RetrogeneDB ID:

retro_lafr_66

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_60:9834368..9835934(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000029279
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LPCAT2
Ensembl ID:ENSLAFG00000003965
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_66
CTCGCTCACCAAGGACTCCGAGTCGCCCGTGGAGGGGACAAGGTGATGGAGGCGGCCTCTGAAGCAGAGCCATGGGAATC
CAGGCGCATCCAGTTGAGGAGCAAGTCCTTATACCCACCGGCGGTGGCCAACCCCTTTGTGCACCAGGTGCGCATCAGTG
CCTGGGGCTGGGTGCGCACCATCCTCTTGGGGGTTGTGCTGGTGCCTGTGCGGGTGTCCTGCATCGCCTTCCTCTTCATC
TTCATCTGGCCCGTGGCCACACTTGCCACCATTGGCCGTCCTATTCAACCTGCCCAGCCCGCCTCGAATTGGAGAAGACA
ACTGACGCAACCAGCTCTTAAGTTCCTGTTTCGGGCTATGCTCTTTTTGGTGGGGTTCGTGGTTAAAGTGAAAGGGAAAA
AGGCAACACGAGACGAGGCCCCCATCTTAGTGGTGGCGCCGCACACCACCTTCTTTGACGTAATCGCCTGTGTTGTGGCA
GGATTGCCATCCGTGGTCTCAGCTAGTGGAAACATGAGGATCCCAGGGGTTGGGAAAGTCATGCTGTCCACGCAGCCAGT
ACTTGTGACCCGGGATGACCCCAATTCCAGGAGGAGTACCCGGAAAGAAATCGTGAGGCGCGTGACATCCGGAAAGAAGT
GGCCACAGATCCTGATTTTCCCAGAAGGAGTGTGTACTAATCGCTCCTGTCTGGTCACTTTTAAACTTGGGGCCTTCTCT
CCAGGTGTTCCGGTGCAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGACACGGTGACCTGGACCTGGCAGGGGTTTTC
AGCATTACAGGTCTTTATGCTGACCCTGAGTCAACTCTTCACTAGGGTGACAGTTGAGTTTATGTCTGTTTATACCCCAA
ATGATGACGAAAAAGAAGATCCCATCCTCTTTGCCAATGCAGTGCGGATCAACATGGCAAATGCTCTGGGCGTGCCAGTG
ACAGATCACACTTACGAAGACTGCAAACTGATGATTTCTGCAGGTCACCTTCAACTACCCATGGAAGCCGGTTTGGTGGA
ATTTACGAAAATTAGCCAGAAATTGAAGTTAGATTGGGATAATATTCATCAGCGTTTGGATGAATATGCTGCAATTGCAG
TTGCCTCAAAAGGAGGAAAGATAGGAATTGAAGAGTTTGCAAGCTTCTTAAAACTCCCAGTTTCAAAACCCCTGCAACAA
CTTTTTGCCCTCTTTGACAGAAATAATGATGGCAGCATAGACTTCAGAGAGTATGTGATAGGCCTGACTGTCCTGTGCAA
CCCTGACAACACTAAAAAGATTCTGAAAATGTCCTTTAAGCTTTTTGATCTTGATAAGGATGGTTTCATAACAGAAAAGG
AGTTAACTTCTATACTGCGGGCAGCTTTTGGAGTGCCAGATCTTGATGCTTCCAAGCTCTTTCAGGAAATAGCTGGAGAG
AACTCAGAGTACATTTCATTCAAAACCTTTAAGAAATTTGGCCTGAAGCATCCAGCATATGCCAAGTTATTTAGTTCATA
CCTAGACCTCCAGGCAGCCCATATATTTTCATTACCACAAGTAGTA

