RetrogeneDB ID:

retro_ptro_3185

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:12784331..12784850(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL35
Ensembl ID:ENSPTRG00000012152
Aliases:None
Description:mitochondrial ribosomal protein L35 [Source:HGNC Symbol;Acc:14489]


Retrocopy-Parental alignment summary:






>retro_ptro_3185
ATGGCGGCTTCTGCCTTTGTTGGTGCGATGAGGAGCAGCTTCAGGAATCTATGGCTCCTGAATATTTTTGCATCTCCAGC
CCACCGAAACTGTGCCAGGAATGCCTCTCTTATTTCTGCATTGTCTACTGGACGTTTTAGTCATATTCGGACACCATTTG
TTTCCTCCACTCCCAGGCTGATCACATCTGTCAGAAACCTGACATGTGGGCATACTGCAGTGATCCCCAACAGAGTGGCC
CCCTTGCTTCCAAGTGTCCTGAAGCTGCCAGTCAGAACTGTAATATACGTCAGTACACAAAAAGGCAAGAGAAAAACTGT
GAAAGCTGTTATCTATAGGTTTTTTCGACTTCATTCTGGCCTTTGGGTGAGGAGAAAGGCTGGTTATAAGAAAAAATTCT
GGAAAAAGACACCTGCAAGAAAAAAGCAATTGAGGGAATTTGTGTTCTGCGATAAAACCCAGAGTAAACTCTTAGATAAA
ATGACAGTGTCCTTCTGGAAGAGGTGAAACTTGTATGCT

ORF - retro_ptro_3185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.88 %
Parental protein coverage: 97.74 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRLTTSERNLTCG
MAASAF.GA.R.....L..LNI.AS...RNC..NASLISALSTGRFSHI.TP.VSSTPRL.TS.RNLTCG
RetrocopyMAASAFVGAMRSSFRNLWLLNIFASPAHRNCARNASLISALSTGRFSHIRTPFVSSTPRLITSVRNLTCG
ParentalHTSAILNRVAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCGLWVRRKAGYKKKLWKKTPAR
HT..I.NRVAP.LPSVLKLPVR...Y.S..KGKRKTVKAVI.RF.RLH.GLWVRRKAGYKKK.WKKTPAR
RetrocopyHTAVIPNRVAPLLPSVLKLPVRTVIYVSTQKGKRKTVKAVIYRFFRLHSGLWVRRKAGYKKKFWKKTPAR
ParentalKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWHS
KK.LREFVFC.KTQSKLLDKMT.SFWKR.N...
RetrocopyKKQLREFVFCDKTQSKLLDKMTVSFWKR*NLYA

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 7 .44 RPM
SRP007412_cerebellum 0 .00 RPM 5 .56 RPM
SRP007412_heart 0 .00 RPM 16 .03 RPM
SRP007412_kidney 0 .00 RPM 9 .94 RPM
SRP007412_liver 0 .00 RPM 5 .30 RPM
SRP007412_testis 0 .00 RPM 2 .53 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3185 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3185 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3185 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4784
Gorilla gorilla retro_ggor_2979
Pongo abelii retro_pabe_3724

Parental genes homology:
Parental genes homology involve 11 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000194671 retrocopy
Dasypus novemcinctus ENSDNOG000000083291 retrocopy
Homo sapiens ENSG000001323134 retrocopies
Gorilla gorilla ENSGGOG000000267693 retrocopies
Macropus eugenii ENSMEUG000000047731 retrocopy
Mus musculus ENSMUSG000000529621 retrocopy
Otolemur garnettii ENSOGAG000000040481 retrocopy
Pan troglodytes ENSPTRG00000012152 4 retrocopies
Rattus norvegicus ENSRNOG000000085461 retrocopy
Tupaia belangeri ENSTBEG0000001536610 retrocopies
Tarsius syrichta ENSTSYG000000077132 retrocopies



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