RetrogeneDB ID:

retro_lafr_719

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_32:11307319..11307666(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS20
Ensembl ID:ENSLAFG00000002515
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_719
GCTTTTAAGGACACTAGAAAGACACCCGTGGAATCAGAGATGGCCATCCACCAGATAAGAATTACTCTAACCACCCACAG
TGTAAAATCCCTGGACAAGCTGTGTGTTGACTTGATTAGAGGCACAAAGAAGAACCTCAAAGTGAAGGGACCGGTTCAGA
TGCCTACCAAGGCTCTGAGAATCACTACAAAGAAAATTCCTTGTGGAGAAGGTTCTGAAACCTGAGATTGTTTCCAGATG
AGAATCCACAAGCAACTCATCAACTTGCACAGTCCTTCCAAGATCATTAGGAGATCACTTCCATTAGTATTGAGCCAGGA
GCAGAGACCGAAGTCACCATTGCAGAT

ORF - retro_lafr_719 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.27 %
Parental protein coverage: 98.32 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCG
AFKDT.KTPVE.E.AIH.IRITLT...VKSL.K.C.DLIRG.K.KNLKVKGPV.MPTK.LRITT.K.PCG
RetrocopyAFKDTRKTPVESEMAIHQIRITLTTHSVKSLDKLCVDLIRGTK-KNLKVKGPVQMPTKALRITTKKIPCG
ParentalEGSKTWDRFQMRIHKRLIDLHSPSEIVK-QITSISIEPGVEVEVTIAD
EGS.T.D.FQMRIHK.LI.LHSPS.I....ITSISIEPG.E.EVTIAD
RetrocopyEGSET*DCFQMRIHKQLINLHSPSKIIR<EITSISIEPGAETEVTIAD

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_719 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 14 parental genes, and 149 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000608717 retrocopies
Canis familiaris ENSCAFG0000002988420 retrocopies
Callithrix jacchus ENSCJAG000000166314 retrocopies
Cavia porcellus ENSCPOG0000001169710 retrocopies
Echinops telfairi ENSETEG000000033943 retrocopies
Gorilla gorilla ENSGGOG0000000183721 retrocopies
Loxodonta africana ENSLAFG00000002515 8 retrocopies
Myotis lucifugus ENSMLUG000000290592 retrocopies
Macaca mulatta ENSMMUG000000213141 retrocopy
Mustela putorius furoENSMPUG0000001045215 retrocopies
Nomascus leucogenys ENSNLEG0000000121419 retrocopies
Otolemur garnettii ENSOGAG0000000776010 retrocopies
Rattus norvegicus ENSRNOG000000085557 retrocopies
Sus scrofa ENSSSCG0000000624912 retrocopies



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