RetrogeneDB ID:

retro_lafr_22

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_6:93032353..93035671(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000002055
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:IPO5
Ensembl ID:ENSLAFG00000016190
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_22
ATGGCGGCTACCGGGCTTGCGGGTTTCTCCGCTGCCGTGTCGGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTCAT
CAATCCAAGCTGTATGGTGCGGAGGCAGGCCGAGGAGATCTATGAAAATATCCCGGGTCTGTGTAAGACTACGTTCCTCA
TAGATGCCGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAAGTCTATCCAAACCTACCTCCTGATGTTCAGAGGGACGTCAAGATTGAACTAATACTGGCTGTGAAGTT
AGAAACACATGCCAGCATGAGGAAAAAACTTTGCGATATTTTTGCGGTGCTGGCCAGGAATTTGATAGATGAGGATGGCA
CTAACCACTGGCCCGAAGGTTTGAAATTCCTGATTGATTCCATCTACTCTAAAAATGTGGTTCTATGGGAAGTTGCAATT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGAGCGGCACGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGTATTCAAGATCAGGAGCATCCAGCTATCAGGACATTATCCGCTAGAGCTGCAGCTGCATTTGTCCTTGCTAATGAGA
ATAATGTCGCTCTTTTCAAAGACTTTGCAGACTTGCTGCCAGGAATCTTACAGGCTGTGAATGACTCCTGCTACCAGGAT
GATGATTCCGTCCTGGAATCCCTTGTTGAGATTGCTGATACTGTTCCTAAGTACTTGGGCCCTTATTTAGAAGATACTCT
GCAGCTGAGTTTAAAGTTATGCGGCGACTCTAGGCTTAGTAATCTGCAACGCCAGCTGGCTCTTGAAGTAATAGTGACCT
TGTCTGAAACGGCAACCCCAATGTTGAAGAAATATACAAATATTATTGCACAGGCTATCCCTCACATATTAGCGATGATG
GTTGATCTACAAGATGACGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
CGAGAGTGCACTAGACAGACTGGCTTGTGGACTCGGTGGAAAAGTGGTTTTACCAATGACCAAGGAGCATATCATGCAGA
TGCTTCAGAGCCCTGACTGGAAATATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAGCAA
ATGGAATCAACTCTAGATGAAATGGTTAACTCTGTTTTGCATTTTCTTCAGGATCCTCACCCGAGGGTGAGGGCTGCAGC
CTGTAGTACACTTGGACAGATGGCTACAGATTTTGCACCTAGTTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTT
TGTTGCGTACCATGGAAAATCAAGGTAATCAGCGCGTGCAATCACATGCAGCTTCTGCTCTTATTATTTTTATCGAAGAC
TGCCCCAAATCATTGCTAGCTCTATATTTAGATAGCATGGTGAAAAACTTACATTCCATCCTGGTGATTAAACTGCAAGA
ATTGATTCGGAATGGAACAAAGTTGGCCTTGGAACAGCTTGTGACAACCATTGCCTCAGTTGCAGATACAATAGAAGAAG
AATTTGTTCCGTACTATGATATATTTATGCCCTCTCTAAAGCACATTGTTGAGCTTGCTGTTCAAAAGGAACTCAAGCTT
CTGAAAGGAAAAACTATTGAATGCATCAGCCATGTTGGCCTTGCTGTTGGGAAGGAAAAATTTATGCAAGATGCATCAAA
CGTGATGCAGCTGTTGTTGAAGACACAATCAGACTTAAATAACATGGAAGATGATGACCCTCAGATCTCTTACATGGTTT
CAGCATGGGCTAGGATGTGTAAAATTCTTGGCAAAGATTTTCAACAGTACCTTCCACTGGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTCGCTCTCTTAGACACGCAGGATGTGGAGAATATGAGTGATGATGATGGCTGGCAGTT
TGTAAATCTTGGAGACCAGCAGAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCGACTGCTTGCCAGATGTTGG
TTTACTATGCTAAGGAGTTAAGGGAAGGATTTGTGGAATATACGGAACAAGTTGTGAAGCTGATGGTTCCCTTACTGAAG
TTTTATTTCCACGACAATGTTCGAGTGGCAGCAGCAGAGTCCATGCCTTTTCTGCTAGAATGTGCAAAAATTAATGGACC
GGAGTATCTTGCACTGATGTGGCAATTCATATGTGATCCCTTAATCAAGGCTATTGGGACGGAACCTGATGCAGATGTAC
TCTCAGAAATAATGAATTCTTTTGCAAAGTCCATCGAAGTAATGGGAGATGGGTGTCTCAATGATGAGCACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAGCTCGAAGGGCACTTTAAAAACCAAGAATTGCGACAGGTTAAAAGGCAGGAAGAAAA
CTACGACCAGCAGATTGAAATGTCTCTGCAAGACGAGGATGAATGCGATGTTTATATTCTAACCAAAGTATCAGATATCT
TGCACTCATTATTTAGTACTTACAAGGAAAAGATCTTACCATGGTTTGAACAGCTACTTCCGTTAATTGTAAATCTAATT
TGTTCAAGTAGGCCATGGCCAGACAGACAGTGGGGACTATGCATATTTGATGATATCATAGAGCACTGCAGTCCGACCTC
GTTTAAATACGTAGACTATTTTCGGTGGCCAATGCTACTAAACATGCGGGACAATAACCCTGAAGTCAGGCAAGCTGCTG
CCTATGGCCTGGGAGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCTAAAACCAAAAAAAGTGTCATTGCTACAGAGAATTGTATCTCAGCAATAGGGAAGAT
TTTGAGGTTTAAGCCTAACTGTGTGAATGTGGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAGGATA
AAGAGGAAGCTCTTCAGACTTTGAGTTTTCTCTGTGACTTAATTGAAAATAACCACCCAGTTGTACTTGGTCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCTGAAGGAAAAATTAATGAGACAATTAACTGTGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTTGTGCGCCAGGTCCAGACTGATGACGAGTTATGGTTGGAATGCGCATCCCAACTTGATGAGGAAC
AGCAGGCAGCCTTACAGGCGTTGCTAAATTTTGCTTGA

