RetrogeneDB ID:

retro_ptro_1198

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:17:77123706..77124075(+)
Located in intron of:ENSPTRG00000009702
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF5A
Ensembl ID:ENSPTRG00000008674
Aliases:None
Description:eukaryotic translation initiation factor 5A [Source:HGNC Symbol;Acc:3300]


Retrocopy-Parental alignment summary:






>retro_ptro_1198
GGCTTTGTGGTACTCAAAGGCCGGCCACGTAAGATCGTCGAGATGTCTACTTCGATGACTGGCAAGCATGGCCATGCCAA
GGTCCACCTGGTTGGTACTGACATCTTTACTGGGAAGAAATATGGAGATATCTGCCTGTCAATTCATAACATGGATGTCC
CCAGCATCAAAAGGAATGACTTCCAGCTGATTGGCATCCAGGATGGGCACCTATCACTGCTCCAGGACAGCATGGAGGTG
CGAGAGGACCTTCGTCTGCATGAGGGAGACCTTGTCAAAGAGACTGAGCAGAAGTACAGCTGTGGAGAAGAGATCCTGAT
CATGGTGCTGTCTGCCATGACCGAGGAGGCAGCTGCTGCAATCAAGGCT

ORF - retro_ptro_1198 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.8 %
Parental protein coverage: 66.85 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGY
GFVVLKGRP.KIVEMSTS.TGKHGHAKVHLVG.DIFTGKKY.DIC.S.HNMDVP.IKRNDFQLIGIQDG.
RetrocopyGFVVLKGRPRKIVEMSTSMTGKHGHAKVHLVGTDIFTGKKYGDICLSIHNMDVPSIKRNDFQLIGIQDGH
ParentalLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKA
LSLLQDS.EVREDLRL.EGDL.KE.EQKY.CGEEILI.VLSAMTEEAA.AIKA
RetrocopyLSLLQDSMEVREDLRLHEGDLVKETEQKYSCGEEILIMVLSAMTEEAAAAIKA

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 113 .09 RPM
SRP007412_cerebellum 0 .00 RPM 78 .72 RPM
SRP007412_heart 0 .00 RPM 76 .57 RPM
SRP007412_kidney 0 .00 RPM 130 .79 RPM
SRP007412_liver 0 .00 RPM 257 .98 RPM
SRP007412_testis 0 .00 RPM 105 .07 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1198 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1198 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1198 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1788
Pongo abelii retro_pabe_1468

Parental genes homology:
Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001325073 retrocopies
Gorilla gorilla ENSGGOG000000120322 retrocopies
Monodelphis domestica ENSMODG000000066522 retrocopies
Otolemur garnettii ENSOGAG000000142301 retrocopy
Pan troglodytes ENSPTRG00000008674 3 retrocopies
retro_ptro_1198 , retro_ptro_442, retro_ptro_504,
Pan troglodytes ENSPTRG000000156211 retrocopy
Sus scrofa ENSSSCG000000179391 retrocopy
Tursiops truncatus ENSTTRG000000097831 retrocopy



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