RetrogeneDB ID:

retro_ptro_2219

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:182219293..182219687(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13
Ensembl ID:ENSPTRG00000008480
Aliases:None
Description:ribosomal protein L13 [Source:HGNC Symbol;Acc:10303]


Retrocopy-Parental alignment summary:






>retro_ptro_2219
ATCACCCCGACCCCTGTTCCTGGGCCCATCCAGCCCATAGTAAGGTGTCTCGTGGTAAGGCATCATACCAAAGTAGGCAG
GGTCTGCAGCTTGGAGGAGCTAAGGGTAGCTGGCATTCACAAGAAGCTGGGCCAAACCATTGGCATCTCTGTGGAGCCAA
GATGACAGAACAAGTCCACTGAGTCCCGCAGGCCAATGCACGGCAGCTAAAGGTGCATGGGACCAAACTCATCCTCTCCC
CAGGAAGCCCTTGGCCCCCAAGAAGAGAGACAGTTCAGCAGAAGAACTGAAATTGGCCACCAGATTGACCAGACCCGTTG
CGCCCATCAGGAATGTCCACAGGAAGGAGAAAGCCTAAATCATCACCAAGGAGGAGAACTTCAAAGCCTTTGCC

ORF - retro_ptro_2219 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.8 %
Parental protein coverage: 63.98 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalIAPRPASGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESL-QANV
I.P.P..GPI.PIVRC..VR.HTKV..GR..SLEELRVAGIHKK...TIGISV.PR..NKSTES..QAN.
RetrocopyITPTPVPGPIQPIVRCLVVRHHTKV--GRVCSLEELRVAGIHKKLGQTIGISVEPR*QNKSTESR<QANA
ParentalQRLKEYRSKLIL-FPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFA
..LK....KLIL..PRKP.APKK.DSSAEELKLAT.LT.PV.PIRNV..KEKA..IT.EE.NFKAFA
RetrocopyRQLKVHGTKLIL<LPRKPLAPKKRDSSAEELKLATRLTRPVAPIRNVHRKEKA*IITKEE-NFKAFA

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 178 .87 RPM
SRP007412_cerebellum 0 .00 RPM 146 .69 RPM
SRP007412_heart 0 .00 RPM 85 .37 RPM
SRP007412_kidney 0 .00 RPM 338 .80 RPM
SRP007412_liver 0 .00 RPM 301 .87 RPM
SRP007412_testis 0 .00 RPM 39 .31 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2219 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2219 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2219 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3281
Gorilla gorilla retro_ggor_2231

Parental genes homology:
Parental genes homology involve 17 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000170721 retrocopy
Canis familiaris ENSCAFG000000198405 retrocopies
Callithrix jacchus ENSCJAG000000096725 retrocopies
Cavia porcellus ENSCPOG000000273484 retrocopies
Echinops telfairi ENSETEG000000150574 retrocopies
Felis catus ENSFCAG000000033384 retrocopies
Homo sapiens ENSG0000016752612 retrocopies
Microcebus murinus ENSMICG000000081914 retrocopies
Myotis lucifugus ENSMLUG000000109506 retrocopies
Monodelphis domestica ENSMODG000000036634 retrocopies
Mus musculus ENSMUSG0000000074023 retrocopies
Nomascus leucogenys ENSNLEG0000001577413 retrocopies
Ornithorhynchus anatinus ENSOANG000000067291 retrocopy
Otolemur garnettii ENSOGAG000000264443 retrocopies
Pan troglodytes ENSPTRG00000008480 12 retrocopies
Pteropus vampyrus ENSPVAG000000151306 retrocopies
Rattus norvegicus ENSRNOG0000001533514 retrocopies



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