RetrogeneDB ID:

retro_lafr_898

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_46:3225077..3226124(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000032437
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000003044
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_898
ACCCCCGGGGTCTCTTCCAGGACTTCAACCCCCAGTAAGTTCCTCATCTACACCTGCCTGCTGCTCTTCTCCGTGCTGCT
GCCCCTCCGCCTGGACGGCGTCATCCAGTGGAGCTACTGGGCCGTCTTCGCGCCCATATGGCTGTGGAAGCTCATGGTCA
TCGCGGGCGCCTCTGTGGGCGCAGGTGTTTGGGCGCGCAACCCTCGCTACCGCACCGAGGGGGAGGCTTGTGTGGAGTTC
AAAGCCATGTTGATCTCCGTGGGCATCCACCTGCTGCTGCTCATGTTCGAGGTCCTGGTGTGCGACAGGGTGGAGAGGGG
GACCCACTTCTGGCTGCTGGTCTTCATGCCGCTCTTCTTTGTGTCCCCCGTGTCCGTGGCCGCCTGCGTCTGGGGTTTCC
GACATGATCGGTCGCTGGAGCTGGAGATCCTGTGCTCTGTCAACATCCTGCAGTTCATCTTCATCGCTCTGAGGCTGGAC
AGGATTATCCACTGGCCGTGGCTGGTGGTGTTCGTGCCGCTGTGGGTCCTCATGTCCTTCCTCTGCCTGGTCGTGCTCTA
TTACATCGTCTGGTCGCTGCTCTTCCTGCGGTCCCTGGATGTGGTTGCGGAGCAGCGTAGAACACACGTGACCATGGCTG
TGAGCTGGATAACGATCGTCGTGCCCCTTCTCACCTTCGAGGTCCTGCTGGCTCACAGAGTGGACGGTCACAATACATTC
TCTTATATATCCATATTTGTCCCCCTTTGGCTGTCACTAATAACCTTAATGGCCACGACATTTAGGCGAAAGGGGGGCAA
TCATTGGTGGTTTGGTATTCGCAGAGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATACGGGAACA
TTTCATATGACCTCCATCATGAAGATAGTGAAGATATTGAAGAAACATCGGTTCCAGAAGCCCCTAAAATTGCCCCGATG
TTTGGAAAGAAGGCCAGGGTAGTTATAACCCAGAGCCCTGGGAAATATGTTCCCCCACCTCCCAAGTTAAATATAGACAT
GCCAGAT

ORF - retro_lafr_898 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.36 %
Parental protein coverage: 99.71 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTPHCQFHIFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFTPIWLWKLMVIVGASVGTGVWARNPQY
TP........PSKFLIY.CLLLFSVLL.LRLDG.IQWSYWAVF.PIWLWKLMVI.GASVG.GVWARNP.Y
RetrocopyTPGVSSRTSTPSKFLIYTCLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLMVIAGASVGAGVWARNPRY
ParentalRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLE
R.EGE.CVEFKAMLI.VGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLE
RetrocopyRTEGEACVEFKAMLISVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLE
ParentalVRFPVFNNAIYKIIIKNSLGQLFEDPKVVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHI
.......N....I.I...L......P..VV.VPLW.LMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.
RetrocopyLEILCSVNILQFIFIALRLDRIIHWPWLVVFVPLWVLMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHV
ParentalTMALSWMTIVVPLLTFEILLGHKLDGH-AFSCIPIFVPLHLSLITLMATTFGQKGGNRWWFGIRKDFCQF
TMA.SW.TIVVPLLTFE.LL.H..DGH..FS.I.IFVPL.LSLITLMATTF..KGGN.WWFGIR.DFCQF
RetrocopyTMAVSWITIVVPLLTFEVLLAHRVDGHNTFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQF
ParentalLLEIFPFLREYGNISYDLHHEDNEETEESPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
LLEIFPFLREYGNISYDLH...........VPE.PKIAPMF.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyLLEIFPFLREYGNISYDLHXXXXXXXXXTSVPEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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_898 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 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG00000003044 1 retrocopy
retro_lafr_898 ,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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