RetrogeneDB ID:

retro_lafr_791

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_39:3674676..3676950(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000030124
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSLAFG00000017825
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_791
ATGGCGCTCAGGCGGCGCCGTGTCAAAGTCTATATCCTGAACGATCACCGGGAATGGGACGACCTAGGCACCGGGTTGAT
CTCATCTACTTACGTGGGGCGGCTGCAGGGAGTGTCCCTGCTAGTTCGTTCCGAGTGCAACGGCTCCCTAATCTGGGAGT
CGAAGATAAATACACACACACGGTATCAGAAACAACAGGAGTCATTGATTGTTTGGTCGGAAGCCGAGAACCACGGTCTG
GCGCTAAGTTTCCAGGAACGAGCCGGCTGTCAGGCAATCTGGAAGGACATTTGCCGCGTTCAAGGTAAAGACCCCTCCGC
CGAAATCACACAAGACCTTTTGGATGAATCAGAAGAGGAACAATTTGATGAAATACCAGACACCAGTAATCTGGTTGTCC
TGCCTAATTGTGAACTCAACAATCTTGAACAGATTGCTGGCTTAGTTAACACAGTTCTTGCCTCGCCTATCCGTAGGGAA
AGGCTGGCTCTGATCTTGGAAAATGAGAACTATATTAAAAAACTACTGCAGTTGTTCCACACTTGTGAGACGCTAGAGAA
CACCGAAGGCTTGCACCATTTGCATGCCATTATTAAAGGAATCTTATTCCTCAACAAGACATCTCTGTTTGAGATCATGT
TTTCTGATGAATGCATCATGGATGTGGTGGGATGCCTTGAATACGACCCTGCTTTGGCTCAGCCTAAAAGGCATAGGGAA
TTCTTGACCCAAGTTGCAAAGTTCAAGGAAGTTATACCAATAACAGACTGTGAACTTAAGCAAAAAATACGTCAGACCCA
CAGGCTACAGTACATTCACGATATCTTATTGCCTATACCATCCATGTTTGAAGAGAATATGCTTTCTGCTCTTACTACTT
GTATTTTCTTCAACAAAGTTGAGATAGTCAACTTACTGCAGAACAATGACAAGTTTTTGTCTGAGGTTTTTGCACAGTTA
ACAGCTAAGACCACAGCTGATGATCAACTGCGTGAATTGGTGTTTTTTTTAAAGGAATTCTGTGCATTTTCTCAGACCTT
ACAACCACAAAGCAAGGATGCATTATTCCAAAAGTTCACAAGATTGGGAATTCTTCCTGCTCTTAAAAGTGTCATAGGCA
TGGACAATCTGCAGATAAGGTCAGCTGCTACAGATATATTTGTCTATCTAGTGGAGCGTAGTCCATCCATGATCCGACGA
TTTATAATGGACGAAGCCCTGCTCTGCAAAGATGGTAACCTTTTAATTACTATAATAATTGAACAAATGATCGGTGATAC
TGACCCTGAGCTAGGAGGTGCTGTTCAATTAATGGGGCTTCTTCGTTCTTTACTTGATCCAGACAACATGCTGGCTGTAC
CTAGTGAAAGACAAAGAAGTGAATTTCTAAATTTCTTCTACAAACGTTGCATGCATGTCTTGATAGGGCCACTTTTGGCC
AGCACTTCAGAAGACAAATGTGAAAAGGATAATACAGGTGGAGCTAGCAAAAATTGCCCCGATAATTATCAGACAGCACA
ACTGCTTGCCATAATTTTAGAGCTGCTCACGTTTTGTGTACAACATCACGCATATTACATAAAAAATTATATTTTGAACA
AAGACTTGCTAAGAAGAATCTTGATCCTGATGAACTCAAAGCACACTTTCCTGATCTTGTGTGCTGTTCGCTTTATGAGA
AGGATGATTGGCCGTAAAGATGAACTTTATAATTGTTACATCATCAAGGGAAATCTTTTTGAGCCAGTCATAAATGCTCT
TCTGAATAACGGGACTCGGTACAATATGTTGAATTCAGCTGTAATTGAGCTGTTTGAATACATAAGAGTGGAAAATATTA
AGTCTCTTGTTGCACATATAGTTGAGAAGTTTTATAAGGCAGTTGAATCGATTGAATATGTTCAGACATTCAAAGGACTG
AAGATTAAATATGAACAAGAGAAAGAGAGACAAAGTCAAGTACAGAAGAATTTGCATCCTATACTGCCTAGCAAAATACT
TTATGAAGGTGCCAATGTCTTTGAGGAGATAGAAGAAGTGAGTTTTAAGGAAGATAAAGAGGAAGGAGGAGCAATTATGC
CGCCATTGGAAACTCCTGCGCCAAAAGACCACTTTCCAAATCATTGTGGTAACATGACGGAGATTGAAAAAAGAAAAGTC
AATGCAGACAAGACCAACCTTCAGGAAAAAGCATCTGGTGACTTCAAATTTACTCCATCGCTTTCTGCCGGTGTTGCTAA
TGGAACAAGTAGTCCAGATGGTAGCAGTGTGGTT

