RetrogeneDB ID:

retro_lafr_1018

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_6:78010601..78012487(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000011105
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL13
Ensembl ID:ENSLAFG00000008122
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1018
CCTCTTTCTCCAGCATTCTTCTGTCTGTGCAAGAGGAAGGTTTTCACATGAAAGTGTCTCTTGGTAACGGCGAAATGGGC
GTCTCTGCCCATTTGCAGCCTTGCAAGGCAGGAACCACGCGCTTTTTTACCAGCAATACTCACAGCTCGGTGGTATTGCA
AGGTTTTGATCAGCTTAGAGTAGAAGGATTGCTTTGCGATGTGACCCTGGTACCAGGTGATGGAGATGAAATCTTCCCTG
TTCACAGAGCTATGATGGCGTCTGCTAGTGATTATTTCAAAGCCATGTTTACGGGTGGAATGAAAGAACAAGATTTAATG
TGCATTAAGCTTCATGGAGTGAACAAGGTTGGTCTGAAGAAAATCATTGATTTTATTTATACTGCGAAACTGTCTCTTAA
TATGGACAATCTTCAAGACACACTTGAAGCTGCCAGCTTTTTGCAGATTTTACCTGTTTTGGACTTCTGTAAAGTATTTC
TTATATCAGGGGTCTCTTTAGATAACTGTGTTGAGGTTGGACGGATTGCTAACACCTACAATCTTATAGAAGTGGACAAA
TATGTTAATAATTTCATCCTGAAGAATTTTCCTGCATTGTTGAGTACTGGGGAGTTCCTGAAACTCCCTTTTGAGCGGCT
TGCCTTTGTGCTTTCCAGTAATAGTCTTAAGCACTGTACTGAACTTGAACTCTTCAAGGCTGCCTGTCGCTGGCTAAGGT
TGGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAACATTCGATTTCCACTGATGACACCGCAGGACCTCATC
AATTACGTGCAAACTGTAGATTTCATGAGAACGGACAATACCTGTGTGAATTTGCTTTTGGAAGCTAGCAATTACCAGAT
GATGCCATATATGCAGCCAGTGATGCAGTCAGACAGAACTGCCATTCGATCTGACTCGACTCACTTGGTTACATTAGGAG
GAGTTTTGAGGCAACAGTTGGTTGTCAGTAAAGAATTAAGAATGTATGATGAAAGGGCACAAGAATGGAAATCTTTAGCC
CCGATGGATGCTCCTCGTTACCAGCATGGCATTGCTGTCATTGGAAACTTTCTTTATGTGGTTGGTGGTCAAAGTAATTA
TGATACGAAAGGAAAAACCGCTGTTGATACTGTTTTTAGATTTGATCCTCGGTATAATAAATGGAAGCAAGTTGCATCAT
TAAATGAAAAGCGCACATTCTTCCACTTGAGCGCCCTCAAAGGATATTTGTATGCGGTTGGTGGGCGAAGTGCAGCTGGT
GAACTGGCCACAGTAGAATGTTACAACCCAAGAATGAATGAGTGGAGCTATGTTGCAAAGATGAGTGAACCCCACTATGG
CCATGCTGGAACAGTGTATGGAGGTTTAATGTATATTTCAGGCGGAATTACTCATGACACTTTCCAAAATGAGCTCATGT
GCTTTGACCCAGATACAGACAAGTGGACACAGAAAGCTCCAATGACTACAGTCAGAGGTCTGCATTGCATGTGTACAGTT
GGAGACAAACTCTATGTCATTGGTGGCAATCACTTCAGGGGAACAAGTGATTATGATGACGTTCTAAGCTGTGAATACTA
TTCACCAACCCTTGACCAGTGGACACCAATTGCTGCTATGTTAAGAGGTCAGAGTGATGTTGGAGTTGCTGTCTTTGAAA
ATAAAATTTATGTTGTTGGTGGGTACTCTTGGAATAACCGTTGTATGGTAGAAATTGTCCAGAAATATGACCCAGAAAAA
GATGAGTGGCACAAAGTTTTTGACCTTCCAGAGTCACTTGGTGGCATTCGAGCTTGTACCCTCACAGTTTTTCCACCTGA
AGAAAACCCTGGATCACCTTCTAGAGAATCTCCTCTTTCAGCACCT

