RetrogeneDB ID:

retro_lafr_536

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_2:82796217..82797083(-)
Located in intron of:ENSLAFG00000017550
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSLAFG00000022011
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_536
CCCAAACATGAAAGGGACAGGAGGTCTTCGAGAATTGACCCTATCAGATCACCCAACATGGCTGGAGGACTGTTTGCTGT
CAGCAAGAATATTTTGAGTACCTTGGAACCTATGATACTGGAATGGAAGTGTGGGGAGGTGAAAACCTAGAACTGTCTTT
TAGGGTGTGGCAGTGTGGTGGTAAGTTGGAGATCCATCCGTGCTCCCACGTGGGCCACGTATTCCCAAAGCGGGCACCGT
ATGCTCGGCCCAATTTCCTACAGAATACTGCCCGGGCAGCAGAAGTATGGATGGATGAGTACAAACAGCATTTCTACAAT
CGAAACCCTCCAGCAAGAAAAGAAGCTTATGGTGATATTTCTGAAAGAAAATTATTACGAGAACGGCTGAGGTGCGAGAA
CTTTGACTGGTATTTGAAAAATGTATTTTCTAATTTACATGTTCCAGAGGATAGGCCGGGCTGGCATGGAGCAGTTCGCA
GTACTGGGATTTCTTCTGAATGTTTAGATTATAATTCTCCTGACAACAGCCCCACAGGTGCGAACCTTTCGCTGTTTGGA
TGCCATGGCCAAGGAGGAAATCAATTCTTTGAATATACTTCAAACAAAGAAATAAGGTTTAATTCTGTGACAGAGTTATG
TGCGACAGTCCCTGAGCAAAAGACTTTTGTGGGAATGCTAACTTGTCCTAAAGATGGGTTCCCTATTCCAGCAAATATTA
TTTGGCATTTTAAAGAAGATGGAACCATTTTTCATCCACACTCAGGGCTGTGTCTGAGTGCTTATCGAACACCTGAGGGC
CGGGCGGATGTACAAATGAGAACTTGTAATGCTCTAGATAAAAATCAAATCTGGAGGTTTGAGAAG

ORF - retro_lafr_536 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.42 %
Parental protein coverage: 55.49 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPERERRRMRSPIDVIRSPTMAGGLFAVSK-KYFEYLGSYDTGMEVWGGENLEFSFRIWQCGGTLETHPCS
P..ER.R..S.ID.IRSP.MAGGLFAVSK..YFEYLG.YDTGMEVWGGENLE.SFR.WQCGG.LE.HPCS
RetrocopyPKHERDRRSSRIDPIRSPNMAGGLFAVSK<EYFEYLGTYDTGMEVWGGENLELSFRVWQCGGKLEIHPCS
ParentalHVGHVFPKKAPYSRNKALANSVRAAEVWMDEYKELYYHRNPHARLEPFGDVTERRQLRAKLQCKDFRWFL
HVGHVFPK.APY.R...L.N..RAAEVWMDEYK...Y.RNP.AR.E..GD..ER..LR..L.C..F.W.L
RetrocopyHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKQHFYNRNPPARKEAYGDISERKLLRERLRCENFDWYL
ParentalETVYPELHVPEDRPGFFGMLQNKGLKEYCFDYNPPKDDQISGHQVLLYHCHGMGQNQFFEYTSQNEIRYN
..V...LHVPEDRPG..G.....G....C.DYN.P.D....G....L..CHG.G.NQFFEYTS..EIR.N
RetrocopyKNVFSNLHVPEDRPGWHGAVRSTGISSECLDYNSP-DNSPTGANLSLFGCHGQGGNQFFEYTSNKEIRFN
ParentalTRQPEGCVSAPAESDILFMELCKETA---PENQKFIFREDGSLFHVLSKKCVQAERKAPGDSVVPLLRDC
....E.C...P.......M..C.......P.N....F.EDG..FH..S..C..A.R...G...V......
RetrocopyS-VTELCATVPEQKTFVGMLTCPKDGFPIPANIIWHFKEDGTIFHPHSGLCLSAYRTPEGRADVQMRTCN
ParentalTNSERQKWFFKE
.....Q.W.F..
RetrocopyALDKNQIWRFEK

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_536 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 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG00000022011 1 retrocopy
retro_lafr_536 ,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,


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