RetrogeneDB ID:

retro_lafr_1036

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_6:67607252..67607781(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSLAFG00000005569
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1036
ATGGTTCACTACTCACTTCACCCAGAAAATCCCACAAAAGCATGCAAATCAAGAGGTTCAAATCTTCGGGTCCTTTTCGA
GAACACCCATGAAACCGCCCAGGCCATCAAGAATATGCATATCCAAAAAGCCATCTAGTATCTGAAAGATGTCACTTTAT
ACAAGTATGTGTGCTGTTCCAACATTACAATAGTAGAGTTGATAGGTGTGCACAGGCCTAACAATGGGGCCAGATATAGT
GTTGATGGCCCAAAAAGAGTGCCAAATTTTTGCTGCACATGCTTAAAAATGCAGAGTAATGTTAAACTTAAGGGTTTGGG
TGTAGATTCTCTGGTCATTGAGCACATCTATGTGAACAAAGCCCCCAAGATGTGCCACCATATTTACAGAGCTCATGATC
ATATTAACCCATACATGAGCTTCCCTGCCACATTGAGATGATCCTTACTGAAAAAGAACAATTGTTCCTAAACCAGAAGA
GGAGGTTGCACAAAAGAAAAAGATACCCAAGAAGAAACTGAAGAAACAA

ORF - retro_lafr_1036 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.27 %
Parental protein coverage: 96.74 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQ-CVPFRRYNGGVGR
MV.YSL.PENPTK.CKSRGSNLRV.F.NT.ETAQAIK.MHI.KA..YLKDVTL.K..CV.F..YN..V.R
RetrocopyMVHYSLHPENPTKACKSRGSNLRVLFENTHETAQAIKNMHIQKAI*YLKDVTLYKY<CVLFQHYNSRVDR
ParentalCAQAKQWGWTQGRWPKKSAEFLLHM-LKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINP
CAQA.QWG.....WPKKSA.FLLHM.LK...SN..LKGL.VDSLVIEHI.VNKAPKM....YRAH..INP
RetrocopyCAQA*QWGQI*C*WPKKSAKFLLHM>LK-MQSNVKLKGLGVDSLVIEHIYVNKAPKMCHHIYRAHDHINP
ParentalYMS-SPCHIEMILTEKEQ-IVPKPEEEVAQKKKISQKKLKKQ
YMS..PCHIEMILTEKEQ.IVPKPEEEVAQKKKI..KKLKKQ
RetrocopyYMS<LPCHIEMILTEKEQ<IVPKPEEEVAQKKKIPKKKLKKQ

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_1036 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 17 parental genes, and 340 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Homo sapiens ENSG0000026568133 retrocopies
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG00000005569 16 retrocopies
Macropus eugenii ENSMEUG0000001670926 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pan troglodytes ENSPTRG0000001001251 retrocopies
Sus scrofa ENSSSCG0000002964230 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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