RetrogeneDB ID:

retro_ptro_2329

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:19535000..19535883(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL5
Ensembl ID:ENSPTRG00000000963
Aliases:None
Description:ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]


Retrocopy-Parental alignment summary:






>retro_ptro_2329
ATGGGGTTTGTTAAAGTTGTCAAGAGTAAGGCCTACTTTAAGAGATACTAAGTGAAATGTAGAAGACAATGACAGGGTAA
AACTGATTACTATGCTCAGAAATCCTTGGTGATATAAGATAAAAATAAGTATAACATGCCTAAATACAGGGTGATAGTTT
GTGTAACAGATAGAGATATCATTTGTCAGATTGCTTATGCCCATATAGGAGGGAATATGATAATGTATGCAGCTTATGCA
TATGAGCTGCCAAAACATGGTGTGAAGGTTGGCCTGACAAATTATGCTATAGCATACTGTACTGGCCTCCTGCTGGCCTG
CAGACTTCTCAGTAGGTTTGGCATGGACAAGATCTAAGAAGTCCAAGTAGAGATGAATGGAGATGAATACAATGTAAAAA
CCATTGATGGTCAGCCAGGTGCCTTTACCTGCTATTTGGATGCAGGCCTTGCCAGAACTACCGATAAACTTTTATGGGGT
CCTGAAAGGAGTTGTGGATGGAGGTTTGTTGATTCCTCACAATATTAAACGATTTCCTGGTTATGATTCTGAAAGCAAGA
AATTTAATGCAGAAGTACATCAAAAGCACATTATGGATCCAAATGCTGCAGACTACATGTGTTATCTAATAGAAAAAGAT
GAAGATGCTGACAAGAAATGTTTCTCTTAATACATAAAGAACAGCATAACTTCAGACATGAAGGAGATGTACAAGAAAGC
TCATGCTGCTATATAAGAGAATCCAGTCTATGAGAGGAAGCCCGAGAAAGAAGTTTAAAAAAAGAAGTGGAACCATCTGA
AAATGTCCCTTGCCCAGAAGAAAGATCAGGTAGCTCAAAAGAAGACAAGCTTCCTCAGAGCTCAGGAGCAGGCTGCCAAG
AGC

ORF - retro_ptro_2329 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.52 %
Parental protein coverage: 100. %
Number of stop codons detected: 7
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
MGFVKVVK.KAYFKRY.VK.RR...GKTDYYA.K.LVI.DKNKYN.PKYR.IV.VT.RDIICQIAYA.I.
RetrocopyMGFVKVVKSKAYFKRY*VKCRRQ*QGKTDYYAQKSLVI*DKNKYNMPKYRVIVCVTDRDIICQIAYAHIG
ParentalGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPG
G.MI..AAYA.ELPK.GVKVGLTNYA.AYCTGLLLA.RLL.RFGMDKI.E.QVE..GDEYNV..IDGQPG
RetrocopyGNMIMYAAYAYELPKHGVKVGLTNYAIAYCTGLLLACRLLSRFGMDKI*EVQVEMNGDEYNVKTIDGQPG
ParentalAFTCYLDAGLARTTTGNKV-FGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR
AFTCYLDAGLAR..T..K...G.LKG.VDGGL.IPH..KRFPGYDSESK.FNAEVH.KHIM..N.ADYM.
RetrocopyAFTCYLDAGLAR--TTDKL>YGVLKGVVDGGLLIPHNIKRFPGYDSESKKFNAEVHQKHIMDPNAADYMC
ParentalYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDR
YL.E.DEDA.KK.FS.YIKNS.T.D.M.EMYKKAHAAI.ENPVYE.KP.KEV.KK.WN..KMSLAQKKD.
RetrocopyYLIEKDEDADKKCFS*YIKNSITSD-MKEMYKKAHAAI*ENPVYERKPEKEV*KKKWNHLKMSLAQKKDQ
ParentalVAQKKASFLRAQERAAES
VAQKK.SFLRAQE.AA.S
RetrocopyVAQKKTSFLRAQEQAAKS

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 144 .07 RPM
SRP007412_cerebellum 0 .00 RPM 175 .59 RPM
SRP007412_heart 0 .00 RPM 212 .10 RPM
SRP007412_kidney 0 .00 RPM 383 .05 RPM
SRP007412_liver 0 .00 RPM 204 .59 RPM
SRP007412_testis 0 .00 RPM 178 .94 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2329 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2329 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2329 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3430
Gorilla gorilla retro_ggor_2318
Pongo abelii retro_pabe_2841

Parental genes homology:
Parental genes homology involve 14 parental genes, and 141 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000028521 retrocopy
Echinops telfairi ENSETEG000000098898 retrocopies
Homo sapiens ENSG0000012240630 retrocopies
Gorilla gorilla ENSGGOG0000000269924 retrocopies
Macropus eugenii ENSMEUG000000063613 retrocopies
Myotis lucifugus ENSMLUG000000089561 retrocopy
Monodelphis domestica ENSMODG000000116351 retrocopy
Nomascus leucogenys ENSNLEG000000105002 retrocopies
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
Otolemur garnettii ENSOGAG000000132466 retrocopies
Petromyzon marinus ENSPMAG000000020401 retrocopy
Pongo abelii ENSPPYG0000000115232 retrocopies
Pan troglodytes ENSPTRG00000000963 30 retrocopies
Sarcophilus harrisii ENSSHAG000000064171 retrocopy



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