RetrogeneDB ID:

retro_ptro_1839

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:162251521..162251751(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS12
Ensembl ID:ENSPTRG00000018618
Aliases:None
Description:Pan troglodytes ribosomal protein S12 (RPS12), mRNA. [Source:RefSeq mRNA;Acc:NM_001252509]


Retrocopy-Parental alignment summary:






>retro_ptro_1839
CATGTTTGCATCCAGCTTTGGTCTGTGATGAGCCTGTGTATGTCATGTTGGTGGCCCTTTGTGCTGAACACCAAATCTAC
CTAAGTAAGGTTGATGACCGTAAGAAACTAGGGGAAGAGATAGGCCTCAGAGAGGGAAAACCCTATAAAGTCATTGGTTG
CAATTGTGTAGTAGTTAAGGACTATGGCAAAGAATCTCAGGCCAAGGATGTCATTGAAGAGTACTTCAGA

ORF - retro_ptro_1839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.49 %
Parental protein coverage: 62.12 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHLCVL-ASNCDEPMYVKLVEALCAEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGK
H.C...A..CDEP.YV.LV.ALCAEHQI.L.KVDD.KKLGE..GL....REGKP.KV.GC.CVVVKDYGK
RetrocopyHVCIQ<ALVCDEPVYVMLV-ALCAEHQIYLSKVDDRKKLGEEIGL----REGKPYKVIGCNCVVVKDYGK
ParentalESQAKDVIEEYFK
ESQAKDVIEEYF.
RetrocopyESQAKDVIEEYFR

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 180 .07 RPM
SRP007412_cerebellum 0 .00 RPM 84 .75 RPM
SRP007412_heart 0 .00 RPM 79 .60 RPM
SRP007412_kidney 0 .00 RPM 293 .11 RPM
SRP007412_liver 0 .00 RPM 168 .52 RPM
SRP007412_testis 0 .00 RPM 63 .12 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1839 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1839 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1839 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2722
Gorilla gorilla retro_ggor_1894

Parental genes homology:
Parental genes homology involve 28 parental genes, and 271 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
Bos taurus ENSBTAG000000013607 retrocopies
Callithrix jacchus ENSCJAG0000000286534 retrocopies
Cavia porcellus ENSCPOG000000004294 retrocopies
Dasypus novemcinctus ENSDNOG0000000621431 retrocopies
Equus caballus ENSECAG000000015998 retrocopies
Echinops telfairi ENSETEG0000000685414 retrocopies
Felis catus ENSFCAG000000284027 retrocopies
Gorilla gorilla ENSGGOG0000001223422 retrocopies
Gadus morhua ENSGMOG000000194551 retrocopy
Loxodonta africana ENSLAFG0000000793311 retrocopies
Microcebus murinus ENSMICG000000052525 retrocopies
Myotis lucifugus ENSMLUG000000011375 retrocopies
Macaca mulatta ENSMMUG000000132371 retrocopy
Mustela putorius furoENSMPUG000000147711 retrocopy
Mus musculus ENSMUSG000000619831 retrocopy
Nomascus leucogenys ENSNLEG000000146114 retrocopies
Oryctolagus cuniculus ENSOCUG0000000160614 retrocopies
Otolemur garnettii ENSOGAG0000000130920 retrocopies
Pelodiscus sinensis ENSPSIG000000034571 retrocopy
Pan troglodytes ENSPTRG00000018618 25 retrocopies
Pteropus vampyrus ENSPVAG0000001720112 retrocopies
Rattus norvegicus ENSRNOG000000164115 retrocopies
Sorex araneus ENSSARG000000031702 retrocopies
Sarcophilus harrisii ENSSHAG000000089056 retrocopies
Tarsius syrichta ENSTSYG0000001009724 retrocopies
Vicugna pacos ENSVPAG000000115043 retrocopies



Copyright © RetrogeneDB 2014-2017