RetrogeneDB ID:

retro_lafr_276

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_11:49445607..49446328(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMX
Ensembl ID:ENSLAFG00000005568
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_276
AAGGGTCCACTTCCAGTAAAAACATGACCACCACCATGAAGTAGAGGTCCTCCTCCTAAATGATCTGCCCCTTCAGGACC
AGTTAGCAGAACTGTGTCATGTGGAAGAAATTGTTACAGTGGCCCACCACAAAGAGAACCACTGCCCTCTCATAGAGATG
CTTATTTGTCCCCAAGAGATGATGGGTGTTCTACTAAAGACAGCTATTCATGCAGAGATTACCCAAATTCTTATGATACA
AGAGATTTTGCACCACCACCAAGAGATTATACATATTGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCATCCAG
AGGCTATAGTGATAGAGATGGCTATGGTCGTGACTGTGACTATTCAGATCATCCAAGTGACGTTACTACAGAAACTCCTA
TGAGAGTTATAGTAATTCATCTAGTGCTCCACGTACAAGAGGGTCCCTGACATTTTCTGGTGGAAGCAGTTGCTAAGATG
ACTACAGCAGCCCACATGACGGACTTTTGTAGAAGAAGAGATAACTACTCAAGGCCGCCGAGGTGATCTTTACTCAAGTG
GCCAGGATCGGGTTGGTGGATGAGAAAGAGGGCTTGCCCATTCTATGGAAAGGGGGTACCGTCCTCCACGTGATTCCTAT
AGCAGTTCAAGCTGCAAAGCGCCAAGAGGTAGTGGCTGTGGAGGAAGTCGATCTGATGGAGGAGGATGCATAAGCAGATA
C

ORF - retro_lafr_276 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.85 %
Parental protein coverage: 61.64 %
Number of stop codons detected: 5
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDGYSTKDSY
.GP.P....PPP....P.......SG...R..VS.GR..Y.GPP.REPLPS.RD.YLSPRDDG.STKDSY
RetrocopyKGPLPVKT*PPP*SRGPPPK*SAPSGPVSRT-VSCGRNCYSGPPQREPLPSHRDAYLSPRDDGCSTKDSY
ParentalSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS-YRDSYESYG
S.RDYP.S.DTRD.APPPRDYTY.DYGHSSSRDDYPSRGYSDRDGYGRD.DYSDHPS....YR.SYESY.
RetrocopySCRDYPNSYDTRDFAPPPRDYTYCDYGHSSSRDDYPSRGYSDRDGYGRDCDYSDHPSDVT<YRNSYESYS
ParentalNSRSAPPTRGPPPSYGGSSRYDDYSSSRDG-YGGSRDSYS-SSRSDLYSSGRDRVGRQERGLPPSMERGY
NS.SAP.TRG.....GGSS..DDYSS..DG.....RD.YS...R.DLYSSG.DRVG..ERGL..SMERGY
RetrocopyNSSSAPRTRGSLTFSGGSSC*DDYSSPHDG>FCRRRDNYS>GRRGDLYSSGQDRVGG*ERGLAHSMERGY
ParentalPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
.PPRDSYSSSS..APRG.G.GGSRSD.GG..SRY
RetrocopyRPPRDSYSSSSCKAPRGSGCGGSRSDGGGCISRY

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_276 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
retro_btau_36,
Canis familiaris ENSCAFG000000189624 retrocopies
retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus ENSCPOG000000121641 retrocopy
retro_cpor_778,
Dasypus novemcinctus ENSDNOG000000171993 retrocopies
retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii ENSDORG000000154811 retrocopy
retro_dord_793,
Echinops telfairi ENSETEG000000131781 retrocopy
retro_etel_1952,
Felis catus ENSFCAG000000047791 retrocopy
retro_fcat_1903,
Homo sapiens ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla ENSGGOG000000069441 retrocopy
retro_ggor_657,
Loxodonta africana ENSLAFG00000005568 3 retrocopies
retro_lafr_1188, retro_lafr_276 , retro_lafr_35,
Loxodonta africana ENSLAFG000000070031 retrocopy
retro_lafr_1091,
Microcebus murinus ENSMICG000000068562 retrocopies
retro_mmur_1252, retro_mmur_661,
Myotis lucifugus ENSMLUG000000132095 retrocopies
retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica ENSMODG000000140541 retrocopy
retro_mdom_1231,
Mustela putorius furoENSMPUG000000018552 retrocopies
retro_mputfur_1539, retro_mputfur_956,
Mus musculus ENSMUSG000000311342 retrocopies
retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus ENSOCUG000000072201 retrocopy
retro_ocun_3,
Otolemur garnettii ENSOGAG000000078395 retrocopies
retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps ENSOPRG000000165931 retrocopy
retro_opri_372,
Pongo abelii ENSPPYG000000207713 retrocopies
retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus ENSRNOG000000008661 retrocopy
retro_rnor_268,
Sorex araneus ENSSARG000000003971 retrocopy
retro_sara_169,
Ictidomys tridecemlineatus ENSSTOG000000062112 retrocopies
retro_itri_1205, retro_itri_1346,
Tupaia belangeri ENSTBEG000000011541 retrocopy
retro_tbel_1919,
Tarsius syrichta ENSTSYG000000095551 retrocopy
retro_tsyr_15,
Tursiops truncatus ENSTTRG000000073221 retrocopy
retro_ttru_1450,


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