RetrogeneDB ID:

retro_lafr_999

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_59:4462668..4463258(+)
Located in intron of:ENSLAFG00000003535
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EI24
Ensembl ID:ENSLAFG00000010888
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_999
CTTTGGGTGCTTAGCGAAGTTGTCAGTGCTATTTGGTTCCAAGATGTAGCTGATCTAACATCTGAGGTAGCAGGGAGGAA
GCCTCACCCACTCCCTAGTGTCAGCAAAGTAACCACTGAGAAGCTCTTCAGCCTTTTGCTGCAGCATCTTTTCTTTCTCC
CAGGGATGTTTATAAGTCTCTTCCCCACCCATCTTGCTGGTCAGCTCTTAGTCTCCTCATGTGTTCCTTCTGCATTCACT
GGACTGCTTTGAATACCGCTGATTCAATAAGGTAACTGAAACATACCAGTGGCTGTCAGACACAGAAAGGAACGGGACTT
ACTACTTTGGATTGGTTTGCCTTTGGCTTTCCTCACAGCCATGCATTTCTCACACATTATCAGTGGCTGCCTCTTTCCTT
TACTCATTATCAGCACCAATGAAGCAAAGACCCCCTTATTTCAGTTGCGCCTCTATTCCTTGGTGGTCTTCTCAAGCAAC
AGCCTCTTCTACAAGACGGTCTACCTGCAGTCTGCTCTGAGTAGCTCAACCTCTGCAGGAAGTTCCCATCACCACATCCA
TCTCCTGCCAAGCTGAAGGCTGCTGCAGGC

ORF - retro_lafr_999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.38 %
Parental protein coverage: 58.03 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalLFVLSKVVNAIWFQDIADLAFEVSGRKPHPFPSVSKIIADMLFNLLLQALFLLQGMFVSLFPIHLVGQL-
L.VLS.VV.AIWFQD.ADL..EV.GRKPHP.PSVSK.....LF.LLLQ.LF.L.GMF.SLFP.HL.GQL.
RetrocopyLWVLSEVVSAIWFQDVADLTSEVAGRKPHPLPSVSKVTTEKLFSLLLQHLFFLPGMFISLFPTHLAGQL<
ParentalVSLL-HMSLLYSLYCFEYRWFNKGIEMHQRLSNIERNWPYYFG-FGLPLAFLTAMQSSYIISGCLFSILF
.SLL.H..LL.SL.CFEYR.FNK..E..Q.LS..ERN..YYFG..GLPLAFLTAM..S.IISGCLF....
RetrocopyLSLL<HVFLLHSLDCFEYR*FNKVTETYQWLSDTERNGTYYFG<IGLPLAFLTAMHFSHIISGCLF----
ParentalPLFIISANEAKTPGKAYLFQLRLFSLVVFLSNRLFHKTVYLQSALSSSTSA-EKFPSPHPSPAKLKAAAG
PL.IIS.NEAKTP....LFQLRL.SLVVF.SN.LF.KTVYLQSALSSSTSA..KFPSPHPSPAKLKAAAG
RetrocopyPLLIISTNEAKTP----LFQLRLYSLVVFSSNSLFYKTVYLQSALSSSTSA<RKFPSPHPSPAKLKAAAG

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_999 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 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009902 retrocopies
Bos taurus ENSBTAG000000072022 retrocopies
Canis familiaris ENSCAFG000000108981 retrocopy
Choloepus hoffmanni ENSCHOG000000126693 retrocopies
Cavia porcellus ENSCPOG000000072722 retrocopies
Dasypus novemcinctus ENSDNOG000000023624 retrocopies
Equus caballus ENSECAG000000158611 retrocopy
Erinaceus europaeus ENSEEUG000000032741 retrocopy
Felis catus ENSFCAG000000151001 retrocopy
Homo sapiens ENSG000001495473 retrocopies
Loxodonta africana ENSLAFG00000010888 15 retrocopies
Microcebus murinus ENSMICG000000030233 retrocopies
Myotis lucifugus ENSMLUG000000015831 retrocopy
Macaca mulatta ENSMMUG000000100093 retrocopies
Nomascus leucogenys ENSNLEG000000074513 retrocopies
Oryctolagus cuniculus ENSOCUG000000146701 retrocopy
Otolemur garnettii ENSOGAG000000018386 retrocopies
Ochotona princeps ENSOPRG000000134912 retrocopies
Procavia capensis ENSPCAG000000127621 retrocopy
Pongo abelii ENSPPYG000000040333 retrocopies
Pan troglodytes ENSPTRG000000044444 retrocopies
Pteropus vampyrus ENSPVAG000000045321 retrocopy
Rattus norvegicus ENSRNOG000000303911 retrocopy
Sarcophilus harrisii ENSSHAG000000173331 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000042992 retrocopies
Tarsius syrichta ENSTSYG000000047472 retrocopies



Copyright © RetrogeneDB 2014-2017