 0 .00 RPM 50 .83 RPM
SRP007412_kidney 0 .00 RPM 102 .20 RPM
SRP007412_liver 0 .00 RPM 70 .61 RPM
SRP007412_testis 0 .00 RPM 34 .46 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3018 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3018 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3018 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
Canis familiaris ENSCAFG000000192542 retrocopies
Callithrix jacchus ENSCJAG000000109573 retrocopies
Cavia porcellus ENSCPOG000000022382 retrocopies
Homo sapiens ENSG000001600758 retrocopies
Gorilla gorilla ENSGGOG000000044211 retrocopy
Loxodonta africana ENSLAFG000000020764 retrocopies
Macropus eugenii ENSMEUG000000151701 retrocopy
Myotis lucifugus ENSMLUG000000165172 retrocopies
Macaca mulatta ENSMMUG000000015511 retrocopy
Monodelphis domestica ENSMODG000000066163 retrocopies
Mustela putorius furoENSMPUG000000143942 retrocopies
Mus musculus ENSMUSG000000290381 retrocopy
Otolemur garnettii ENSOGAG000000244302 retrocopies
Pongo abelii ENSPPYG000000020001 retrocopy
Pan troglodytes ENSPTRG00000000034 16 retrocopies
Pteropus vampyrus ENSPVAG000000176954 retrocopies
Rattus norvegicus ENSRNOG000000178292 retrocopies
Sus scrofa ENSSSCG000000033482 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
Tursiops truncatus ENSTTRG000000170512 retrocopies



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