RetrogeneDB ID:

retro_lafr_1071

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_65:2545508..2545759(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MYCBP
Ensembl ID:ENSLAFG00000020514
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1071
TACAAAGCCACCCACTGGAAGCATGAGCAGTTCCGGAGGAACTTAGAGAAGTTGGAGGGGCTGGACACGCTTACCAAGGT
GTTAGTAGCCTTATATAAAAAACCAGAGAAACCTAATAGTGCTTTGGATTTTTTAAAGCATGTCTTAGGAGCTGCAACCG
CAGAAAATCAGCAGTAGAGCTGCTTAGCCTAGAATTGGCAGAAATAAAAGAGGGATATGAATCTATTGTATAAGAAAATT
AAAAAACAAAA

ORF - retro_lafr_1071 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.94 %
Parental protein coverage: 92.31 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYKAADSKREQFRRYLEKSGVLDTLTKVLVALYEEPEKPNSALDFLKHHLGAATPENPE-IELLRLELAEM
YKA...K.EQFRR.LEK...LDTLTKVLVALY..PEKPNSALDFLKH.LGAAT.EN....ELL.LELAE.
RetrocopyYKATHWKHEQFRRNLEKLEGLDTLTKVLVALYKKPEKPNSALDFLKHVLGAATAENQQ<VELLSLELAEI
ParentalKEKYEAIVEENKKLK
KE.YE.IV.EN.K.K
RetrocopyKEGYESIV*EN*KTK

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_1071 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 19 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000306221 retrocopy
Choloepus hoffmanni ENSCHOG000000131363 retrocopies
Callithrix jacchus ENSCJAG000000365581 retrocopy
Cavia porcellus ENSCPOG000000204471 retrocopy
Homo sapiens ENSG000002141142 retrocopies
Gorilla gorilla ENSGGOG000000058102 retrocopies
Loxodonta africana ENSLAFG00000020514 2 retrocopies
retro_lafr_1071 , retro_lafr_903,
Macropus eugenii ENSMEUG000000003151 retrocopy
Mus musculus ENSMUSG000000286471 retrocopy
Nomascus leucogenys ENSNLEG000000118142 retrocopies
Oryctolagus cuniculus ENSOCUG000000222032 retrocopies
Otolemur garnettii ENSOGAG000000244353 retrocopies
Pongo abelii ENSPPYG000000015151 retrocopy
Pan troglodytes ENSPTRG000000005652 retrocopies
Rattus norvegicus ENSRNOG000000171662 retrocopies
Sus scrofa ENSSSCG000000036492 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000215472 retrocopies
Tarsius syrichta ENSTSYG000000056901 retrocopy
Tursiops truncatus ENSTTRG000000095831 retrocopy



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