RetrogeneDB ID:

retro_lafr_651

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_28:20421534..20422311(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000028598
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000028081
Aliases:None
Description:Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G3TW48]


Retrocopy-Parental alignment summary:






>retro_lafr_651
GCCAGCAGCAAGATGCCCTGGTTCTAGGGCTGGGAAATCACCAGGAAGGGAAGGGAATGTGACAGGCATGACACTGCTGG
ATGCACTGGACTCCATCATTCCCCCTGCCCCCCCCCCCACCAACAAGCCCCTGCATCTGCCCCTGCAAGATGTGCACAAG
ATTGGGGGCATTGGCACTGTACCTGTGGGTCGAGTAGAAATAGGCTTCCTCAAGCCTGGCACGATGGGGACCTTTGCCCC
CTGCAATATCACCACTGAGGTCAAGTCTGTGGAAATGCACCTTGAGGCCTTGGCTGAGGCCTTGCCTGGTGACAACGTGG
GCTTCAATGTGAAGAACATGTCAGTGAGGGACATCAGGCGGGGCAATGTGACGGGAACAGCAAGAACAACCTGCCCTCGG
AGGTGGGAAGCTTCCTCTCCCAGGTGATCATTTTCAACCACCCCAGCAACATTGCAGACGGCTACTCCCCAGTTCTGGAC
TGCCACACAGCCCACATGGCCTGCAAGTTTGCTGAGCTAAAGGAGAAGATCGACCGGTGCTCAGGCAAGAACCTTGAAGA
CAACCCCAAAGCCCTGAAGTCCGGGGACTCGGCCATCATCCACATGATCCCGTGCAAGCCCATGTGCGTGGAAAGCTTCT
CAGAGTACCCACCCCTTGGCCGCTTCGCTGTGTGTGGCATGAGGCAGACAGTGGCTGTTGGGGTCATCAAGGCCGTGGAG
AAAAAAGCAGCTACTGGTGGCAGAGTCACCAAGTCAGCCGTGAAAGCAGCCAAGAAG

ORF - retro_lafr_651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.89 %
Parental protein coverage: 55.72 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalASSKMPWFKGWEITRK-EGNVTGMTLLDALDSIIPPARP-TNKPLRLPLQDVYKIGGIGTVPVGRVETGF
ASSKMPWF.GWEITRK.EGNVTGMTLLDALDSIIPPA.P.TNKPL.LPLQDV.KIGGIGTVPVGRVE.GF
RetrocopyASSKMPWF*GWEITRK>EGNVTGMTLLDALDSIIPPAPPPTNKPLHLPLQDVHKIGGIGTVPVGRVEIGF
ParentalLKPGMVVTFAPCNITTEVKSVEMHHEALAEALPGDNVGFNVKNVSVRDIRRGNVTG-DSKNDPPSEVGSF
LKPG...TFAPCNITTEVKSVEMH.EALAEALPGDNVGFNVKN.SVRDIRRGNVTG..SKN..PSEVGSF
RetrocopyLKPGTMGTFAPCNITTEVKSVEMHLEALAEALPGDNVGFNVKNMSVRDIRRGNVTG<NSKNNLPSEVGSF
ParentalLSQVIILNHPGNIAAGYSPVLDCHTAHITCRFAELKEKIDRRSGKKLEDNPKALKSGDSAIIHMIPCKPM
LSQVII.NHP.NIA.GYSPVLDCHTAH..C.FAELKEKIDR.SGK.LEDNPKALKSGDSAIIHMIPCKPM
RetrocopyLSQVIIFNHPSNIADGYSPVLDCHTAHMACKFAELKEKIDRCSGKNLEDNPKALKSGDSAIIHMIPCKPM
ParentalCVESFSEYPPLGRFAVRDMRQTVAVGVIKAVEKKAAAGGKVTKSAMKAAKK
CVESFSEYPPLGRFAV..MRQTVAVGVIKAVEKKAA.GG.VTKSA.KAAKK
RetrocopyCVESFSEYPPLGRFAVCGMRQTVAVGVIKAVEKKAATGGRVTKSAVKAAKK

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_651 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 43 parental genes, and 389 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000778614 retrocopies
Bos taurus ENSBTAG000000145343 retrocopies
Canis familiaris ENSCAFG000000122221 retrocopy
Canis familiaris ENSCAFG000000132491 retrocopy
Callithrix jacchus ENSCJAG000000100516 retrocopies
Cavia porcellus ENSCPOG0000000406715 retrocopies
Dipodomys ordii ENSDORG000000096291 retrocopy
Equus caballus ENSECAG000000203632 retrocopies
Erinaceus europaeus ENSEEUG000000003423 retrocopies
Echinops telfairi ENSETEG0000000423614 retrocopies
Felis catus ENSFCAG0000003097714 retrocopies
Homo sapiens ENSG0000015650827 retrocopies
Gorilla gorilla ENSGGOG0000002567520 retrocopies
Latimeria chalumnae ENSLACG000000029521 retrocopy
Loxodonta africana ENSLAFG00000028081 1 retrocopy
retro_lafr_651 ,
Macropus eugenii ENSMEUG0000000501823 retrocopies
Microcebus murinus ENSMICG0000001531921 retrocopies
Myotis lucifugus ENSMLUG0000001353724 retrocopies
Myotis lucifugus ENSMLUG000000167601 retrocopy
Macaca mulatta ENSMMUG0000000485215 retrocopies
Monodelphis domestica ENSMODG000000185334 retrocopies
Mustela putorius furoENSMPUG000000038166 retrocopies
Mustela putorius furoENSMPUG0000000427110 retrocopies
Mustela putorius furoENSMPUG000000082893 retrocopies
Mus musculus ENSMUSG0000003774215 retrocopies
Nomascus leucogenys ENSNLEG000000014766 retrocopies
Nomascus leucogenys ENSNLEG000000100602 retrocopies
Ornithorhynchus anatinus ENSOANG000000049081 retrocopy
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
Otolemur garnettii ENSOGAG000000046308 retrocopies
Otolemur garnettii ENSOGAG0000000915210 retrocopies
Ochotona princeps ENSOPRG000000166856 retrocopies
Pongo abelii ENSPPYG000000167771 retrocopy
Pan troglodytes ENSPTRG000000183471 retrocopy
Sus scrofa ENSSSCG000000044894 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000288621 retrocopy
Tupaia belangeri ENSTBEG0000001215151 retrocopies
Tupaia belangeri ENSTBEG0000001717016 retrocopies
Tursiops truncatus ENSTTRG0000000011419 retrocopies
Tursiops truncatus ENSTTRG000000018351 retrocopy
Vicugna pacos ENSVPAG000000076379 retrocopies
Drosophila melanogaster FBgn00005571 retrocopy



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