RetrogeneDB ID:

retro_lafr_315

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_12:54545218..54545982(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSLAFG00000000972
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_315
AGCTTATTTCTTCAGACACCTCAAATCGTAACAGATAAAGATTACTCTGTGATGGCCAATTCTCAGACTGTGGTGGTAAC
AGCAGGAGTTCATCAGCAAGCGGGGGAGAGTCATCTCAATCTGGTGCAGAGGAATGTTAATGTCTTCAAACTCACTATTC
CTCAGATCATCAAGTACAGTCCCAACTGCATCGTAATTGTGGTTTCCAACCCAGCAAGTATTCTTACATATGTTACCTGG
AAACTAAGTGGATTACCCAAGCACCGTGCGATTGGAAGTGGTTGTAACCTGGATTCTGCTAGATTTTGCTATCATATGGC
TGAAAAACTTGGCATTCATCCCAGGAGCTGCCATGGATGGATTTTGGGAAAACATAACAACTCAAGTGTGGCAGTGTAGA
GTGGCGTGAACATGGCAGGGGTTTCTTTCCAGGAACTAAATCCAGAGAGGAGGACAGACAATGACAGTGAAGACTGGGAG
GAAGTGCATAAAATGGTGGTTGAAAGTGCCTATGAAATCATCAAGCTAAAAGGATACACCACCTGGGCTACTGGATTAAG
TGTGGCTGATCTGATTGAATCCATGTTGAAAACCTATCCAGGATTCACCCAGTGTCAACGATGATGAAGAGGATGGATAG
CATTGAGAATGAAGTCTTCCTGAGCCTACCATGTATCCTGAATGGTTGGGGGTTAACAAGTGTTATCAACCAGAAGCTGA
AGGATGATGAGGTTGTTGAACCCGAGAAGAGCACAGACACTGTG

ORF - retro_lafr_315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.64 %
Parental protein coverage: 76.58 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLFLQTPKIVADKDYSVTANSKVVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSN
SLFLQTP.IV.DKDYSV.ANS..VVVTAGV.QQ.GES.LNLVQRNVNVFK..IPQI.KYSP.CI.IVVSN
RetrocopySLFLQTPQIVTDKDYSVMANSQTVVVTAGVHQQAGESHLNLVQRNVNVFKLTIPQIIKYSPNCIVIVVSN
ParentalPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAG
P..ILTYVTWKLSGLPKHR.IGSGCNLDSARF.Y.MAEKLGIHP.SCHGWILG.H..SSVAV.SGVN.AG
RetrocopyPASILTYVTWKLSGLPKHRAIGSGCNLDSARFCYHMAEKLGIHPRSCHGWILGKHNNSSVAV*SGVNMAG
ParentalVSLQELNPEMGTDNDSENWKEVHKLVVESAYEVIKLKGYTNWAIGLSVADLIESMLK-NLSRIHPVSTMV
VS.QELNPE..TDNDSE.W.EVHK.VVESAYE.IKLKGYT.WA.GLSVADLIESMLK.NLSRIHPVSTM.
RetrocopyVSFQELNPERRTDNDSEDWEEVHKMVVESAYEIIKLKGYTTWATGLSVADLIESMLK<NLSRIHPVSTMM
ParentalKGMYGIENEVFLSLPCVLNARGLTSVINQKLKDDEVAQLKKSADTL
K.M..IENEVFLSLPC.LN..GLTSVINQKLKDDEV....KS.DT.
RetrocopyKRMDSIENEVFLSLPCILNGWGLTSVINQKLKDDEVVEPEKSTDTV

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_315 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 19 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
Canis familiaris ENSCAFG000000121959 retrocopies
Cavia porcellus ENSCPOG000000071381 retrocopy
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
Felis catus ENSFCAG000000126391 retrocopy
Gorilla gorilla ENSGGOG000000157581 retrocopy
Loxodonta africana ENSLAFG00000000972 2 retrocopies
retro_lafr_197, retro_lafr_315 ,
Loxodonta africana ENSLAFG000000113071 retrocopy
Macropus eugenii ENSMEUG000000048251 retrocopy
Microcebus murinus ENSMICG000000171832 retrocopies
Myotis lucifugus ENSMLUG000000121551 retrocopy
Macaca mulatta ENSMMUG000000026794 retrocopies
Monodelphis domestica ENSMODG000000177861 retrocopy
Mustela putorius furoENSMPUG000000001725 retrocopies
Mus musculus ENSMUSG000000302464 retrocopies
Otolemur garnettii ENSOGAG000000047639 retrocopies
Pteropus vampyrus ENSPVAG000000024623 retrocopies
Rattus norvegicus ENSRNOG000000130003 retrocopies
Sus scrofa ENSSSCG000000005761 retrocopy



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