ORF - retro_lafr_791 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.93 %
Parental protein coverage: 93.07 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQARDT
M...RRRVKVY.LN..R.WDD.GTG..SSTYV..L.G.SLLVR.E..GSL..ESKIN..T.YQKQQ....
RetrocopyMALRRRRVKVYILNDHREWDDLGTGLISSTYVGRLQGVSLLVRSECNGSLIWESKINTHTRYQKQQ--ES
ParentalLIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCE
LIVWSEAEN..LALSFQE.AGC..IW..IC.VQGKDPS.E.TQDL.DESEEE.F.E.P.TS.L..LP.CE
RetrocopyLIVWSEAENHGLALSFQERAGCQAIWKDICRVQGKDPSAEITQDLLDESEEEQFDEIPDTSNLVVLPNCE
ParentalLNKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKAT
LN.LE.IA.LV..VL.SPIRRE.LAL.LENE.YIKKLLQLF..CE.LENTEGLHHL..II.GILFLNK..
RetrocopyLNNLEQIAGLVNTVLASPIRRERLALILENENYIKKLLQLFHTCETLENTEGLHHLHAIIKGILFLNKTS
ParentalLFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILP
LFE.MFSDECIMDVVGCLEYDPALAQPKRHREFLT..AKFKEVIPITD.EL.QKI.QT.R.QYI.DI.LP
RetrocopyLFEIMFSDECIMDVVGCLEYDPALAQPKRHREFLTQVAKFKEVIPITDCELKQKIRQTHRLQYIHDILLP
ParentalTPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQ
.PS.FEEN.LS.LT..IFFNKVEIV..LQ...KFLSEVFAQLT...T.DD..RELV.F.KEFCAFSQTLQ
RetrocopyIPSMFEENMLSALTTCIFFNKVEIVNLLQNNDKFLSEVFAQLTAKTTADDQLRELVFFLKEFCAFSQTLQ
ParentalPQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINV
PQ..DA.F.....LGILPAL..V.GMD.LQ.RSAATDIF.YLVE.SPSM.R.F.M.EA....D..LLI..
RetrocopyPQSKDALFQKFTRLGILPALKSVIGMDNLQIRSAATDIFVYLVERSPSMIRRFIMDEALLCKDGNLLITI
ParentalIIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLANTSEDKYE
IIEQMI.DTDPELGGAVQLMGLLR.L.DP.NMLA.......SEFLNFFY..CMHVL..PLLA.TSEDK.E
RetrocopyIIEQMIGDTDPELGGAVQLMGLLRSLLDPDNMLAVPSERQRSEFLNFFYKRCMHVLIGPLLASTSEDKCE
ParentalKDNIVGSNKNNTVCPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCA
KDN..G..KN...CPDNYQTAQLLA.ILELLTFCV.HH.Y.IKNYI.NKDLLRR.L.LMNSKHTFL.LCA
RetrocopyKDNTGGASKN---CPDNYQTAQLLAIILELLTFCVQHHAYYIKNYILNKDLLRRILILMNSKHTFLILCA
ParentalLRFMRRIIGLKDEFYNRYITKGNLFEPVVNALLDNGTRYNLLNSAVVELFEFIRVEDIKSLTAHIVENFY
.RFMRR.IG.KDE.YN.YI.KGNLFEPV.NALL.NGTRYN.LNSAV.ELFE.IRVE.IKSL.AHIVE.FY
RetrocopyVRFMRRMIGRKDELYNCYIIKGNLFEPVINALLNNGTRYNMLNSAVIELFEYIRVENIKSLVAHIVEKFY
ParentalKALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKALEEDEEMWFNEDEEEEGKAVVA
KA.ESIEYVQTFKGLK.KYEQEK.RQ.Q.......IL.S......A...EE.EE..F.ED..EEG.A...
RetrocopyKAVESIEYVQTFKGLKIKYEQEKERQSQVQKNLHPILPSKILYEGANVFEEIEEVSFKED-KEEGGAIMP
ParentalPVEKSKPEDDFPDSYEKFMETKKAKESEDKENLPKRTSSGGFKFTFSHSASAANGTNSANSKSVV
P.E...P.D.FP.......E..K.K...DK.NL.....SG.FKFT.S.SA..ANGT.S....SVV
RetrocopyPLETPAPKDHFPNHCGNMTEIEKRKVNADKTNLQEK-ASGDFKFTPSLSAGVANGTSSPDGSSVV

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_791 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 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000038431 retrocopy
retro_amel_48,
Bos taurus ENSBTAG000000005451 retrocopy
retro_btau_232,
Canis familiaris ENSCAFG000000028601 retrocopy
retro_cfam_226,
Equus caballus ENSECAG000000138191 retrocopy
retro_ecab_23,
Echinops telfairi ENSETEG000000024201 retrocopy
retro_etel_1699,
Felis catus ENSFCAG000000264571 retrocopy
retro_fcat_13,
Homo sapiens ENSG000001380411 retrocopy
retro_hsap_4799,
Loxodonta africana ENSLAFG00000017825 1 retrocopy
retro_lafr_791 ,
Myotis lucifugus ENSMLUG000000038751 retrocopy
retro_mluc_994,
Macaca mulatta ENSMMUG000000070011 retrocopy
retro_mmul_238,
Mustela putorius furoENSMPUG000000024351 retrocopy
retro_mputfur_92,
Nomascus leucogenys ENSNLEG000000093381 retrocopy
retro_nleu_1112,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
retro_ocun_9,
Otolemur garnettii ENSOGAG000000098371 retrocopy
retro_ogar_140,
Pan troglodytes ENSPTRG000000119331 retrocopy
retro_ptro_3191,
Sus scrofa ENSSSCG000000083981 retrocopy
retro_sscr_1187,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,


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