ORF - retro_lafr_1018 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.75 %
Parental protein coverage: 96.03 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPLSPAYISL-VEEQDQHMKLSLGSSEMGLSSHLQSSKAGATRIFTSNTHSSVVLQGFDQLRLEGLLCDVT
PLSPA...L.V.E...HMK.SLG..EMG.S.HLQ..KAG.TR.FTSNTHSSVVLQGFDQLR.EGLLCDVT
RetrocopyPLSPAFFCL<VQEEGFHMKVSLGNGEMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRVEGLLCDVT
ParentalLMPGDTDDAFPVHRVMMASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLKKIIDFIYTAKLSLNMDNLQ
L.PGD.D..FPVHR.MMASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGLKKIIDFIYTAKLSLNMDNLQ
RetrocopyLVPGDGDEIFPVHRAMMASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQ
ParentalDTLEAASFLQILPVLDFCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYINNFVLKNFTALLSTGEFLKL
DTLEAASFLQILPVLDFCKVFLISGV.LDNCVEVGRIANTYNL.EVDKY.NNF.LKNF.ALLSTGEFLKL
RetrocopyDTLEAASFLQILPVLDFCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEFLKL
ParentalPFERLAFVLSSNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVDFMRTD
PFERLAFVLSSNSLKHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTD
RetrocopyPFERLAFVLSSNSLKHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFMRTD
ParentalNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKTHEWKSLAPM
NTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE...EWKSLAPM
RetrocopyNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWKSLAPM
ParentalDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGYLYA
DAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKW.QVASLNEKRTFFHLSALKGYLYA
RetrocopyDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWKQVASLNEKRTFFHLSALKGYLYA
ParentalVGGRNAAGELPTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDTDKW
VGGR.AAGEL.TVECYNPR.NEW.YVAKMSEPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPDTDKW
RetrocopyVGGRSAAGELATVECYNPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKW
ParentalIQKAPMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDVGVAVF
.QKAPMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDVGVAVF
RetrocopyTQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVF
ParentalENKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSRESPLSAP
ENKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSRESPLSAP
RetrocopyENKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPLSAP

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_1018 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 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG000000182721 retrocopy
retro_cfam_422,
Callithrix jacchus ENSCJAG000000024471 retrocopy
retro_cjac_3406,
Cavia porcellus ENSCPOG000000112681 retrocopy
retro_cpor_590,
Equus caballus ENSECAG000000082371 retrocopy
retro_ecab_622,
Loxodonta africana ENSLAFG00000008122 1 retrocopy
retro_lafr_1018 ,
Myotis lucifugus ENSMLUG000000273931 retrocopy
retro_mluc_204,
Macaca mulatta ENSMMUG000000022931 retrocopy
retro_mmul_42,
Mustela putorius furoENSMPUG000000017301 retrocopy
retro_mputfur_169,
Mus musculus ENSMUSG000000367821 retrocopy
retro_mmus_121,
Nomascus leucogenys ENSNLEG000000147361 retrocopy
retro_nleu_1031,
Oryctolagus cuniculus ENSOCUG000000019931 retrocopy
retro_ocun_254,
Pongo abelii ENSPPYG000000206581 retrocopy
retro_pabe_60,
Pteropus vampyrus ENSPVAG000000159891 retrocopy
retro_pvam_1485,
Rattus norvegicus ENSRNOG000000140291 retrocopy
retro_rnor_154,
Sus scrofa ENSSSCG000000126371 retrocopy
retro_sscr_51,
Ictidomys tridecemlineatus ENSSTOG000000120351 retrocopy
retro_itri_124,
Tarsius syrichta ENSTSYG000000025211 retrocopy
retro_tsyr_19,
Tursiops truncatus ENSTTRG000000140981 retrocopy
retro_ttru_26,
Vicugna pacos ENSVPAG000000030911 retrocopy
retro_vpac_8,


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