RetrogeneDB ID:

retro_lafr_1079

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_66:11120873..11121363(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM204A
Ensembl ID:ENSLAFG00000016774
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1079
ATGTGGCGTGAGCTGCTACCTCTTGGCCTAAATGAAAGTGATGTTGAGTTAAATTCTGAAGATGAAGCCGTATCAGAAAG
CTCTGGACTTCACTTACAGGAAGCTAAAGATGAGATGACTAGAGAAACAGAAATCTCAGATTTCCCGAGAGACAGACCAA
AAACCGAAACAGAGCCAAATGCAAATGCCTATACAGAGTACCCTTCCAGAACTTCCTTACACATGCGGGATAAATCTCAG
TAACTGCATAAAAATCATTCTGAACTGCAAACCTCAACCTCGAGATTCAGGAGGAAAAAAGGAAATGCTCCAGGAAAGGT
AAATTGAAGCAAGAAGCGACACCTCGTAGTGAACATCCTCTAACGAAACCCAGCGGAAGGCGCTTACTCAGTATTTTGGA
GTCGGTTCAATCCCCTGTAAAAAAGGAATCAACGACAAGTCAGGTCTTGAAAAAAGCATAGCCCAGGCTGTGCAAGAATG
GGATATTGAG

ORF - retro_lafr_1079 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.41 %
Parental protein coverage: 72.1 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMWSGLLPPGLNESDVELSSEDEAKSENSGLHLLEAEEDQMTRKTEISDFPTDGPKTETEANTNAYEECPS
MW..LLP.GLNESDVEL.SEDEA.SE.SGLHL.EA..D.MTR.TEISDFP.D.PKTETE.N.NAY.E.PS
RetrocopyMWRELLPLGLNESDVELNSEDEAVSESSGLHLQEAK-DEMTRETEISDFPRDRPKTETEPNANAYTEYPS
ParentalGISLHTWNRFQELHKKHSEQKTSASRFRRK-KRKRSRKGKLKNEETSCSEQ-SSNETQWKELTQYFGVND
..SLH.....Q.LHK.HSE..TS.SRFRRK.KRK.SRKGKLK.E.T..SE..SSNETQ.K.LTQYFGV..
RetrocopyRTSLHMRDKSQ*LHKNHSELQTSTSRFRRK<KRKCSRKGKLKQEATPRSEH<SSNETQRKALTQYFGVG-
ParentalRFDPPVKKKKIDKSGLEKSIDQAVEEWNIE
....P.KK...DKSGLEKSI.QAV.EW.IE
Retrocopy--SIPCKKGINDKSGLEKSIAQAVQEWDIE

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_1079 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 24 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000001019912 retrocopies
Callithrix jacchus ENSCJAG000000195651 retrocopy
Cavia porcellus ENSCPOG000000027471 retrocopy
Dasypus novemcinctus ENSDNOG000000013832 retrocopies
Dipodomys ordii ENSDORG000000020741 retrocopy
Echinops telfairi ENSETEG000000038552 retrocopies
Homo sapiens ENSG000001656691 retrocopy
Gorilla gorilla ENSGGOG000000105661 retrocopy
Loxodonta africana ENSLAFG00000016774 4 retrocopies
Macropus eugenii ENSMEUG000000026741 retrocopy
Myotis lucifugus ENSMLUG000000274541 retrocopy
Macaca mulatta ENSMMUG000000127411 retrocopy
Monodelphis domestica ENSMODG000000093783 retrocopies
Mustela putorius furoENSMPUG000000032391 retrocopy
Oryctolagus cuniculus ENSOCUG000000051501 retrocopy
Otolemur garnettii ENSOGAG000000285411 retrocopy
Procavia capensis ENSPCAG000000115011 retrocopy
Pongo abelii ENSPPYG000000026941 retrocopy
Pan troglodytes ENSPTRG000000029841 retrocopy
Pteropus vampyrus ENSPVAG000000046212 retrocopies
Sorex araneus ENSSARG000000008193 retrocopies
Sarcophilus harrisii ENSSHAG000000116013 retrocopies
Tarsius syrichta ENSTSYG000000091471 retrocopy
Tursiops truncatus ENSTTRG000000033511 retrocopy



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