RetrogeneDB ID:

retro_pabe_1250

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:15:48742583..48743035(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS13
Ensembl ID:ENSPPYG00000003456
Aliases:None
Description:ribosomal protein S13 [Source:HGNC Symbol;Acc:10386]


Retrocopy-Parental alignment summary:






>retro_pabe_1250
ATGGGTCGCATGCATGCTCCTGGGAAGGGCCTGTCCCAGTTGGCTTTGCCCTATCGCCACAGCATCCCCACTTGGCTGAA
GTTGACATCTGACGATGTGAAGGAGCAGATTTACAAAGTGGCCAAGAAGGGCCTGACTCCTTCACAAATTGGTGTGATCC
TGAGAGAGTCACATAGTGTTGCACAAGTATGTTTTGTGACAGGCAATAAAATCTTCAGAAATCTGAAGTCTAAGGGACTT
GCTCCTGATCTCCCTGAAGATCTATACCTTTAATTAAGAAAGCAGTCGCTGTTCAAAAGCATCTTGAGAGGAGCAGAAAG
GATAAGGATGCTAAATTCCATCTGATTCTGATAGAGAGCCGGATTCACCACTTGGCTCCATATTACAAGACCAAGCCAGT
CCTCCCTCCCAATTGGAAATATGAATCATCTACAGCCTCTGCCCTGGTAGCA

ORF - retro_pabe_1250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNK
MGRMHAPGKGLSQ.ALPYR.S.PTWLKLTSDDVKEQIYK.AKKGLTPSQIGVILR.SH.VAQV.FVTGNK
RetrocopyMGRMHAPGKGLSQLALPYRHSIPTWLKLTSDDVKEQIYKVAKKGLTPSQIGVILRESHSVAQVCFVTGNK
ParentalILRILKSKGLAPDLPEDLY-HLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNW
I.R.LKSKGLAPDLPEDLY..LIKKAVAV.KHLER.RKDKDAKF.LILIESRIH.LA.YYKTK.VLPPNW
RetrocopyIFRNLKSKGLAPDLPEDLY<PLIKKAVAVQKHLERSRKDKDAKFHLILIESRIHHLAPYYKTKPVLPPNW
ParentalKYESSTASALVA
KYESSTASALVA
RetrocopyKYESSTASALVA

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 55 .79 RPM
SRP007412_cerebellum 0 .00 RPM 116 .62 RPM
SRP007412_heart 0 .03 RPM 114 .36 RPM
SRP007412_kidney 0 .00 RPM 124 .83 RPM
SRP007412_liver 0 .03 RPM 128 .71 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1250 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1250 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1250 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1499

Parental genes homology:
Parental genes homology involve 34 parental genes, and 157 retrocopies.

Species Parental gene accession Retrocopies number
Caenorhabditis elegans C16A3.91 retrocopy
Ailuropoda melanoleuca ENSAMEG000000028953 retrocopies
Bos taurus ENSBTAG000000403085 retrocopies
Choloepus hoffmanni ENSCHOG000000087214 retrocopies
Callithrix jacchus ENSCJAG000000095641 retrocopy
Cavia porcellus ENSCPOG000000000233 retrocopies
Dipodomys ordii ENSDORG000000025073 retrocopies
Equus caballus ENSECAG0000001492812 retrocopies
Felis catus ENSFCAG000000053702 retrocopies
Homo sapiens ENSG000001107006 retrocopies
Gorilla gorilla ENSGGOG000000074503 retrocopies
Latimeria chalumnae ENSLACG000000171741 retrocopy
Loxodonta africana ENSLAFG000000268813 retrocopies
Macropus eugenii ENSMEUG000000149862 retrocopies
Microcebus murinus ENSMICG000000037168 retrocopies
Myotis lucifugus ENSMLUG000000097513 retrocopies
Macaca mulatta ENSMMUG000000225472 retrocopies
Monodelphis domestica ENSMODG000000070786 retrocopies
Mustela putorius furoENSMPUG000000133161 retrocopy
Mus musculus ENSMUSG0000009086219 retrocopies
Ornithorhynchus anatinus ENSOANG000000076871 retrocopy
Oryctolagus cuniculus ENSOCUG000000055366 retrocopies
Otolemur garnettii ENSOGAG000000021287 retrocopies
Ochotona princeps ENSOPRG000000001625 retrocopies
Pongo abelii ENSPPYG00000003456 6 retrocopies
Pteropus vampyrus ENSPVAG000000128063 retrocopies
Rattus norvegicus ENSRNOG000000205022 retrocopies
Sarcophilus harrisii ENSSHAG000000040523 retrocopies
Sus scrofa ENSSSCG000000133815 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000089965 retrocopies
Tupaia belangeri ENSTBEG000000077177 retrocopies
Tarsius syrichta ENSTSYG0000001311411 retrocopies
Tursiops truncatus ENSTTRG000000163213 retrocopies
Vicugna pacos ENSVPAG000000014635 retrocopies



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