RetrogeneDB ID:

retro_ptro_865

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:13:50090641..50090983(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL34
Ensembl ID:ENSPTRG00000016353
Aliases:None
Description:ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]


Retrocopy-Parental alignment summary:






>retro_ptro_865
ATGGTCCCGCGTTTGACACACCGACATAGGCTTTCCTACAATACAACCTCTAACAAAACTAAGCTGTCTGGAACCCCTGG
TAACAGAATCATTTACCTTTATACCAAGAAGGTTGGGAAAGCACCAACATCTACATGTGGTATGTGCCCAGGCAGACTTT
GAGGGGTTCATGCTGTAAGACCTAAAATTCCTATGAGATTGTCCAAAACAAAGAAACATGTCAGCAGGGCCTATGGTGGT
TCCATGTATGCTAAATGTGTTCATGACAGGATCAAGCATGCTTTCCTTATCGAGGAAGAGAAAATCATTGTGAAAGTGTT
GAAGGCACAAGCACAGAGTCAG

ORF - retro_ptro_865 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 97.44 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKT
MV.RLT.R.RLSYNT.SNKT.LS.TPGNRI.YLYTKKVGKAP.S.CG.CPGRL.GV.AVRPK..MRLSKT
RetrocopyMVPRLTHRHRLSYNTTSNKTKLSGTPGNRIIYLYTKKVGKAPTSTCGMCPGRL*GVHAVRPKIPMRLSKT
ParentalKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQ
KKHVSRAYGGSM.AKCV.DRIK.AFLIEE.KI.VKVLKAQAQSQ
RetrocopyKKHVSRAYGGSMYAKCVHDRIKHAFLIEEEKIIVKVLKAQAQSQ

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 97 .95 RPM
SRP007412_cerebellum 0 .04 RPM 85 .36 RPM
SRP007412_heart 0 .00 RPM 66 .98 RPM
SRP007412_kidney 0 .03 RPM 223 .00 RPM
SRP007412_liver 0 .00 RPM 113 .88 RPM
SRP007412_testis 0 .00 RPM 50 .79 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_865 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_865 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_865 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1265
Gorilla gorilla retro_ggor_995

Parental genes homology:
Parental genes homology involve 17 parental genes, and 183 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000001117926 retrocopies
Gadus morhua ENSGMOG000000099821 retrocopy
Loxodonta africana ENSLAFG000000326156 retrocopies
Macropus eugenii ENSMEUG000000093613 retrocopies
Microcebus murinus ENSMICG0000000218032 retrocopies
Macaca mulatta ENSMMUG000000119011 retrocopy
Monodelphis domestica ENSMODG000000206013 retrocopies
Mustela putorius furoENSMPUG0000000887317 retrocopies
Otolemur garnettii ENSOGAG000000067741 retrocopy
Pongo abelii ENSPPYG0000001498818 retrocopies
Pelodiscus sinensis ENSPSIG000000032951 retrocopy
Pan troglodytes ENSPTRG00000016353 31 retrocopies
Sarcophilus harrisii ENSSHAG000000013571 retrocopy
Sarcophilus harrisii ENSSHAG000000020523 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002596414 retrocopies
Tupaia belangeri ENSTBEG0000000357424 retrocopies
Xenopus tropicalis ENSXETG000000210951 retrocopy



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