RetrogeneDB ID:

retro_pabe_1947

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2a:46501707..46502174(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000012368
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSPPYG00000008108
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_pabe_1947
ATGGCGCCAAAAGCGGAGAAGGAAGCTCCTGCCCCTCCTAAAGCAGCCAAAGCGAATGCTTTAAAGGCCAAGAAGGCAGT
GTTGAAGGGTGTCCACAGCCACAAAAAAAAAACAAGATCCACACGTCACCCACCTTCCGGAGGCCCAAGACACTGAGACT
CCAGAGGCAGCCCAAATATCCTCGGAAGAGCGCCCCCAGGAGAAACAAGCTTGACCATTATGCTATCATCAAGTTTCCGC
TGACCACTGAGTCTGCCATGAAGAAGATAGAAGACGACAACACTCTTGTGTCCATTGTGGATGTTAAAGCCACCATCAAG
CACCAGATCAAACAGGCTGTGAAGAAGCTCTATGACATTGATGTGGCCAAAGTCAACACCCTGATTCAGCCTGACGGAAA
GAAGGCAAATGTTCGACTGGCTCCTAATTATAATGCTTGAGATGTTGCCAACAAAATTGGGATCATC

ORF - retro_pabe_1947 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.25 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPKAKKEAPAPPKAEAKA-KALKAKKAVLKGV-HSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRR
MAPKA.KEAPAPPKA.AKA....K.......G........KI.TSPTFRRPKTLRL.RQPKYPRKSAPRR
RetrocopyMAPKAEKEAPAPPKA-AKA<ECFKGQEGSVEGCPQPXXXXKIHTSPTFRRPKTLRLQRQPKYPRKSAPRR
ParentalNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKAN-KHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAY
NKLDHYAIIKFPLTTESAMKKIED.NTLV.IVDVKA..KHQIKQAVKKLYDIDVAKVNTLI.PDG.KKA.
RetrocopyNKLDHYAIIKFPLTTESAMKKIEDDNTLVSIVDVKATIKHQIKQAVKKLYDIDVAKVNTLIQPDG-KKAN
ParentalVRLAPDYDALDVANKIGII
VRLAP.Y.A.DVANKIGII
RetrocopyVRLAPNYNA*DVANKIGII

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 84 .59 RPM
SRP007412_cerebellum 0 .00 RPM 123 .67 RPM
SRP007412_heart 0 .00 RPM 136 .34 RPM
SRP007412_kidney 0 .00 RPM 189 .50 RPM
SRP007412_liver 0 .00 RPM 164 .09 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1947 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1947 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1947 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2271
Gorilla gorilla retro_ggor_140

Parental genes homology:
Parental genes homology involve 20 parental genes, and 463 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG000000131267 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Felis catus ENSFCAG0000000402135 retrocopies
Homo sapiens ENSG0000019824257 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pongo abelii ENSPPYG00000008108 49 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG000000177689 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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