RetrogeneDB ID:

retro_pabe_1308

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:15:69387233..69387485(-)
Located in intron of:ENSPPYG00000006609
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF5A2
Ensembl ID:ENSPPYG00000014294
Aliases:None
Description:Eukaryotic translation initiation factor 5A-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R898]


Retrocopy-Parental alignment summary:






>retro_pabe_1308
GAAGATATTTGTCCTTCTATTCACAACATGGATGTTCCAAATATTCAGAGACATGATTATCAACTGATACGCATTCAAGA
TAGTTGCCTTTCCCTGCTGACAGAAGCTGATGGAGTTCCTGAGGATCTTAAACTGCCAGAAAGTGAACTAGGCAAATAAA
TACAAGGAAAATACAATGCAGGTGAAGATGTACAGGTGTCTGTCATGTGTGCAATGAGTGAAGAATATGCTGTAGCCATA
AAACCCTGCAAA

ORF - retro_pabe_1308 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.52 %
Parental protein coverage: 54.9 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEDICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMC
EDICPS.HNMDVPNI.R.DYQLI.IQD..LSLLTE...V.EDLKLPE.ELGK.I.GKYNAGEDVQVSVMC
RetrocopyEDICPSIHNMDVPNIQRHDYQLIRIQDSCLSLLTEADGVPEDLKLPESELGK*IQGKYNAGEDVQVSVMC
ParentalAMSEEYAVAIKPCK
AMSEEYAVAIKPCK
RetrocopyAMSEEYAVAIKPCK

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 2 .27 RPM
SRP007412_cerebellum 0 .00 RPM 1 .95 RPM
SRP007412_heart 0 .00 RPM 1 .54 RPM
SRP007412_kidney 0 .00 RPM 1 .76 RPM
SRP007412_liver 0 .00 RPM 0 .58 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1308 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1308 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1308 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1591
Pan troglodytes retro_ptro_1070

Parental genes homology:
Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000053631 retrocopy
Cavia porcellus ENSCPOG000000125941 retrocopy
Dasypus novemcinctus ENSDNOG000000148012 retrocopies
Homo sapiens ENSG000001635771 retrocopy
Loxodonta africana ENSLAFG000000132251 retrocopy
Macropus eugenii ENSMEUG000000074732 retrocopies
Nomascus leucogenys ENSNLEG000000052921 retrocopy
Oryctolagus cuniculus ENSOCUG000000166571 retrocopy
Pongo abelii ENSPPYG000000079071 retrocopy
Pongo abelii ENSPPYG00000014294 2 retrocopies
retro_pabe_1308 , retro_pabe_1640,
Pan troglodytes ENSPTRG000000156211 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000081302 retrocopies



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