RetrogeneDB ID:

retro_pabe_2461

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:114222995..114223340(+)
Located in intron of:ENSPPYG00000029772
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CDC42
Ensembl ID:ENSPPYG00000001755
Aliases:None
Description:cell division cycle 42 [Source:HGNC Symbol;Acc:1736]


Retrocopy-Parental alignment summary:






>retro_pabe_2461
ACAGATGTATTTCTAGTCTGTTTCTCAGTGGTCTCTCCATGTTCATTTTAAAGTATGAAAGAAAAGTGAGGGCCTGAGAT
AACTCACCACTGTCCAAAGGCTCCTTTCTTGCTTGTCACGACCCAAACTGATCTCAGAGGGTCTATTATTGAGAAAATTA
CCAAGAACAAACAGAAGCCTATCACTCCAGAGACTGCTGAAAAGCCGGCCCACAACCTGAAGGCTGTCAAGTATATGGAT
GGTCCTGTACCCACACAGCAAGACCTAAAGAATGGATTGGACAAAGCAATATTGGCTATCCTGGAGCCTCCAGAACTGAA
GAAGAGCTGCAAGCCTATGCTGCTA

ORF - retro_pabe_2461 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.09 %
Parental protein coverage: 61.26 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEK
TDVFLVCFSVVSP.SF...KEK..PEITHHCPK.PFLLV.TQ.DLR...S.IEK..KNKQKPITPETAEK
RetrocopyTDVFLVCFSVVSPCSF*SMKEK*GPEITHHCPKAPFLLVTTQTDLRG--SIIEKITKNKQKPITPETAEK
ParentalLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL
.A..LKAVKY......TQ..LKN..D.AILA.LEPPE.KKS....LL
RetrocopyPAHNLKAVKYMDGPVPTQQDLKNGLDKAILAILEPPELKKSCKPMLL

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 56 .18 RPM
SRP007412_cerebellum 0 .49 RPM 63 .11 RPM
SRP007412_heart 0 .00 RPM 45 .03 RPM
SRP007412_kidney 0 .17 RPM 103 .42 RPM
SRP007412_liver 0 .06 RPM 72 .40 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2461 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2461 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2461 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2968
Gorilla gorilla retro_ggor_2057
Macaca mulatta retro_mmul_1900

Parental genes homology:
Parental genes homology involve 21 parental genes, and 75 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000147075 retrocopies
Choloepus hoffmanni ENSCHOG0000000530610 retrocopies
Callithrix jacchus ENSCJAG000000059126 retrocopies
Cavia porcellus ENSCPOG000000065434 retrocopies
Equus caballus ENSECAG000000191801 retrocopy
Echinops telfairi ENSETEG000000044431 retrocopy
Felis catus ENSFCAG000000048534 retrocopies
Gorilla gorilla ENSGGOG000000244395 retrocopies
Macaca mulatta ENSMMUG000000220098 retrocopies
Monodelphis domestica ENSMODG000000160783 retrocopies
Mustela putorius furoENSMPUG000000159992 retrocopies
Mus musculus ENSMUSG000000066993 retrocopies
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
Otolemur garnettii ENSOGAG000000142611 retrocopy
Pongo abelii ENSPPYG00000001755 6 retrocopies
Pongo abelii ENSPPYG000000087632 retrocopies
Pongo abelii ENSPPYG000000117913 retrocopies
Pongo abelii ENSPPYG000000124392 retrocopies
Rattus norvegicus ENSRNOG000000135361 retrocopy
Sorex araneus ENSSARG000000051843 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000008054 retrocopies



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