ORF - retro_lafr_22 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.57 %
Parental protein coverage: 55.03 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKVRILIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIG
K...LI..GTKL.LEQ.VT.IASVADT.EE.FVPYYD.FMPSLKHIVE.AVQKEL.LL.GKTIECIS..G
RetrocopyKLQELIRNGTKLALEQLVTTIASVADTIEEEFVPYYDIFMPSLKHIVELAVQKELKLLKGKTIECISHVG
ParentalLAVGKEKFMQDASDVMQLLLKTQTDFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTAA
LAVGKEKFMQDAS.VMQLLLKTQ.D.N.MEDDDPQISYM.SAWARMCKILGK.FQQYLP.V..PL.KTA.
RetrocopyLAVGKEKFMQDASNVMQLLLKTQSDLNNMEDDDPQISYMVSAWARMCKILGKDFQQYLPLVIEPLIKTAS
ParentalIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVK
.KP.VALLDTQD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVK
RetrocopyAKPDVALLDTQDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVK
ParentalLMVPLLKFYFHERVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAK
LMVPLLKFYFH..VRVAAAESMP.LLECA...GPEYL..MW.F.CD.LIKAIGTEPD.DVLSEIM.SFAK
RetrocopyLMVPLLKFYFHDNVRVAAAESMPFLLECAKINGPEYLALMWQFICDPLIKAIGTEPDADVLSEIMNSFAK
ParentalCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDI
.IEVMGDGCLN.EH.EELGGILKAKLE.HFKNQELRQVKRQ.E.YD.Q.E.SLQDED..DVYILTKVSDI
RetrocopySIEVMGDGCLNDEHLEELGGILKAKLEGHFKNQELRQVKRQEENYDQQIEMSLQDEDECDVYILTKVSDI
ParentalLHSIFSSYKEKVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVC
LHS.FS.YKEK.LPWFEQLLPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY..YF..PML....
RetrocopyLHSLFSTYKEKILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVDYFRWPMLLNMR
ParentalDNSPEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQAADSRTKENINATENCISAVGKMMKFKPD
DN.PEVRQAAAYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.S.TK....ATENCISA.GK...FKP.
RetrocopyDNNPEVRQAAAYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTKKSVIATENCISAIGKILRFKPN
ParentalCVNVDEVLPHWLSWLPLHEDKEEAVQTFSYLCDLIESNHPIVLGPNNTNLPKIFKIIADGEMHEAIKHED
CVNVDEVLPHWLSWLPLHEDKEEA.QT.S.LCDLIE.NHP.VLGPNN.NLPKI..IIA.G...E.I..ED
RetrocopyCVNVDEVLPHWLSWLPLHEDKEEALQTLSFLCDLIENNHPVVLGPNNSNLPKIISIIAEGKINETINCED
ParentalPCAKRLANVVRQVQTSGGLWTECVGQLSLEQQGAIQELLNSA
PCAKRLANVVRQVQT...LW.EC..QL..EQQ.A.Q.LLN.A
RetrocopyPCAKRLANVVRQVQTDDELWLECASQLDEEQQAALQALLNFA

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_22 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 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG000000393741 retrocopy
retro_btau_104,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG000000060611 retrocopy
retro_chof_11,
Cavia porcellus ENSCPOG000000048272 retrocopies
retro_cpor_265, retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG00000016190 1 retrocopy
retro_lafr_22 ,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG000000306622 retrocopies
retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys ENSNLEG000000078312 retrocopies
retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,


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