RetrogeneDB ID:

retro_pabe_3013

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:143757437..143757698(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSPPYG00000025953
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_pabe_3013
ATATCCATAGTGATCCTTGAGAAGTTCCAGCATATTTTGCAAGTACTCAACACTAACATCAATGGGCGGTGGAAAATAGC
CTTTGTCATCACTGCCATTAAGGGTGTGGGTTGAAGATATGCTCACATGGTGTTGAGGAAAGCAGACATTGACATCACCA
AGAGGGCAGGAGAACTCACTGAGGATGAGGTGGAACCTGTGATCACCATTATACAAAATCTACACCAGTACAAGATCCCA
GACTGGTCCTTAAACAGACAG

ORF - retro_pabe_3013 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.76 %
Parental protein coverage: 57.24 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
.S.VI.EKFQHIL.VLNTNI.GR.KIAF.ITAIKGVG.RYAH.VLRKADID.TKRAGELTEDEVE.VITI
RetrocopyISIVILEKFQHILQVLNTNINGRWKIAFVITAIKGVG*RYAHMVLRKADIDITKRAGELTEDEVEPVITI
ParentalMQNPRQYKIPDWFLNRQ
.QN..QYKIPDW.LNRQ
RetrocopyIQNLHQYKIPDWSLNRQ

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 151 .44 RPM
SRP007412_cerebellum 0 .00 RPM 115 .40 RPM
SRP007412_heart 0 .00 RPM 185 .68 RPM
SRP007412_kidney 0 .00 RPM 391 .53 RPM
SRP007412_liver 0 .00 RPM 335 .61 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3013 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3013 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3013 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3674

Parental genes homology:
Parental genes homology involve 34 parental genes, and 203 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000029181 retrocopy
Ailuropoda melanoleuca ENSAMEG000000016232 retrocopies
Bos taurus ENSBTAG000000026482 retrocopies
Canis familiaris ENSCAFG000000009507 retrocopies
Choloepus hoffmanni ENSCHOG000000037465 retrocopies
Callithrix jacchus ENSCJAG000000216505 retrocopies
Cavia porcellus ENSCPOG000000196754 retrocopies
Dasypus novemcinctus ENSDNOG0000001208413 retrocopies
Dipodomys ordii ENSDORG000000138256 retrocopies
Erinaceus europaeus ENSEEUG000000102978 retrocopies
Felis catus ENSFCAG000000040137 retrocopies
Homo sapiens ENSG000002315002 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Macropus eugenii ENSMEUG0000001677011 retrocopies
Myotis lucifugus ENSMLUG000000073602 retrocopies
Macaca mulatta ENSMMUG000000038671 retrocopy
Monodelphis domestica ENSMODG000000142104 retrocopies
Mustela putorius furoENSMPUG000000023066 retrocopies
Mus musculus ENSMUSG000000086682 retrocopies
Nomascus leucogenys ENSNLEG0000000684010 retrocopies
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Otolemur garnettii ENSOGAG000000062257 retrocopies
Procavia capensis ENSPCAG000000058542 retrocopies
Pongo abelii ENSPPYG00000025953 14 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Pteropus vampyrus ENSPVAG000000019026 retrocopies
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
Sus scrofa ENSSSCG000000015025 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000241713 retrocopies
Tupaia belangeri ENSTBEG0000001270840 retrocopies
Tursiops truncatus ENSTTRG000000043023 retrocopies



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