RetrogeneDB ID:

retro_lafr_546

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_20:26920625..26921033(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3A
Ensembl ID:ENSLAFG00000021624
Aliases:None
Description:Histone H3 [Source:UniProtKB/TrEMBL;Acc:G3T157]


Retrocopy-Parental alignment summary:






>retro_lafr_546
ATGGCTCGTACAAAGCAGACTGACCACAAATCAGCCAGTGGTAAAGAACCCAGTAAGCAAGTGGCCGCAAAAGCCACTTG
CAAGAGTGCGCCCTCTACCTGAGGGATGAAGAGACCTCATCATCGTAGGCCTGGTACCGTGGCACTCCTGGAAATCAGCC
GTTATCGGAAATCCACTGAACTTCCGATTCACAAACTTCCCTTCCAAGACCTGCTGCAAGATATTGCTCAGGACTTCAAA
ACAGATCTGTGTTTCCAGAGCACAGCTATTGGTGCTTTGCAATAGGCAAGTGAGGGGTGCCTGGTTGACCTTTTTGAAGA
CATCAACCTGTGTGCTATCCATGCCAAACATGTGACAATTATGCCAAAAGACATCCAGCTACCATGCCATATACTTGGAG
AATGTGCT

ORF - retro_lafr_546 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
MARTKQT..KS..GK.P.KQ.A.KA..KSAPST.G.K.PH..RPGTVAL.EI.RY.KSTEL.I.KLPFQ.
RetrocopyMARTKQTDHKSASGKEPSKQVAAKATCKSAPST*GMKRPHHRRPGTVALLEISRYRKSTELPIHKLPFQD
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
L...IAQDFKTDL.FQS.AIGALQ.ASE..LV.LFED.NLCAIHAK.VTIMPKDIQL...I.GE.A
RetrocopyLLQDIAQDFKTDLCFQSTAIGALQ*ASEGCLVDLFEDINLCAIHAKHVTIMPKDIQLPCHILGECA

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_546 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 15 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097653 retrocopies
Choloepus hoffmanni ENSCHOG0000000966110 retrocopies
Cavia porcellus ENSCPOG000000047077 retrocopies
Gorilla gorilla ENSGGOG000000229287 retrocopies
Loxodonta africana ENSLAFG000000080833 retrocopies
Loxodonta africana ENSLAFG00000021624 4 retrocopies
Myotis lucifugus ENSMLUG0000001544710 retrocopies
Mus musculus ENSMUSG0000006074319 retrocopies
Oryctolagus cuniculus ENSOCUG000000246442 retrocopies
Oreochromis niloticus ENSONIG000000199755 retrocopies
Ochotona princeps ENSOPRG000000159522 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000242268 retrocopies
Tupaia belangeri ENSTBEG0000000617713 retrocopies
Vicugna pacos ENSVPAG000000115315 retrocopies



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