RetrogeneDB ID:

retro_ptro_1367

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:19:39265873..39266646(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000022576
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSPTRG00000022025
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_ptro_1367
GTGGCTTCCGGTCCCAAGCAGCATCTGAAGCGGGTAGCAGCTCCACAACATTGGATGCTGGATAAATTGACTGGTGTGTT
TGCTGCTCGTCCATCCACTGGTCCCCAAAAGCTGAGAGAGTGTCTCCCTCATATTTTCCTGAGGAACAGACTTAAGTATG
CCCTGACAGGAGATGAAGTGAAGAAGATTTGCATGCAGTGGTTCATTAAGGTAGATGGCAAGGTTCGAACTGATAGAACA
ACCTACCCTATTGGATTTATGGATGTCATCAGCATTGACAAGACGGGGGAGGGTTTCCGTCTGATCTATGGCATCAATTG
TCGCTTTGCTGTACATCGTGTTACACCTGAGGAAGTCAAGCACAAGTTATGCAAAATGAGAAAAATCTTTGTGTGCACAA
AAGGAACCCCTCACCTGGTGATTCACGATGCTCACACTATCCGCCACCCTGATTCCCTCATTAAAGTGAACGACACCATT
CGGATTGATTTGGAGACTGGCAAGATCACTGCTTTGAAGTTCGACACTGGTAACCTGTGTTTGGTGACTGGAGGTGCTAA
CTAGGGAAGAATTGGTGTGATCACCAATAGAGAGAGGCACCCTGGATCTTTTGACACGATTCACGTGAAAGATGCCAACA
GCAACAGCTTTTCCATCATTTTTGTTATTGACAAGGGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCCGC
TTCACCATTGCTGAAGGGAGAGACAAGAGACTGCAGCCAAACAGAGCAGTGGA

ORF - retro_ptro_1367 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFI
.A.GPK.HLKRVAAP.HWMLDKLTGVFA.RPSTGP.KLRECLP.I.FLRNRLKYALTGDEVKKICMQ.FI
RetrocopyVASGPKQHLKRVAAPQHWMLDKLTGVFAARPSTGPQKLRECLPHI-FLRNRLKYALTGDEVKKICMQWFI
ParentalKIDGKVRTD-ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
K.DGKVRTD..TYP.GFMDVISIDKTGE.FRLIY....RFAVHR.TPEE.K.KLCK.RKIFV.TKG.PHL
RetrocopyKVDGKVRTDRTTYPIGFMDVISIDKTGEGFRLIYGINCRFAVHRVTPEEVKHKLCKMRKIFVCTKGTPHL
ParentalVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVH
V.HDA.TIR.PD.LIKVNDTI.IDLETGKIT...KFDTGNLC.VTGGAN.GRIGVITNRERHPGSFD..H
RetrocopyVIHDAHTIRHPDSLIKVNDTIRIDLETGKIT-ALKFDTGNLCLVTGGAN*GRIGVITNRERHPGSFDTIH
ParentalVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRL-AAKQSSG
VKDAN.NSF....S.IFVI.KGNKPWISLPRGKGIR.TIAE.RDKRL.AAKQSSG
RetrocopyVKDANSNSF----SIIFVIDKGNKPWISLPRGKGIRFTIAEGRDKRL<AAKQSSG

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 132 .82 RPM
SRP007412_cerebellum 0 .00 RPM 129 .52 RPM
SRP007412_heart 0 .00 RPM 90 .29 RPM
SRP007412_kidney 0 .05 RPM 231 .18 RPM
SRP007412_liver 0 .00 RPM 130 .28 RPM
SRP007412_testis 0 .00 RPM 9 .06 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1367 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1367 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1367 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2052
Gorilla gorilla retro_ggor_1479
Macaca mulatta retro_mmul_43

Parental genes homology:
Parental genes homology involve 26 parental genes, and 246 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
Bos taurus ENSBTAG000000188005 retrocopies
Canis familiaris ENSCAFG000000171512 retrocopies
Callithrix jacchus ENSCJAG000000041922 retrocopies
Cavia porcellus ENSCPOG000000063373 retrocopies
Equus caballus ENSECAG000000108526 retrocopies
Homo sapiens ENSG000001298241 retrocopy
Homo sapiens ENSG0000019803419 retrocopies
Loxodonta africana ENSLAFG000000026544 retrocopies
Macropus eugenii ENSMEUG0000000796916 retrocopies
Meleagris gallopavo ENSMGAG000000096711 retrocopy
Microcebus murinus ENSMICG0000001660658 retrocopies
Monodelphis domestica ENSMODG000000110701 retrocopy
Mustela putorius furoENSMPUG0000000529411 retrocopies
Mus musculus ENSMUSG0000003132013 retrocopies
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
Otolemur garnettii ENSOGAG000000118082 retrocopies
Procavia capensis ENSPCAG000000007613 retrocopies
Pongo abelii ENSPPYG0000002046224 retrocopies
Pan troglodytes ENSPTRG00000022025 9 retrocopies
Pan troglodytes ENSPTRG000000224701 retrocopy
Pteropus vampyrus ENSPVAG0000001288221 retrocopies
Rattus norvegicus ENSRNOG000000032011 retrocopy
Sus scrofa ENSSSCG000000124055 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000286928 retrocopies
Vicugna pacos ENSVPAG000000109524 retrocopies



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