RetrogeneDB ID:

retro_lafr_441

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_16:41268543..41270481(-)
Located in intron of:ENSLAFG00000009994
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSLAFG00000000523
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_441
ATGGCAGACAGTCTCCCCACAGAGTTTGATGTGGTTATAATAGGGACAGGTTTGCCTGAATCCATCCTTGCAGCTGCAAG
TTCAAGAAGTGGCCAGAGGGTTCTGCATGTTGACTCCAGAAGTTACTATGGAGGGAACTGGGCTAGCTTCAGCTTTTCAG
GATTGCTATCCTGGTTGAAGGAATATCAGGAAAACTGTGTTGATGGGGAAGAAAGTACAGCTGCATGGCAAGGCCTGATC
CATGAAACAGAAGAAGCCATTACTCTTCGCAAGAAAGATGAAACCATTCAACACGTGGAAGTTTTTTGTTATGCCAGTCA
AGATTTGGATGACAGTGTTGAAGAGGTTGGTGCTTTGCAGAAAAATCCTTGCTCAGTGGCATCTAGTACCCTCACTGAAA
CTCTGGATTCTGCATGCTTGGGCGAAGACGAGCACTTAGTACACGTTCCTAGCTATGAAAGGCCCGCCCAAGACACTTCA
AAAAGTGATGGAGAGATTTCGCTAGATGTAAATGACGTCAAGGAACCCCCGGAGAAAGGAAACGATGGTGGAGACAGAGC
TCGTGCTCACGCGGTTTCAGATGCAGACAAAGATGAAAACAAACCTGCAGGAGAAGGCAACACAGACCAGCCAACAAGAA
ACCGGATTACTTACTCTCAGATAGTTAAAGAAGGCAGGAGGTTTAATATTGATTTGGTATCGAAGCTGCTGTATTCTCAA
GGATTGCTGATTGACCTTTTAATCAAATCAAATGTCAGTCGATATGCAGAATTTAAAAATGTCACAAGGATTCTTGCATT
TTGGGAAGGAAAAGTTGAACAAGTGCCTTGTTCCAGAGCAGATGTCTTCAATAGCAAAGAACTCACTATGGTTGAAAAGA
GGATGCTCATGAAATTTCTCACGTTTTGCGTTGACTATGAGCAACATCCTGATGAATACGAAGCTTTCAAGCAATGCTCA
TTTTCAGAGTACTTAAAAACTAAAAAATTAACTCCAAATCTCCAACATTTTGTACTGCACTCAATTGCAATGACATCAGA
GTCATCTTGCACTACGATAGATGGCCTTAAAGCAACAAAAAACTTCCTTCAGTGTCTTGGACGGTTCGGCAACACTCCCT
TCTTATTTCCCTTGTATGGCCAAGGAGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTCTTTGGCGGAATCTATTGT
CTTCGGCATAAGGTACACTGCCTTATAGTTGACAAAGAATCTGGGAGATGTAAAGCAGTTATAGATCACTTTGGCCAAAG
GATAAATGCCAAGTATTTTATTGTGGAGGATAGCTACCTTTCTGAGGAAACATGTGCACATGTGCAGTATAAGCAGATCT
CTAGGGCAGTGCTCATTACAGACCAATCTATACTGAAGACAGATTCAGACCAGCAGATTTCTGTTTTGATAGTGCCTCCA
GTAGAAGCAGGGACCTGTGCTGTTCGGGTCATTGAATTATGTTCTTCAACCATGACATGCATGAAAGACACCTATCTGGT
GCATTTGACGTGTTCATCTTCTAAAACAGCAAGAGAAGATTTAGAATCAGTGGTGAAGAAATTATTCACCCCATATGCTG
AAACGGAAGTAGACAAGGAAGCGCTTGAAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCAGGA
ATCAGCAGAAGCTCATATAATGGCTTGCCTTCCAACGTTTATGTCTGTTCTGGGCCTGACTCTGGTCTGGGAAGTGAGCA
TGCTGTCAAGCAAGCTGAAACACTTTTCCATGAGATCTTTCCAAGTGAAGAATTCTGCCCCCCGCCTCCAAATCCAGAAG
ACATTGTCTTTGATGGTGATGATAGGCAACCAGAGGCTCCTGGAACCAATAAGACAATAATGGCTGAACCAGAATCCTCT
GAAGAAAGCAAAACCCTA

