RetrogeneDB ID:

retro_lafr_592

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_24:38487469..38488750(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSLAFG00000002565
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_592
AGCCGGAAGCGCATGAAGGACAGGTCCGAGTCAGTTTACGAGGCACTCTTCCTGAGGGGGGAGGACAGCGACGTGCAGAT
TCGCGCATTGGGGGAGGAGTGGAACTTGCACAGGGTCTACTTGTGCCAGTCAGGCTACTTCTCAAGTATGTTCAGCGGCG
CCTGGCGGGAGACAACCATGAACATGATCGAGCTGCAGATGCCCGACGAGAACATCGATCGGGATTCCCTGCACGAGGCT
TTCGGCTCGCTGTACCGTGACGCTGTGCTCATCCCGCCCAGCCGAGTAATAGCCATCCTGGCCACAGCCAGCATGCTGCA
GTTCGACAAGCTGATTCAGCAGTGCGAGGAGGTAATGAAGGAAACGGTTGGTGCCCAGACCGTGTGTGGCTACTACTACT
CTGCCGAGAGCTACGGGCTCCAAAGTGTCAGGACCATGTGCTTCCAGTGGCTGCTGGACAACCTGATGACCCAGCGTAGT
GAAGAGTTATTGCGAGAAGTCAGCAAGGATCTTATGAAAGAACTCATTGCCTCTTCAGAGCTCTTGGTGCTTGAGGTGGA
GATGGACGTGTACATCACCCTGAAAAAATGGATGTTTCTGCAGCTGCAGCCAACATGGAGGGGGCCGCGCAGAACTCTAC
TGTCGAACGCTGACGTATGGTTTGCCAGGCAAAGGAGGGAGGCGGAGGGTGCCCCTTTTCTGGAGACCGAGCAGGGCACT
GCCTTCGTGCCGGTCTTCCGGCAGCTGCGGCTTGCCTACATAATCTGTGACCTGCCTTCTGCCCGTGTCCTCGACCAGGA
CTCACTAATCCCTGCTGCATGGCTGACCCCGGTGTATAAAGAGCAGTGGCTCGCTCTGCTCCGAGCTGAGCAGACGAGGG
ATCTCGGGCCCATGAACGTGTATGTATCTGATCTTGAGAGGACCAGCATGCGGTGTGGCGGCCAGCTTCTCAGAGATGAA
CAGTGCAGCTGGCGGTGGGCCGGCTTCAACTTCGGCTGGGACCTAGTGGTGTGCTACACTAACCGGCGAATCATTTTCCG
GCGCAGTGCCCTAAACAAGTCCTGTGGCCTCGGGGTCAGCTTACTATGGCAGAGAAAAGTCGCGTTCCGCCTGCGTCTGG
CCTCTTTGGACAGGGCTGGAAGAGCCATGTTCAGGAAGGACACTGAATACCAGGTGCTTTCCTTGAGAAAGGATCAAGAG
CTAGAGGTCGTGAACCTGGAGGACCAAGAGGTGATCTTCCCCATGTATGTGGCCTGTAACTTCCTGTACCTCCCTCCAGA
G

ORF - retro_lafr_592 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.72 %
Parental protein coverage: 81.02 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMNIIELEIPDQ
SRK..K..S...Y..LFL.GE.SD..I.ALGEEW.LH..YLCQSGYFSSMFSG.W.E..MN.IEL..PD.
RetrocopySRKRMKDRSESVYEALFLRGEDSDVQIRALGEEWNLHRVYLCQSGYFSSMFSGAWRETTMNMIELQMPDE
ParentalNIDIEALQVAFGSLYRDDVLIKPSRVIAILAAACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGTYGL
NID...L..AFGSLYRD.VLI.PSRVIAILA.A.MLQ.D.LIQQC.E.MKET....TVCGYY.SA..YGL
RetrocopyNIDRDSLHEAFGSLYRDAVLIPPSRVIAILATASMLQFDKLIQQCEEVMKETVGAQTVCGYYYSAESYGL
ParentalDSVKKKCLEWLLNNLMTHQNVELLRELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSL
.SV...C..WLL.NLMT....ELLRE.S...MK.LI.SS.L.V..VEMDVY..LKKWMFLQL.P.W.G..
RetrocopyQSVRTMCFQWLLDNLMTQRSEELLREVSKDLMKELIASSELLVLEVEMDVYITLKKWMFLQLQPTWRGPR
ParentalKQLLTETDVWLSKRRKDFEGIAFLETEQGKPFVSVFRHLRLQYIISDLASARIIEQDALVPSEWLSSVYK
..LL...DVW....R...EG..FLETEQG..FV.VFR.LRL.YII.DL.SAR...QD.L.P..WL..VYK
RetrocopyRTLLSNADVWFARQRREAEGAPFLETEQGTAFVPVFRQLRLAYIICDLPSARVLDQDSLIPAAWLTPVYK
ParentalQQWFAMLRAEQDSEVGPQEINKEELEGHSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNT
.QW.A.LRAEQ....GP.......LE..SMRCG..L..D....WRW.GFNFG.DL.V.YTNR.IIF.R..
RetrocopyEQWLALLRAEQTRDLGPMNVYVSDLERTSMRCGGQLLRDEQCSWRWAGFNFGWDLVVCYTNRRIIFRRSA
ParentalLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCN
LN..C...VSL...R..AFRLRLAS.D..G.......T.YQ.L.L.KDQE..V.NL.....IFP.Y..CN
RetrocopyLNKSCGLGVSLLWQRKVAFRLRLASLDRAGRAMFRKDTEYQVLSLRKDQELEVVNLEDQEVIFPMYVACN
ParentalFLYISPE
FLY..PE
RetrocopyFLYLPPE

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_592 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 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG00000002565 3 retrocopies
retro_lafr_220, retro_lafr_592 , retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,


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