RetrogeneDB ID:

retro_ptro_2868

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:4844941..4845548(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS5
Ensembl ID:ENSPTRG00000011591
Aliases:None
Description:ribosomal protein S5 [Source:HGNC Symbol;Acc:10426]


Retrocopy-Parental alignment summary:






>retro_ptro_2868
ATGACCAAGTGGGAGACAGCAGCACCAGAGATGGTAGAAACCCCCAACATCCAGCTCTTTGGGAGGTGGAGCACCGATGA
TGTGCAGATCAATGACATTTCCCTGAAGGATTACATTGCAGTGGAGGAGAAGTATACCAAGTACCTGCTTCACAGTGCAG
GGTGGTATGCCCTCCAAGCATTTCCACAAAACACAGTGCCCCATCTTGGAGCACCTCACTAACTCCATGATGATGCATGG
CCACAATAATGGCAAGAAACCCATGACCATGCACATTGTCAAGCATGCTTTTGAGATCGTCCACCTGCTCACGAATGAGA
ACACTCTTCGAGTCCTGGTGAATGCCGTCATCAACAGTGGTCCCTGGGAGGACTCTACATGCATTGGGTGAGCCAAGACC
ATGAGATGACAGGCTGTGGATGTGTACCCACTGCATGGCATGAATCAGGCCATCTGGCTGCTGTGCAGAGGCACTTGTGA
GGCTTTCTTCCAGAACATCAAGACCATTGCTGAGTGCCTGGAAGATGAGCTCATCAATGCCACCAGGGGCTCCTCCAACT
CCTATGTCATCAAGAAGGATGAGCTAGAGCATGTGGCCAAGTCCAAC

ORF - retro_ptro_2868 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.98 %
Parental protein coverage: 99.51 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYA-AKRFRKAQCPIV
MT.WETAAP...ETP.I.LFG.WSTDDVQINDISL.DYIAV.EKY.KYL.HSAG.YA..K.F.K.QCPI.
RetrocopyMTKWETAAPEMVETPNIQLFGRWSTDDVQINDISLKDYIAVEEKYTKYLLHSAGWYA>SKHFHKTQCPIL
ParentalERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAV
E.LTNSMMMHG.NNGKK.MT..IVKHAFEI.HLLT.EN.L.VLVNA.INSGP.EDST.IG.A.T.R.QAV
RetrocopyEHLTNSMMMHGHNNGKKPMTMHIVKHAFEIVHLLTNENTLRVLVNAVINSGPWEDSTCIG*AKTMR*QAV
ParentalDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDELERVAKSN
DV.PL...NQAIWLLC.G..EA.F.NIKTIAECL.DELINA..GSSNSY.I.KKDELE.VAKSN
RetrocopyDVYPLHGMNQAIWLLCRGTCEAFFQNIKTIAECLEDELINATRGSSNSYVI-KKDELEHVAKSN

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 140 .24 RPM
SRP007412_cerebellum 0 .04 RPM 130 .70 RPM
SRP007412_heart 0 .00 RPM 66 .74 RPM
SRP007412_kidney 0 .05 RPM 286 .75 RPM
SRP007412_liver 0 .00 RPM 233 .10 RPM
SRP007412_testis 0 .00 RPM 37 .83 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2868 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2868 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2868 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000023661 retrocopy
Callithrix jacchus ENSCJAG000000003046 retrocopies
Echinops telfairi ENSETEG000000135431 retrocopy
Homo sapiens ENSG000000838455 retrocopies
Gorilla gorilla ENSGGOG000000042584 retrocopies
Macropus eugenii ENSMEUG000000154003 retrocopies
Myotis lucifugus ENSMLUG000000126411 retrocopy
Macaca mulatta ENSMMUG000000087293 retrocopies
Mustela putorius furoENSMPUG000000083081 retrocopy
Ornithorhynchus anatinus ENSOANG000000119211 retrocopy
Otolemur garnettii ENSOGAG000000130882 retrocopies
Procavia capensis ENSPCAG000000110342 retrocopies
Pongo abelii ENSPPYG000000105007 retrocopies
Pan troglodytes ENSPTRG00000011591 6 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000059351 retrocopy
Tupaia belangeri ENSTBEG000000169552 retrocopies
Tarsius syrichta ENSTSYG000000000762 retrocopies
Tursiops truncatus ENSTTRG000000019911 retrocopy



Copyright © RetrogeneDB 2014-2017