ORF - retro_lafr_441 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.74 %
Parental protein coverage: 98.77 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMANNLPSEFDVIVIGTGLPESVIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEHQESS-DAV
MA..LP.EFDV..IGTGLPES..AAA.SRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKE.QE...D..
RetrocopyMADSLPTEFDVVIIGTGLPESILAAASSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENCVDGE
ParentalNESPTWQEQILENEEAIALSKKDRTIQHVEVFCYASQDLHEDVEEAGALQKNRAPLTAVNPTEAADSVFL
.....WQ..I.E.EEAI.L.KKD.TIQHVEVFCYASQDL...VEE.GALQKN.........TE..DS..L
RetrocopyESTAAWQGLIHETEEAITLRKKDETIQHVEVFCYASQDLDDSVEEVGALQKNPCSVASSTLTETLDSACL
ParentalPKEDESLSTVSCEIPAEQPPSSNPESAPEVNDVEAVEEKENDGNDKTCVQATSEKETGENVPTAENTAEQ
..........S.E.PA.....S..E....VNDV....EK.NDG.D.....A.S.....EN.P..E....Q
RetrocopyGEDEHLVHVPSYERPAQDTSKSDGEISLDVNDVKEPPEKGNDGGDRARAHAVSDADKDENKPAGEGNTDQ
ParentalPKKNRITYSQIVKEGRRFNIDLVSKLLYSRGLLIELLIKSNVSRYAEFKNVTRILAFRDGRVEQVPCSRA
P..NRITYSQIVKEGRRFNIDLVSKLLYS.GLLI.LLIKSNVSRYAEFKNVTRILAF..G.VEQVPCSRA
RetrocopyPTRNRITYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSNVSRYAEFKNVTRILAFWEGKVEQVPCSRA
ParentalDVFNSKQLTMVEKRMLMKFLTFCMDYEEHPDEYKAYEEMTFSEYLKTQKLTPNLQYFVLHSIAMTSEATS
DVFNSK.LTMVEKRMLMKFLTFC.DYE.HPDEY.A.....FSEYLKT.KLTPNLQ.FVLHSIAMTSE...
RetrocopyDVFNSKELTMVEKRMLMKFLTFCVDYEQHPDEYEAFKQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSC
ParentalTTIDGLKATKNFLRCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLHHSVQCLVVDKDSGKCKAI
TTIDGLKATKNFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCL.H.V.CL.VDK.SG.CKA.
RetrocopyTTIDGLKATKNFLQCLGRFGNTPFLFPLYGQGEIPQCFCRMCAVFGGIYCLRHKVHCLIVDKESGRCKAV
ParentalIDQFGQRIISKHFIVEDSYFSEKTCSNVQYRQISRAVLITDRSVLKADSDQQISILTVPASKPGTFAVRV
ID.FGQRI..K.FIVEDSY.SE.TC..VQY.QISRAVLITD.S.LK.DSDQQIS.L.VP....GT.AVRV
RetrocopyIDHFGQRINAKYFIVEDSYLSEETCAHVQYKQISRAVLITDQSILKTDSDQQISVLIVPPVEAGTCAVRV
ParentalIELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQELFTPYTETEIENDEGKKPRLLWALYFNMRDSSD
IELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV..LFTPY.ETE.......KPRLLWALYFNMRDSS.
RetrocopyIELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYAETEVDKEALEKPRLLWALYFNMRDSSG
ParentalISRNSYNDLSSNIYICSGPDCGLGNDNAVKQAEALFQQICPNEDFCPPPPNPEDIVLDGDSLQPEPSESS
ISR.SYN.L.SN.Y.CSGPD.GLG...AVKQAE.LF..I.P.E.FCPPPPNPEDIV.DGD..QPE.....
RetrocopyISRSSYNGLPSNVYVCSGPDSGLGSEHAVKQAETLFHEIFPSEEFCPPPPNPEDIVFDGDDRQPEAPGTN
ParentalSILQTNSETPKESPYL
.......E...ES..L
RetrocopyKTIMAEPESSEESKTL

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_441 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 ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG00000000523 1 retrocopy
retro_lafr_441 ,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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