RetrogeneDB ID:

retro_ptro_1467

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:21:15173069..15173487(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23
Ensembl ID:ENSPTRG00000009079
Aliases:None
Description:ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]


Retrocopy-Parental alignment summary:






>retro_ptro_1467
ATGTCAAAGCAAGGACGTGGTAGGTCCTCTGGTGTGAACTTCTGGATTTCCTTGGGTCTTCCAGTAGGAGCTGTGATCAA
CTGCTGACAACACAGGAGCCAAAAACCTGTATATCATCTCCATGAAGGGGATCAAGGGACAGCTGAACAGACTTTCTGCT
GCTAGTGTGGGTGACATGGTGATGGCCACAGTCAAGAAGGGCAAACCAGAGCTCAGAAAAATGGTACATCCAGCAGCGGT
CATTCGACAACCAAAGTCATACCGGAGAAAAGATGGTGTGTTTCTTTATTCCGAAGATAATGCAGGGGTCATAGTGAATA
ATAAAGGCAAAATGAAAGGTTCTGCCATTATAGGACCAGTAGCAAAGGAGTATGCAGACTTGTGGCCCTGGACTGTGTCC
AATGCTCGCAGCATTGCA

ORF - retro_ptro_1467 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKG-RLNRLPAAGVGDMVMATVKKGK
MSK.GRG.SSG..F.ISLGLPVGAVINC......K..Y.....G..G..LNRL.AA.VGDMVMATVKKGK
RetrocopyMSKQGRGRSSGVNFWISLGLPVGAVINC*QHRSQKPVYHLH-EGDQG>QLNRLSAASVGDMVMATVKKGK
ParentalPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWPRIASNAGSI
PELRK.VHPA.VIRQ.KSYRRKDGVFLY.EDNAGVIVNNKG.MKGSAI.GPVAKE.ADLWP...SNA.SI
RetrocopyPELRKMVHPAAVIRQPKSYRRKDGVFLYSEDNAGVIVNNKGKMKGSAIIGPVAKEYADLWPWTVSNARSI
ParentalA
A
RetrocopyA

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 2 .68 RPM 107 .62 RPM
SRP007412_cerebellum 5 .48 RPM 139 .52 RPM
SRP007412_heart 0 .58 RPM 192 .28 RPM
SRP007412_kidney 1 .80 RPM 321 .35 RPM
SRP007412_liver 1 .18 RPM 256 .73 RPM
SRP007412_testis 2 .00 RPM 98 .01 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1467 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1467 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1467 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2522
Gorilla gorilla retro_ggor_1574
Macaca mulatta retro_mmul_1598

Parental genes homology:
Parental genes homology involve 21 parental genes, and 123 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042686 retrocopies
Bos taurus ENSBTAG000000032295 retrocopies
Canis familiaris ENSCAFG000000289551 retrocopy
Choloepus hoffmanni ENSCHOG000000091539 retrocopies
Callithrix jacchus ENSCJAG000000083119 retrocopies
Cavia porcellus ENSCPOG000000100022 retrocopies
Latimeria chalumnae ENSLACG000000044301 retrocopy
Loxodonta africana ENSLAFG000000284504 retrocopies
Macropus eugenii ENSMEUG000000011882 retrocopies
Macaca mulatta ENSMMUG000000045029 retrocopies
Mus musculus ENSMUSG0000007141510 retrocopies
Nomascus leucogenys ENSNLEG000000006427 retrocopies
Ornithorhynchus anatinus ENSOANG000000012301 retrocopy
Oryctolagus cuniculus ENSOCUG000000139156 retrocopies
Otolemur garnettii ENSOGAG000000124457 retrocopies
Ochotona princeps ENSOPRG0000000195710 retrocopies
Pongo abelii ENSPPYG0000000850110 retrocopies
Pan troglodytes ENSPTRG00000009079 9 retrocopies
Rattus norvegicus ENSRNOG0000000410710 retrocopies
Sus scrofa ENSSSCG000000215903 retrocopies
Vicugna pacos ENSVPAG000000056942 retrocopies



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