ORF - retro_lafr_66 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.0 %
Parental protein coverage: 92.53 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLLGIILLPIRALLVALILLLAWPFAAISTACCPEKLTHPIAGWRRKVTQPALKFLGRALFFSMGFIVTVK
LLG..L.P.R....A......WP.A...T...P.....P...WRR..TQPALKFL.RA..F..GF.V.VK
RetrocopyLLGVVLVPVRVSCIAFLFIFIWPVATLATIGRPIQPAQPASNWRRQLTQPALKFLFRAMLFLVGFVVKVK
ParentalGKIASPLEAPIFVAAPHSTFFDGIACVIAGLPSMVSRNENAQVPVIGRLLRAVQPVLVSRVDPDSRKTTI
GK.A...EAPI.V.APH.TFFD.IACV.AGLPS.VS...N...P..G......QPVLV.R.DP.SR..T.
RetrocopyGKKATRDEAPILVVAPHTTFFDVIACVVAGLPSVVSASGNMRIPGVGKVMLSTQPVLVTRDDPNSRRSTR
ParentalNEIIKRATSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFFQL
.EI..R.TSG..WPQIL.FPEG.CTNRSCL.TFK.GAF.PGVPVQPVLLRYPN.LDTVTWTWQG....Q.
RetrocopyKEIVRRVTSGKKWPQILIFPEGVCTNRSCLVTFKLGAFSPGVPVQPVLLRYPNTLDTVTWTWQGFSALQV
ParentalCMLTFCQPFTKVEVEFLPVQVPNDEEKSDPVLFANKVRNIMADALEIPVTDHTYEDCRLMISAGQLTLPM
.MLT..Q.FT.V.VEF..V..PND.EK.DP.LFAN.VR..MA.AL..PVTDHTYEDC.LMISAG.L.LPM
RetrocopyFMLTLSQLFTRVTVEFMSVYTPNDDEKEDPILFANAVRINMANALGVPVTDHTYEDCKLMISAGHLQLPM
ParentalEAGLVEFTKISRKLKLDWDGIRKHLDEYASIARSSKGGRIGIEEFAEYLKLPVSDVLRQLFALFDRNHDG
EAGLVEFTKIS.KLKLDWD.I...LDEYA.IA..SKGG.IGIEEFA..LKLPVS..L.QLFALFDRN.DG
RetrocopyEAGLVEFTKISQKLKLDWDNIHQRLDEYAAIAVASKGGKIGIEEFASFLKLPVSKPLQQLFALFDRNNDG
ParentalSIDFREYVIGLAVLCNPANTEEIIQVAFKLFDVDEDGYITEEEFSTILQASLGVPDLDVSGLFKEIAQGD
SIDFREYVIGL.VLCNP.NT..I....FKLFD.D.DG.ITE.E...IL.A..GVPDLD.S.LF.EIA...
RetrocopySIDFREYVIGLTVLCNPDNTKKILKMSFKLFDLDKDGFITEKELTSILRAAFGVPDLDASKLFQEIAGEN
ParentalS--ISYEEFKSFALKHPEYAKIFTTYLDLQTCHVFSLPEV
S..IS...FK.F.LKHP.YAK.F..YLDLQ..H.FSLP.V
RetrocopySEYISFKTFKKFGLKHPAYAKLFSSYLDLQAAHIFSLPQV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_66 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 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000192721 retrocopy
retro_btau_64,
Callithrix jacchus ENSCJAG000000129021 retrocopy
retro_cjac_2945,
Dasypus novemcinctus ENSDNOG000000068591 retrocopy
retro_dnov_1735,
Dipodomys ordii ENSDORG000000131931 retrocopy
retro_dord_399,
Equus caballus ENSECAG000000096491 retrocopy
retro_ecab_865,
Erinaceus europaeus ENSEEUG000000142771 retrocopy
retro_eeur_109,
Homo sapiens ENSG000000872531 retrocopy
retro_hsap_185,
Gorilla gorilla ENSGGOG000000051441 retrocopy
retro_ggor_266,
Loxodonta africana ENSLAFG00000003965 1 retrocopy
retro_lafr_66 ,
Loxodonta africana ENSLAFG000000114311 retrocopy
retro_lafr_1156,
Myotis lucifugus ENSMLUG000000040081 retrocopy
retro_mluc_88,
Macaca mulatta ENSMMUG000000044781 retrocopy
retro_mmul_392,
Mus musculus ENSMUSG000000331921 retrocopy
retro_mmus_270,
Nomascus leucogenys ENSNLEG000000012581 retrocopy
retro_nleu_994,
Pongo abelii ENSPPYG000000073581 retrocopy
retro_pabe_445,
Pan troglodytes ENSPTRG000000081242 retrocopies
retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus ENSPVAG000000078011 retrocopy
retro_pvam_173,
Rattus norvegicus ENSRNOG000000166431 retrocopy
retro_rnor_309,
Sorex araneus ENSSARG000000119141 retrocopy
retro_sara_88,
Sarcophilus harrisii ENSSHAG000000123831 retrocopy
retro_shar_116,
Tursiops truncatus ENSTTRG000000011821 retrocopy
retro_ttru_188,


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