RetrogeneDB ID:

retro_lafr_166

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_0:86374847..86375209(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000004598
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_166
GGGGTTACTAGAGCCATAATCGGGAAATCTAAGAATATTCTCTTTGTCATCACAAAGCCAGATGTTTATAAGAGCCCAGC
TTCAGATACCTACATAGCTTTTCGGGAAGCCAAGATCCAGGACTTATCTCAGCAAGCACAGCTAGCAGTTGCTGAGAAAT
TCAAAATTCAAGGTGAAGCTGTCTCAACATTCAAGAAAACAAACAAACTGTGCAAGAGGAGAGTGAAGAGGGAGCGGCTA
ATGAAACAGGTGTGGAAGTTAAGGACATAGAACTGGTCACGTCACAAGCAAATGTGTGAAAAGCAAAGGTAGTTTGAGAT
CTGAAGAACAATAGTAATGATATTGTAAATGCTATGATGGAA

ORF - retro_lafr_166 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.45 %
Parental protein coverage: 57.21 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQLAAAEKFKVQGEAVS-NIQENTQ
GVTR..I.KSKNILFVITKPDVYKSPASDTYI.F.EAKI.DLSQQAQLA.AEKFK.QGEAVS.NIQEN.Q
RetrocopyGVTRAIIGKSKNILFVITKPDVYKSPASDTYIAFREAKIQDLSQQAQLAVAEKFKIQGEAVS<NIQENKQ
ParentalTPTVQEESEEEEVDETGVEVKDIELVMSQANVSRAKAVRALKNNSNDIVNAIME
..TVQEESEE....ETGVEVKDIELV.SQANV..AK.V..LKNNSNDIVNA.ME
Retrocopy--TVQEESEEGAANETGVEVKDIELVTSQANV*KAKVV*DLKNNSNDIVNAMME

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_166 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 24 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041753 retrocopies
Bos taurus ENSBTAG000000107012 retrocopies
Canis familiaris ENSCAFG000000001418 retrocopies
Callithrix jacchus ENSCJAG000000107018 retrocopies
Cavia porcellus ENSCPOG000000126543 retrocopies
Dipodomys ordii ENSDORG000000145222 retrocopies
Equus caballus ENSECAG000000152421 retrocopy
Erinaceus europaeus ENSEEUG000000104585 retrocopies
Homo sapiens ENSG000001965316 retrocopies
Loxodonta africana ENSLAFG00000004598 6 retrocopies
Macropus eugenii ENSMEUG000000084123 retrocopies
Microcebus murinus ENSMICG000000164655 retrocopies
Myotis lucifugus ENSMLUG0000000116916 retrocopies
Macaca mulatta ENSMMUG000000030734 retrocopies
Mus musculus ENSMUSG000000613151 retrocopy
Nomascus leucogenys ENSNLEG000000174497 retrocopies
Ochotona princeps ENSOPRG000000017813 retrocopies
Procavia capensis ENSPCAG000000070675 retrocopies
Pongo abelii ENSPPYG000000046706 retrocopies
Pteropus vampyrus ENSPVAG000000080158 retrocopies
Sarcophilus harrisii ENSSHAG000000021751 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000090281 retrocopy
Tursiops truncatus ENSTTRG000000021502 retrocopies
Vicugna pacos ENSVPAG000000040282 retrocopies



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