RetrogeneDB ID:

retro_lafr_98

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_85:6428305..6429796(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000027414
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSLAFG00000002565
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_98
ATGGGGCCCTTGAGCAGCCGGGTCCTGCGAAGCAGGGAACCAGGCCCAGCGGATCCACAGCCAGAAGCCCAGGCGGGCCC
CAGTTACGTATTTGGAAATCGAAAGCGCAAGCAGAGCAGCAGGCCCTGCTTGGGCCCAAAGTCTAAGGAGAACTGCCACA
GGTCTGTAGGCCAGGGGGAGGATCTACAGCAAGTCCTCAGCGCAAGCCCCGGGAAAAAACTTAGGATCACATCCAAATAC
ACTTACGAAACTTTATTTTTGAATGGGGAAACCAGTGACATTAAGATCTGCGCCCTGGGGAAAGTATGGTGTTTACACAA
AATATTTTTATGTCAGTCAGGCTACTTTGCTAGCATGTTCAGAGGTTCTAGGAAAGACTCTCACAAGGATATTATTGAGC
TGGAGATTAATGACCAGAATATAGATGTAGAATCCCTGCATTTTGTACTAGGTTCATTGTACAGGGATGAATATGTCTTA
ATGGAGCCCCTTCAAGTTCCAGGAGTTTTGGCAACAGCATGCTTGCTTCAGGTAGAAGGCTTAATTCAGCAGTGTGATGA
AACCATGAAGGAAACAATTAATGTAAAAACTGTATGTGGCTATTATACAGCAGCAGAGGCCTATGGGTTAGATTCAGTAA
AGACAAATTGCTTTGAATGGCTTCTTCACAACCTGATGACACACCCAAGTATTCAGCTTTACAAAGAACTCAGTATAGAT
CTCATGAATCTGCTTATCTCTTCTTCTAATTTATTAGTAATGCAAAAGGAAATGGATGTATACACCACACTTAAAGAGTG
GATGTTCCTTCACCTCAACCCAGCTTGGAACGGCTCAATGAAACGGCTCTTAGATAATGCAAACAACTGGTTTTACAGGC
ACAAGAAATGTGTTGGTTACACCACCTTTCTCGAAACTGAACAAGGCATAGTCTTTCAACCAGTGTTCAAAAATTTGAGG
TTTCAGCATATCATCTGTGACCTAGCCTCCACGAAAGTTATTGAACAAGATGCTCTAATACCTTCAGAATGGTTATCATC
TATTTACAAACAACAATGGCTTACCTTGCTTAAGGCACAGCAATACAGGGAAATTGGGCCTCGAGTCATCAATGAAACAG
AACTTGAAGGATACAGCATGAGATGTGGTAAAAGGATTGTCAAGGATGGAAAATACTCCTGGAAGTGGTCAGGTTACAAC
TTTGGCTTTCCCTTACATGTCATCTTCACCAGCCATTATATAATTTTCAAGCAAAATATTTTTAGTCTACCATGTGAAGG
TTCTGTCTGTTTACAACCTCTAAGAAACATCACATTCAGATTAAGTTTGGTATATTTTGATTCTACTGGAAAACTAAGTT
TCAGTAAAACAACTGGCTATAAAATCCTTACCTTTGAAAATGATGAGGAACAAGTGGTAATGAAATTGGAGAGCATAGTT
CTGAGCTTCCCTTTATATATATTCTGTAACTTCCTGTTTATATCCTTAGAA

ORF - retro_lafr_98 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.04 %
Parental protein coverage: 83.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEGDEQQRLLNTPRSRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKE
.G...Q..L......KKL..TSKY.Y.TLFLNGE.SDIKICALG..W.LHKI.LCQSGYF.SMF.GS.K.
RetrocopyQGEDLQQVLSASPG-KKLRITSKYTYETLFLNGETSDIKICALGKVWCLHKIFLCQSGYFASMFRGSRKD
ParentalSSMNIIELEIPDQNIDIEALQVAFGSLYRDD-VLIKPSRVIAILAAACMLQLDGLIQQCGETMKETINVK
S...IIELEI.DQNID.E.L....GSLYRD..VL..P..V...LA.AC.LQ..GLIQQC.ETMKETINVK
RetrocopySHKDIIELEINDQNIDVESLHFVLGSLYRDEYVLMEPLQVPGVLATACLLQVEGLIQQCDETMKETINVK
ParentalTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELLRELSINVMKQLIGSSNLFVMQVEMDVYTALKK
TVCGYYT.A..YGLDSVK..C.EWLL.NLMTH....L..ELSI..M..LI.SSNL.VMQ.EMDVYT.LK.
RetrocopyTVCGYYTAAEAYGLDSVKTNCFEWLLHNLMTHPSIQLYKELSIDLMNLLISSSNLLVMQKEMDVYTTLKE
ParentalWMFLQLVPSWNGSLKQLLTETDVWLSKRRKDFEGIAFLETEQGKPFVSVFRHLRLQYIISDLASARIIEQ
WMFL.L.P.WNGS.K.LL.....W.....K......FLETEQG..F..VF..LR.Q.II.DLAS...IEQ
RetrocopyWMFLHLNPAWNGSMKRLLDNANNWFYRHKKCVGYTTFLETEQGIVFQPVFKNLRFQHIICDLASTKVIEQ
ParentalDALVPSEWLSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGHSMRCGRKLAKDGEYCWRWTGFNFGFDLL
DAL.PSEWLSS.YKQQW...L.A.Q..E.GP..IN..ELEG.SMRCG....KDG.Y.W.W.G.NFGF.L.
RetrocopyDALIPSEWLSSIYKQQWLTLLKAQQYREIGPRVINETELEGYSMRCGKRIVKDGKYSWKWSGYNFGFPLH
ParentalVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNL
V..T..YIIFK.N....PC.GSV.LQP.R.I.FRL.L..FDS.GKL..S.TTGY.ILT.E.D.EQVVM.L
RetrocopyVIFTSHYIIFKQNIFSLPCEGSVCLQPLRNITFRLSLVYFDSTGKLSFSKTTGYKILTFENDEEQVVMKL
ParentalDSRLLIFPLYICCNFLYISPE
.S..L.FPLYI.CNFL.IS.E
RetrocopyESIVLSFPLYIFCNFLFISLE

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_98 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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