RetrogeneDB ID:

retro_lafr_729

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_33:22230838..22231469(-)
Located in intron of:ENSLAFG00000017227
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPE
Ensembl ID:ENSLAFG00000014127
Aliases:None
Description:Ribulose-phosphate 3-epimerase [Source:UniProtKB/TrEMBL;Acc:G3TCM6]


Retrocopy-Parental alignment summary:






>retro_lafr_729
GATTTAAGGGCCATGTACCTCTGGATGCTGGGCTCCGGGGCCAATTATCTACACCTGTATGTAATGGATGAGTGTTTTGT
TCCCAGCATCACCTTTGATCACCCTGTGAGAAAGCCTCTGAAAGCACTAGGCCAGGACCCTTTCTTTGACAGGCACGTGA
TGGTGTCCAGGCTGTAATAGTGGGTAAAGCCAATGACTGTAGCAGGTGCCAATCAATATATGCCTTTCAACTTGAGGCTA
CTGAGAACCCAGGGGCTTTGATTAAAGACATTGAGGAGGATGGGATGAAGGTTGATCTTGCCATCAAACCAGGAACTACA
GTTGAGTGTTCGGTGCCATGGGCTAATCAGATAGATACAGGCTTTGATATGACAGTGGAACCTGGCCTTGGAGGGCAGAA
ATTCATGGACAACATGATGCCAAAGGTTCACTGGTCGAGGACCTAGTTCTTGTCTTTGGACATAGAGGTTGATGGCAGAG
TATGTCCTGACACTGTCCATGAGTGTGCAGAGGCAGGAGCTAACATGATTGTGTCTGACACTGCCATTAGGAGGAGTGAA
GAGCTGGATCTGTGATCAACTGGTTAAGAAATGTTCGCTCAGAAGCTGCTCAGAAATGTTCTCTTGATAGA

ORF - retro_lafr_729 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.36 %
Parental protein coverage: 92.54 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSRPEQWVKPMAVAG
.L.A..L.ML.SGA.YLHL.VMD..FVP.ITF.HPV...L.K.LGQDPFFD.H.MVSR...WVKPM.VAG
RetrocopyDLRAMYLWMLGSGANYLHLYVMDECFVPSITFDHPVRKPL-KALGQDPFFDRHVMVSRL**WVKPMTVAG
ParentalANQY-TFHL-EATENPGALIKDIRENGMKVGLAIKPGTTVEYLAPWANQIDMALVMTVEPGFGGQKFMED
ANQY..F.L.EATENPGALIKDI.E.GMKV.LAIKPGTTVE...PWANQID....MTVEPG.GGQKFM..
RetrocopyANQYMPFNL<EATENPGALIKDIEEDGMKVDLAIKPGTTVECSVPWANQIDTGFDMTVEPGLGGQKFMDN
ParentalMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSED-PRSVINLLRNVCSEAAQKR
MMPKVHW.RT.F.SLDIEVDG.V.PDTVH.CAEAGANMIVS..AI.RSE....SVIN.LRNV.SEAAQK.
RetrocopyMMPKVHWSRT*FLSLDIEVDGRVCPDTVHECAEAGANMIVSDTAIRRSEE<AGSVINWLRNVRSEAAQKC
ParentalCLDR
.LDR
RetrocopySLDR

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_729 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 18 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000049653 retrocopies
Bos taurus ENSBTAG000000478062 retrocopies
Canis familiaris ENSCAFG000000138113 retrocopies
Choloepus hoffmanni ENSCHOG000000011105 retrocopies
Dasypus novemcinctus ENSDNOG000000031931 retrocopy
Equus caballus ENSECAG000000000023 retrocopies
Latimeria chalumnae ENSLACG000000028001 retrocopy
Loxodonta africana ENSLAFG00000014127 2 retrocopies
retro_lafr_675, retro_lafr_729 ,
Macaca mulatta ENSMMUG000000105132 retrocopies
Monodelphis domestica ENSMODG000000158276 retrocopies
Mustela putorius furoENSMPUG000000079482 retrocopies
Oryctolagus cuniculus ENSOCUG000000169951 retrocopy
Pongo abelii ENSPPYG000000131324 retrocopies
Pteropus vampyrus ENSPVAG000000144522 retrocopies
Sus scrofa ENSSSCG000000161521 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000103221 retrocopy
Tursiops truncatus ENSTTRG000000009081 retrocopy
Vicugna pacos ENSVPAG000000115851 retrocopy



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