RetrogeneDB ID:

retro_ptro_1201

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:17:2537092..2537708(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A1
Ensembl ID:ENSPTRG00000008694
Aliases:None
Description:Pan troglodytes eukaryotic translation initiation factor 4A, isoform 1 (EIF4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001098575]


Retrocopy-Parental alignment summary:






>retro_ptro_1201
ATGTCAGCAAGTCAGGATTCCCGATCCAGAGACAATGGCCCTAATGGGATGGAGCCTGGAGACGTCAGAGAGAGTAACTG
GAATGAGATTGTAGACAGCTTTGATGACATGAACCTCTTGGAGTCCCTGCTCCGTGGCATCTACGCCTATGGTTTTGAGA
AGCCCTTGCCGTCCAGCAGCGAGCCATTCTACCTTGTATCAAGGGTTATGATGTGATCACTCAAGCCCAGTCTGGGACTG
GAAAACTGCCACATTTGCCACATCAATTCTGCAACAGATTGAATTAGATCTAAAGGCCACCCAGGCTTTGATTCTAGCAC
CCACTCGGGAATTGGCTCAGCAGATATAGAAGGTGGGCATGGCACTCGGAGACTGCATGGGTGCCTCCTATCACGCCTGT
AGAGGGGGCACCCATGTGTGTGCTGAGGTGCAGAAACTGCAGATGGAAGCTCCCCATATAATTGGGGGTACCCCTGGCCA
TGTGTGTGATATGCTTAACTGCAGATACGTGTCTCCCAAATACATCAAGATATTTGTACTGGACAAAGCTGATGAAATGT
TAAGCTGTGGATTCAGGGACCAGATCTATGACATATTCCAAAAGCTCAACAACAAC

ORF - retro_ptro_1201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.06 %
Parental protein coverage: 50.74 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPS-AIQQRAILPCIKG
MSASQDSRSRDNGP.GMEP..V.ESNWNEIVDSFDDMNL.ESLLRGIYAYGFEKP..A.QQRAILPCIKG
RetrocopyMSASQDSRSRDNGPNGMEPGDVRESNWNEIVDSFDDMNLLESLLRGIYAYGFEKPL<AVQQRAILPCIKG
ParentalYDVIAQAQSGTGK-TATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT
YDVI.QAQSGTGK.TATFA.SILQQIELDLKATQAL.LAPTRELAQQI.KV.MALGD.MGAS.HAC.GGT
RetrocopyYDVITQAQSGTGK<TATFATSILQQIELDLKATQALILAPTRELAQQI*KVGMALGDCMGASYHACRGGT
ParentalNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSN
.V.AEVQKLQMEAPHII.GTPG.V.DMLN.RY.SPKYIK.FVLD.ADEMLS.GF.DQIYDIFQKLN.N
RetrocopyHVCAEVQKLQMEAPHIIGGTPGHVCDMLNCRYVSPKYIKIFVLDKADEMLSCGFRDQIYDIFQKLNNN

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 108 .23 RPM
SRP007412_cerebellum 0 .00 RPM 114 .43 RPM
SRP007412_heart 0 .00 RPM 90 .88 RPM
SRP007412_kidney 0 .00 RPM 190 .54 RPM
SRP007412_liver 0 .00 RPM 366 .10 RPM
SRP007412_testis 0 .00 RPM 114 .55 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1201 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1201 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1201 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1796
Gorilla gorilla retro_ggor_1321
Pongo abelii retro_pabe_1474

Parental genes homology:
Parental genes homology involve 16 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000049001 retrocopy
Erinaceus europaeus ENSEEUG000000035811 retrocopy
Felis catus ENSFCAG000000248971 retrocopy
Homo sapiens ENSG0000016196010 retrocopies
Gorilla gorilla ENSGGOG000000247028 retrocopies
Macropus eugenii ENSMEUG000000107802 retrocopies
Myotis lucifugus ENSMLUG000000034153 retrocopies
Macaca mulatta ENSMMUG000000134991 retrocopy
Monodelphis domestica ENSMODG000000070903 retrocopies
Mus musculus ENSMUSG000000597967 retrocopies
Nomascus leucogenys ENSNLEG000000095477 retrocopies
Pan troglodytes ENSPTRG00000008694 10 retrocopies
Pan troglodytes ENSPTRG000000157181 retrocopy
Rattus norvegicus ENSRNOG000000306283 retrocopies
Sorex araneus ENSSARG000000060177 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000248141 retrocopy



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