RetrogeneDB ID:

retro_lafr_1188

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_85:3239662..3240267(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000020970
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMX
Ensembl ID:ENSLAFG00000005568
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1188
GAAGCCAACTGTCCAGGAAAGCTCTCCATTGGTGGGCTCAATACAGAAACAAATACGAAAGCCCTTAAGGCAGTTTTTGG
CAAATATGGACGAAATGTGGAAGTACTCTTGATAAAAGACCGTGAAACCAACAAATCGAGAGGATTGCCTTTTGTCACCT
TTGAAAGCCCGGCAGATGCCAAAGATACAGCCAAAGATAGGAATGGAAAATCCTTAAATGGAAAAGCCATTAAAGTTGAA
CAAACCATTAACGTATCATTTGAAAGTGGTAGACGTGGACCTCCTCCAACCTCCAAGAAGCAGAGGCCCTTCAAGAGGTC
TTAGAGGAGGAAGTATAGGAACCAGGGAACCTCCTTCATATGGGGGGGTGGATAACAGATGATGGTACATATTCCATGAA
TTTTAACATGAGTTCTTTCAAGAGACCTCTTCCAATAAAAAGAGTACCACCACCACGAAATAGAGGTTCTCCTCCTAAAA
GATCTGCCCCTTTGGGACCAGTTCACGGCAGCAGTGGAATAGGAGGAAGAGCTCCTGTATCACATGGAAGGGATAGTTAT
GGAGGCCCACCACAAAGGGTACCCCTGCCCTCTCGTAGACATGTT

ORF - retro_lafr_1188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.39 %
Parental protein coverage: 51.92 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGK
EA..PGKL.IGGLNTETN.KAL.AVFGKYGR.VEVLL.KDRETNKSRG..FVTFESPADAKD.A.D....
RetrocopyEANCPGKLSIGGLNTETNTKALKAVFGKYGRNVEVLLIKDRETNKSRGLPFVTFESPADAKDTAKDRXXX
ParentalSLDGKAIKVEQATKPTFESGRRGPPP-PPRSRGPPRGLRGGRGGSGGTRGPPS-RGGHMDDGG-YSMNFN
................FESGRRGPPP.PPRSRGP.RGLRGG...S.GTR.PPS..GG...D.G.YSMNFN
RetrocopyXXXXXXXXXXXXXXVSFESGRRGPPP>PPRSRGPSRGLRGG---SIGTREPPS>MGGWITDDGTYSMNFN
ParentalMSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDV
MSS...PLP.KR.PPPR..G.PPKRSAP.GPV..SSG.GGRAPVS.GRDSYGGPP.R.PLPSRR.V
RetrocopyMSSFKRPLPIKRVPPPRNRGSPPKRSAPLGPVHGSSGIGGRAPVSHGRDSYGGPPQRVPLPSRRHV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_1188 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 27 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133081 retrocopy
Canis familiaris ENSCAFG000000189624 retrocopies
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
Cavia porcellus ENSCPOG000000121641 retrocopy
Dasypus novemcinctus ENSDNOG000000171993 retrocopies
Dipodomys ordii ENSDORG000000154811 retrocopy
Echinops telfairi ENSETEG000000131781 retrocopy
Felis catus ENSFCAG000000047791 retrocopy
Homo sapiens ENSG000001472747 retrocopies
Gorilla gorilla ENSGGOG000000069441 retrocopy
Loxodonta africana ENSLAFG00000005568 3 retrocopies
retro_lafr_1188 , retro_lafr_276, retro_lafr_35,
Loxodonta africana ENSLAFG000000070031 retrocopy
Microcebus murinus ENSMICG000000068562 retrocopies
Myotis lucifugus ENSMLUG000000132095 retrocopies
Monodelphis domestica ENSMODG000000140541 retrocopy
Mustela putorius furoENSMPUG000000018552 retrocopies
Mus musculus ENSMUSG000000311342 retrocopies
Oryctolagus cuniculus ENSOCUG000000072201 retrocopy
Otolemur garnettii ENSOGAG000000078395 retrocopies
Ochotona princeps ENSOPRG000000165931 retrocopy
Pongo abelii ENSPPYG000000207713 retrocopies
Rattus norvegicus ENSRNOG000000008661 retrocopy
Sorex araneus ENSSARG000000003971 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000062112 retrocopies
Tupaia belangeri ENSTBEG000000011541 retrocopy
Tarsius syrichta ENSTSYG000000095551 retrocopy
Tursiops truncatus ENSTTRG000000073221 retrocopy



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