RetrogeneDB ID:

retro_lafr_328

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_12:60732448..60732942(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSLAFG00000006572
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_328
CCAGCTCCTGTAGAAGTCACATACAAGAACATGAGATTTCTGAAGACACACAGTCCAATCAACACGACCTTAAACAAATT
TATAGAGGAACTTCCGGAATATGGAGTTACCAAGATAGTAAGAGTATGTAAGGCAGCTTGAGACACTGCTCTTGAGGAAG
AAGAAAGCATCCATGTTCGCGATTGGCCTGGTGATGATGGTGCACCGCAGTCCAACCAGAATGTTGATGGCTGGTTAAGT
CCTGTAAAAATTAAGTTTTGTGGAGAACCTGCTGTATTGCCGTTTGTTGTGTGGCAGGTCTTCGGAGCACTCCAGTGCTT
GTTGCCCCGGCATTAGCTGAAGGTGGAATGAGATATGAAGACGCAGTACAGTTCAGGAGACAAAAGCAGCGTGGAGCTTT
CGACAGCAAGGAACTTTTGTGTTTGGAGAAGTAGAGTCCTAAAATGTGGCTGTGGTTCAAAGTCTCCAAGCGTCATAGAA
ACAACTGCTGCATT

ORF - retro_lafr_328 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.4 %
Parental protein coverage: 95.98 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTALVEKEGIHVLDWPFDDGAPP
PAPVEVTYKNMRFL.TH.P.N.TLNKFIEEL..YGVT.IVRVC.A..DTAL.E.E.IHV.DWP.DDGAP.
RetrocopyPAPVEVTYKNMRFLKTHSPINTTLNKFIEELPEYGVTKIVRVCKAA*DTALEEEESIHVRDWPGDDGAPQ
ParentalSNQIVDDWLSLVKIKFREEPG-CCIAVHCVAGLGSRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSK
SNQ.VD.WLS.VKIKF..EP..C.IAV.CVAGL.S..PVLVA.AL.EGGM.YEDAVQF.RQK.RGAF.SK
RetrocopySNQNVDGWLSPVKIKFCGEPA<C-IAVCCVAGLRS-TPVLVAPALAEGGMRYEDAVQFRRQKQRGAFDSK
ParentalQLLYLEKYRPKMRLRFKESNGHRNNCCI
.LL.LEK..PKM.L.FK.S..HRNNCCI
RetrocopyELLCLEK*SPKMWLWFKVSKRHRNNCCI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_328 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 32 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024383 retrocopies
Bos taurus ENSBTAG000000022753 retrocopies
Canis familiaris ENSCAFG000000024903 retrocopies
Callithrix jacchus ENSCJAG000000017433 retrocopies
Cavia porcellus ENSCPOG000000257595 retrocopies
Dasypus novemcinctus ENSDNOG000000185074 retrocopies
Dipodomys ordii ENSDORG000000099606 retrocopies
Equus caballus ENSECAG000000224836 retrocopies
Erinaceus europaeus ENSEEUG000000064773 retrocopies
Echinops telfairi ENSETEG000000081836 retrocopies
Felis catus ENSFCAG000000011993 retrocopies
Homo sapiens ENSG000001122455 retrocopies
Gorilla gorilla ENSGGOG000000225217 retrocopies
Latimeria chalumnae ENSLACG000000071831 retrocopy
Loxodonta africana ENSLAFG00000006572 8 retrocopies
Myotis lucifugus ENSMLUG000000011621 retrocopy
Macaca mulatta ENSMMUG000000027771 retrocopy
Monodelphis domestica ENSMODG000000187015 retrocopies
Mustela putorius furoENSMPUG000000031181 retrocopy
Mus musculus ENSMUSG0000002606410 retrocopies
Nomascus leucogenys ENSNLEG000000004406 retrocopies
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
Ochotona princeps ENSOPRG000000049384 retrocopies
Pongo abelii ENSPPYG000000167435 retrocopies
Pan troglodytes ENSPTRG000000183144 retrocopies
Pteropus vampyrus ENSPVAG000000152252 retrocopies
Rattus norvegicus ENSRNOG000000117714 retrocopies
Rattus norvegicus ENSRNOG000000463704 retrocopies
Tupaia belangeri ENSTBEG0000000995614 retrocopies
Tarsius syrichta ENSTSYG000000046322 retrocopies
Tursiops truncatus ENSTTRG000000041296 retrocopies
Vicugna pacos ENSVPAG000000042779 retrocopies



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