RetrogeneDB ID:

retro_lafr_1234

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_9:58514818..58515703(-)
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:ENSLAFG00000032009
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1234
ATGTCTGGAGCCCTTGACATCCTACAGATGAAGGAGGAGAATGTCCTCTAATTCCTTGCAGCAGGAACCAACTTAGGTGG
CATCAACCTTGACCTCCAAATGGAGCAGTACATCTACAAAAGGAAAAGTGATGGCAACTACATCTCATACCTGAAGAGGA
CCAGGGAGAAGCTTTTGTGGCAGCTCAGGCCATTGTTGCCATTGAAAACCCAACTGATTTCTCTGTTATATCCTCCAAGA
ATACTGGCCAGCAGGCTATGCTAAAGTTTTCTGTTGCCCCTGGCACCGCTCCTATTGCTGGGCACTTCACTCCTGGAACC
TTCACTAACCAGATCCAGGCAGCCCTCTGAGAGCCACATCTTCTGGTGGTTACTGATCCTACAGCTGACCACCAGCCTCT
CACAGAGGCATCTTACATGAACCTGCCCACCATTGCTCTGAGTAAGACAGATTCTCCTCTGAGCTGCTTGGACATTGCCA
TCCCATGCAACAACAAGAGAGCTCACTCAATGGCTCTGATGTGGTGGATGCTGGCCTGGGAAGTTCTGCGCATGTGTGGC
ACCATCTCCCAGGAGCACCCGTGGGAGGTCATGCATGACCTCTACTTCTACAGGGATCTCGAATAAATTAAAAAGGAAAA
GCAGGCTGCAGCTGAAAAGGCTGTAACCAAGGAAGAATTTCAGGGTGAATGGACTGCTCCCTTTCCTGAATTTACTGTTG
CTCAGCCCGAGGTCATAAACTGATCCGAAGGTGTGCAGGTGCCTTCTGTGCCCAGTCAGCAGTTTCCTATTGAACAGTGG
AGTGTTCAGCTTGCAACTGAAGACTGGTCTACAACGCTCCAACGCTCAGGCCACTGAGTAGGTAGAAACCACCACGGGGT
GGTCT

ORF - retro_lafr_1234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLL-LAARAIVAIE
MSGALD.LQMKEE.VL.FLAAGT.LGG.NLD.QMEQYIYKRKSDG.YI..LKRT.EKLL..AA.AIVAIE
RetrocopyMSGALDILQMKEENVL*FLAAGTNLGGINLDLQMEQYIYKRKSDGNYISYLKRTREKLL<VAAQAIVAIE
ParentalNPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASY
NP.D.SVISS.NTGQ.A.LKF..A.G..PIAG.FTPGTFTNQIQAA..EP.LLVVTDP.ADHQPLTEASY
RetrocopyNPTDFSVISSKNTGQQAMLKFSVAPGTAPIAGHFTPGTFTNQIQAAL*EPHLLVVTDPTADHQPLTEASY
ParentalVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEE
.NLPTIAL..TDSPL...DIAIPCNNK.AHS..LMWWMLA.EVLRM.GTIS.EHPWEVM.DLYFYRD.E.
RetrocopyMNLPTIALSKTDSPLSCLDIAIPCNNKRAHSMALMWWMLAWEVLRMCGTISQEHPWEVMHDLYFYRDLE*
ParentalIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTAAQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAA
I.KE.QAAAEKAVTKEEFQGEWTAP.PEFT.AQPEV...SEGVQVPSVP.QQFP.E.WS.Q.ATEDWS..
RetrocopyIKKEKQAAAEKAVTKEEFQGEWTAPFPEFTVAQPEVIN*SEGVQVPSVPSQQFPIEQWSVQLATEDWSTT
Parental-PTAQATEWVGTTTEWS
...AQATE.V.TTT.WS
Retrocopy>SNAQATE*VETTTGWS

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_1234 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 36 parental genes, and 485 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000041831 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000896213 retrocopies
Bos taurus ENSBTAG0000000975719 retrocopies
Canis familiaris ENSCAFG0000000510127 retrocopies
Callithrix jacchus ENSCJAG0000000967515 retrocopies
Cavia porcellus ENSCPOG000000087157 retrocopies
Dasypus novemcinctus ENSDNOG0000000404827 retrocopies
Dipodomys ordii ENSDORG000000082671 retrocopy
Equus caballus ENSECAG000000130625 retrocopies
Erinaceus europaeus ENSEEUG000000052922 retrocopies
Echinops telfairi ENSETEG000000181604 retrocopies
Felis catus ENSFCAG0000000273922 retrocopies
Homo sapiens ENSG000001680282 retrocopies
Gorilla gorilla ENSGGOG0000001503811 retrocopies
Loxodonta africana ENSLAFG00000032009 5 retrocopies
Macropus eugenii ENSMEUG0000000816914 retrocopies
Microcebus murinus ENSMICG0000000451832 retrocopies
Macaca mulatta ENSMMUG000000079302 retrocopies
Macaca mulatta ENSMMUG0000002296519 retrocopies
Monodelphis domestica ENSMODG000000109672 retrocopies
Mustela putorius furoENSMPUG0000000246321 retrocopies
Mus musculus ENSMUSG000000325181 retrocopy
Nomascus leucogenys ENSNLEG0000000562649 retrocopies
Otolemur garnettii ENSOGAG000000288308 retrocopies
Ochotona princeps ENSOPRG0000000450516 retrocopies
Pongo abelii ENSPPYG000000139934 retrocopies
Pan troglodytes ENSPTRG000000228411 retrocopy
Pteropus vampyrus ENSPVAG0000000779419 retrocopies
Rattus norvegicus ENSRNOG0000001864527 retrocopies
Sorex araneus ENSSARG0000001440210 retrocopies
Sarcophilus harrisii ENSSHAG000000068962 retrocopies
Sus scrofa ENSSSCG000000112669 retrocopies
Tupaia belangeri ENSTBEG0000001594654 retrocopies
Tarsius syrichta ENSTSYG000000044586 retrocopies
Tursiops truncatus ENSTTRG0000001449624 retrocopies
Vicugna pacos ENSVPAG000000123074 retrocopies



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