RetrogeneDB ID:

retro_lafr_611

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_25:15871658..15871929(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000001910
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_611
ATTTTGCAAACCGTGAAGCATGTGGAGCCTCAAGTAAAACAAGTTCATCAAAGCCTACCAAAATCTGCCTCCAGGGGTGG
TAGATTTGAGCCCAAAGTGATGAAATGGGATGGTGCATTAATAGTAGGTATAAGCTGTACAGCCAATAAAGGCAAAAATA
AGAGATGCTCGTTGACAAATTATGCCCTTACATCACCCAGACAAGGGAGGATCTCCTTATATAGCAGCTGAAATGAGTGA
GGCTAGAGATTTACTGGAAGGTTAAGCTAAA

ORF - retro_lafr_611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.32 %
Parental protein coverage: 81.03 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVLRAMKHVEPQVKQVFKSLPKSAFSGGYYRGGFEPKMTKREAALILGVSPTANKGK-IRDAHRRIMLLNH
.L...KHVEPQVKQV..SLPKSA..G....G.FEPK..K...ALI.G.S.TANKGK.IRDA...IM.L.H
RetrocopyILQTVKHVEPQVKQVHQSLPKSASRG----GRFEPKVMKWDGALIVGISCTANKGK>IRDAR*QIMPLHH
ParentalPDKGGSPYIAAKINEAKDLLEGQAK
PDKGGSPYIAA...EA.DLLEG.AK
RetrocopyPDKGGSPYIAAEMSEARDLLEG*AK

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_611 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 34 parental genes, and 172 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000122556 retrocopies
retro_amel_1087, retro_amel_155, retro_amel_252, retro_amel_283, retro_amel_744, retro_amel_994,
Bos taurus ENSBTAG000000235131 retrocopy
retro_btau_127,
Canis familiaris ENSCAFG000000327148 retrocopies
retro_cfam_1256, retro_cfam_1306, retro_cfam_1451, retro_cfam_2015, retro_cfam_346, retro_cfam_389, retro_cfam_741, retro_cfam_819,
Callithrix jacchus ENSCJAG0000001279510 retrocopies
retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Cavia porcellus ENSCPOG000000211981 retrocopy
retro_cpor_126,
Dasypus novemcinctus ENSDNOG000000190671 retrocopy
retro_dnov_49,
Dipodomys ordii ENSDORG000000058627 retrocopies
retro_dord_232, retro_dord_295, retro_dord_320, retro_dord_53, retro_dord_586, retro_dord_684, retro_dord_794,
Erinaceus europaeus ENSEEUG000000069559 retrocopies
retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi ENSETEG000000068977 retrocopies
retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis ENSFALG000000082961 retrocopy
retro_falb_28,
Felis catus ENSFCAG000000105917 retrocopies
retro_fcat_1250, retro_fcat_1481, retro_fcat_1603, retro_fcat_1837, retro_fcat_475, retro_fcat_511, retro_fcat_982,
Homo sapiens ENSG000002059818 retrocopies
retro_hsap_1330, retro_hsap_2061, retro_hsap_2062, retro_hsap_2349, retro_hsap_3497, retro_hsap_387, retro_hsap_538, retro_hsap_583,
Gallus gallus ENSGALG000000088521 retrocopy
retro_ggal_17,
Gorilla gorilla ENSGGOG000000091207 retrocopies
retro_ggor_1037, retro_ggor_1483, retro_ggor_1484, retro_ggor_1783, retro_ggor_2365, retro_ggor_491, retro_ggor_517,
Loxodonta africana ENSLAFG00000001910 5 retrocopies
retro_lafr_48, retro_lafr_515, retro_lafr_611 , retro_lafr_881, retro_lafr_929,
Loxodonta africana ENSLAFG000000043432 retrocopies
retro_lafr_287, retro_lafr_942,
Microcebus murinus ENSMICG000000103814 retrocopies
retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus ENSMLUG000000068651 retrocopy
retro_mluc_84,
Macaca mulatta ENSMMUG000000121043 retrocopies
retro_mmul_2142, retro_mmul_2454, retro_mmul_946,
Mustela putorius furoENSMPUG000000023367 retrocopies
retro_mputfur_1099, retro_mputfur_1652, retro_mputfur_287, retro_mputfur_662, retro_mputfur_841, retro_mputfur_848, retro_mputfur_984,
Mus musculus ENSMUSG000000276793 retrocopies
retro_mmus_1446, retro_mmus_3071, retro_mmus_3554,
Oryctolagus cuniculus ENSOCUG000000140435 retrocopies
retro_ocun_1100, retro_ocun_1650, retro_ocun_1869, retro_ocun_334, retro_ocun_398,
Otolemur garnettii ENSOGAG0000000875411 retrocopies
retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Ochotona princeps ENSOPRG000000092565 retrocopies
retro_opri_1127, retro_opri_122, retro_opri_440, retro_opri_529, retro_opri_844,
Procavia capensis ENSPCAG000000149502 retrocopies
retro_pcap_195, retro_pcap_25,
Pongo abelii ENSPPYG000000143282 retrocopies
retro_pabe_2126, retro_pabe_44,
Pan troglodytes ENSPTRG000000300467 retrocopies
retro_ptro_1374, retro_ptro_1719, retro_ptro_2370, retro_ptro_2927, retro_ptro_404, retro_ptro_429, retro_ptro_907,
Rattus norvegicus ENSRNOG000000498191 retrocopy
retro_rnor_2913,
Sus scrofa ENSSSCG000000117702 retrocopies
retro_sscr_651, retro_sscr_891,
Ictidomys tridecemlineatus ENSSTOG000000115081 retrocopy
retro_itri_552,
Tupaia belangeri ENSTBEG0000001508927 retrocopies
retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,
Tarsius syrichta ENSTSYG000000016113 retrocopies
retro_tsyr_112, retro_tsyr_174, retro_tsyr_312,
Tursiops truncatus ENSTTRG000000147006 retrocopies
retro_ttru_1023, retro_ttru_1630, retro_ttru_1830, retro_ttru_662, retro_ttru_704, retro_ttru_962,
Vicugna pacos ENSVPAG000000033871 retrocopy
retro_vpac_533,


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