RetrogeneDB ID:

retro_pabe_3626

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:30903891..30904380(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTL
Ensembl ID:ENSPPYG00000010223
Aliases:None
Description:Ferritin light chain [Source:UniProtKB/Swiss-Prot;Acc:Q5R538]


Retrocopy-Parental alignment summary:






>retro_pabe_3626
ATGAGCTCCCAGATTCGTCAGAATTATTCCACTGACGTGGACGCAGCCGTCAACAGCCTGGTCAATTTGTACCTGCAGGC
CTCCTACACCTACCTCTCTCTGGGCTTCTATTTCGACCACGATGATGTGGCTTTGGAAGGCGTGAGCCACTTCTTCCGCG
AATTGGCCGAGGAAAAGTGCGAGGGCTACGAGCGTCTCCTGAAGATGCAAAACCAGCGTGGCAGCCGTGCTCTCTTCCAG
GACATCAAGAAGCCAGCTGAAGATGAGTGGGGTAAAACCCCGGACGCCATGAAAGCCGCCATGGCCCTGGAGAAAAAACT
GAATCAGGCTCTTTTGGATCTTCATGCCCTGGGTTCTGCTTGCACGGACCCCCGTCTCTGTGACTTCCTGGAGAGTCACT
TCCTAGATGAGTAAGTGAAGTTCATCAAGAAGATGGGTGACCACCTGACCAACCTCCACAGGCTGGCCGGCCCGGAGGCT
GGGCTCGGC

ORF - retro_pabe_3626 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.64 %
Parental protein coverage: 86.24 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSQIRQNYSTDVEAAVNSLVNMYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQ
MSSQIRQNYSTDV.AAVNSLVN.YLQASYTYLSLGFYFD.DDVALEGVSHFFRELAEEK.EGYERLLKMQ
RetrocopyMSSQIRQNYSTDVDAAVNSLVNLYLQASYTYLSLGFYFDHDDVALEGVSHFFRELAEEKCEGYERLLKMQ
ParentalNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSAHTDPHLCDFLETHFLDEEVK
NQRG.RALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSA.TDP.LCDFLE.HFLDE.VK
RetrocopyNQRGSRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSACTDPRLCDFLESHFLDE*VK
ParentalLIKKMGDHLTNLHRLGGPEAGAG
.IKKMGDHLTNLHRL.GPEAG.G
RetrocopyFIKKMGDHLTNLHRLAGPEAGLG

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 98 .31 RPM
SRP007412_cerebellum 0 .00 RPM 54 .48 RPM
SRP007412_heart 0 .03 RPM 53 .34 RPM
SRP007412_kidney 0 .36 RPM 966 .76 RPM
SRP007412_liver 0 .37 RPM 1042 .84 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3626 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3626 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3626 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4665
Pan troglodytes retro_ptro_3101
Gorilla gorilla retro_ggor_2894

Parental genes homology:
Parental genes homology involve 23 parental genes, and 301 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001334333 retrocopies
Canis familiaris ENSCAFG000000038611 retrocopy
Callithrix jacchus ENSCJAG0000000025013 retrocopies
Cavia porcellus ENSCPOG000000205581 retrocopy
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
Felis catus ENSFCAG0000000334837 retrocopies
Gorilla gorilla ENSGGOG000000119999 retrocopies
Loxodonta africana ENSLAFG0000003124811 retrocopies
Macaca mulatta ENSMMUG000000039099 retrocopies
Mustela putorius furoENSMPUG0000000330429 retrocopies
Mus musculus ENSMUSG000000507081 retrocopy
Nomascus leucogenys ENSNLEG0000000471610 retrocopies
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
Pongo abelii ENSPPYG0000000317312 retrocopies
Pongo abelii ENSPPYG00000010223 11 retrocopies
Pan troglodytes ENSPTRG0000001126811 retrocopies
Rattus norvegicus ENSRNOG000000208437 retrocopies
Sus scrofa ENSSSCG0000000315333 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000206397 retrocopies



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