RetrogeneDB ID:

retro_lafr_886

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_44:765612..766191(-)
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:ENSLAFG00000015979
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_886
TTCAGTGGCTGATAAGTCGCAGACCTGAGCTTGGCGGGGTATGAGGAGTTGAAATGTGGCAGCCAGGTGCTGTGAGATGT
TGGCTACCAGTTTGACATCTGCTTCACCTCAGTGCAGAACAGTGCAATCCGGATCCTCTGGAAGGTGCTGGATGCCATTG
ACCAGATGCGGCGGCCAGTAGTGAGGACCTGGCACCTCAATGAGCAGCACTATAGGGGTCTGACTGGCCTTAATAAAGCA
GAAGCCGCTGCCAAGCCCAGTGAGGCCTAGGTAAAGATCTGGAGGTGCTCCTCTGATGTCCCACCACTGCCAATGGAACC
TGACCACCCCTTCTATTGCAACATCACTAAGAATGGTAGGTATGCAGACCTCACTGAAGACCAGTTACCTTCCTATGAGA
ATCTGAAGGACACTATTGCTTGAGCCCTACTCTTTTGGAATGAAGAAATAGTTCCTCAGATCAAGAAGGAGAAACAGGTA
CCGATTGCAGCACATGGTAACAGCCTTCGGGGCATCATCAAACATTTGGAGGGTCTTTCTGAACAGGCTATCGTGGAGTT
GAACCTGCCCTACCATCAG

ORF - retro_lafr_886 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.68 %
Parental protein coverage: 81.43 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFSGWYDADLSPAGQEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERH
FSG...ADLS.AG.EE.K.G.Q.L.D.GY.FDICFTSVQ..AIR.LW.VLDAIDQM..PVVRTW.LNE.H
RetrocopyFSG**VADLSLAGYEELKCGSQVL*DVGYQFDICFTSVQNSAIRILWKVLDAIDQMRRPVVRTWHLNEQH
ParentalYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIA
Y.GLTGLNKAE.AAK..EA.VKIWR.S.DVPP.PMEPDHPFY.NI.K..RYADLTEDQLPS.E.LKDTIA
RetrocopyYRGLTGLNKAEAAAKPSEA*VKIWRCSSDVPPLPMEPDHPFYCNITKNGRYADLTEDQLPSYENLKDTIA
ParentalRALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTMQ
.AL.FWNEEIVPQIK..K.V.IAAHGNSLRGI.KHLEGLSE.AI.ELNLP..Q
Retrocopy*ALLFWNEEIVPQIKKEKQVPIAAHGNSLRGIIKHLEGLSEQAIVELNLPYHQ

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_886 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 21 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000126972 retrocopies
Canis familiaris ENSCAFG000000090621 retrocopy
Callithrix jacchus ENSCJAG000000165751 retrocopy
Cavia porcellus ENSCPOG000000068444 retrocopies
Echinops telfairi ENSETEG000000024671 retrocopy
Homo sapiens ENSG0000017131412 retrocopies
Gorilla gorilla ENSGGOG0000002860213 retrocopies
Loxodonta africana ENSLAFG00000015979 1 retrocopy
retro_lafr_886 ,
Microcebus murinus ENSMICG000000076571 retrocopy
Macaca mulatta ENSMMUG000000200271 retrocopy
Monodelphis domestica ENSMODG000000042424 retrocopies
Mustela putorius furoENSMPUG000000170451 retrocopy
Nomascus leucogenys ENSNLEG0000001380410 retrocopies
Oryctolagus cuniculus ENSOCUG000000056795 retrocopies
Pongo abelii ENSPPYG000000025309 retrocopies
Pan troglodytes ENSPTRG0000000280712 retrocopies
Rattus norvegicus ENSRNOG000000505857 retrocopies
Sus scrofa ENSSSCG000000105171 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000259551 retrocopy
Tupaia belangeri ENSTBEG000000059135 retrocopies
Drosophila melanogaster FBgn00148691 retrocopy



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