RetrogeneDB ID:

retro_pabe_3613

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:12294786..12295001(+)
Located in intron of:ENSPPYG00000020124
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAU
Ensembl ID:ENSPPYG00000003077
Aliases:None
Description:40S ribosomal protein S30 [Source:UniProtKB/Swiss-Prot;Acc:P0C2F0]


Retrocopy-Parental alignment summary:






>retro_pabe_3613
CCAGAAGGTCAAGTCATGCTTTGAGAAGACACAGCCTTGGAGGATGAGTTTTTTTTGGGGATAGTGGGGTGGAGGCCCTG
ACCACTCTGAAAGTAGCCAGCTGTGTGCCTGGAGTTAAATTCCATGGTTTCCTGGCCTGTGCTAGGGAAGTGAGAGTTCA
GACTTCCAAGGTGGCCTACAAGGAGAATAAGAGGTTGAGGAGAAGGAGGAAGAGA

ORF - retro_pabe_3613 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.68 %
Parental protein coverage: 54.14 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPEDQVVLLAGAPLEDEATLG-QCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
PE.QV.L.....LEDE...G...GVEALTTL.VA....G.K.HG.LA.A..VR.QT.KVA..E.K.....
RetrocopyPEGQVML*EDTALEDEXXXG<DSGVEALTTLKVASCVPGVKFHGFLACAREVRVQTSKVAYKENKRLRRR
ParentalRAK
R..
RetrocopyRKR

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 .06 RPM 73 .65 RPM
SRP007412_cerebellum 0 .12 RPM 45 .24 RPM
SRP007412_heart 0 .00 RPM 40 .01 RPM
SRP007412_kidney 0 .00 RPM 115 .75 RPM
SRP007412_liver 0 .00 RPM 138 .84 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3613 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3613 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3613 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 26 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176768 retrocopies
Bos taurus ENSBTAG000000208071 retrocopy
Canis familiaris ENSCAFG000000139347 retrocopies
Callithrix jacchus ENSCJAG000000024321 retrocopy
Dasypus novemcinctus ENSDNOG000000044815 retrocopies
Dipodomys ordii ENSDORG000000036162 retrocopies
Equus caballus ENSECAG000000219562 retrocopies
Echinops telfairi ENSETEG000000105681 retrocopy
Felis catus ENSFCAG000000243679 retrocopies
Loxodonta africana ENSLAFG000000016891 retrocopy
Microcebus murinus ENSMICG000000165962 retrocopies
Myotis lucifugus ENSMLUG000000153703 retrocopies
Macaca mulatta ENSMMUG000000187761 retrocopy
Monodelphis domestica ENSMODG000000100951 retrocopy
Mustela putorius furoENSMPUG000000122371 retrocopy
Mus musculus ENSMUSG000000382741 retrocopy
Oryctolagus cuniculus ENSOCUG000000148783 retrocopies
Otolemur garnettii ENSOGAG000000150134 retrocopies
Pongo abelii ENSPPYG00000003077 2 retrocopies
retro_pabe_2393, retro_pabe_3613 ,
Rattus norvegicus ENSRNOG000000209823 retrocopies
Sarcophilus harrisii ENSSHAG000000001311 retrocopy
Sus scrofa ENSSSCG000000130022 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000033361 retrocopy
Tupaia belangeri ENSTBEG0000000749211 retrocopies
Tursiops truncatus ENSTTRG000000172466 retrocopies
Vicugna pacos ENSVPAG000000052051 retrocopy



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