RetrogeneDB ID:

retro_lafr_328

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_12:60732448..60732942(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSLAFG00000006572
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_328
CCAGCTCCTGTAGAAGTCACATACAAGAACATGAGATTTCTGAAGACACACAGTCCAATCAACACGACCTTAAACAAATT
TATAGAGGAACTTCCGGAATATGGAGTTACCAAGATAGTAAGAGTATGTAAGGCAGCTTGAGACACTGCTCTTGAGGAAG
AAGAAAGCATCCATGTTCGCGATTGGCCTGGTGATGATGGTGCACCGCAGTCCAACCAGAATGTTGATGGCTGGTTAAGT
CCTGTAAAAATTAAGTTTTGTGGAGAACCTGCTGTATTGCCGTTTGTTGTGTGGCAGGTCTTCGGAGCACTCCAGTGCTT
GTTGCCCCGGCATTAGCTGAAGGTGGAATGAGATATGAAGACGCAGTACAGTTCAGGAGACAAAAGCAGCGTGGAGCTTT
CGACAGCAAGGAACTTTTGTGTTTGGAGAAGTAGAGTCCTAAAATGTGGCTGTGGTTCAAAGTCTCCAAGCGTCATAGAA
ACAACTGCTGCATT

ORF - retro_lafr_328 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.4 %
Parental protein coverage: 95.98 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTALVEKEGIHVLDWPFDDGAPP
PAPVEVTYKNMRFL.TH.P.N.TLNKFIEEL..YGVT.IVRVC.A..DTAL.E.E.IHV.DWP.DDGAP.
RetrocopyPAPVEVTYKNMRFLKTHSPINTTLNKFIEELPEYGVTKIVRVCKAA*DTALEEEESIHVRDWPGDDGAPQ
ParentalSNQIVDDWLSLVKIKFREEPG-CCIAVHCVAGLGSRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSK
SNQ.VD.WLS.VKIKF..EP..C.IAV.CVAGL.S..PVLVA.AL.EGGM.YEDAVQF.RQK.RGAF.SK
RetrocopySNQNVDGWLSPVKIKFCGEPA<C-IAVCCVAGLRS-TPVLVAPALAEGGMRYEDAVQFRRQKQRGAFDSK
ParentalQLLYLEKYRPKMRLRFKESNGHRNNCCI
.LL.LEK..PKM.L.FK.S..HRNNCCI
RetrocopyELLCLEK*SPKMWLWFKVSKRHRNNCCI

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_328 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 32 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024383 retrocopies
retro_amel_1102, retro_amel_1344, retro_amel_1590,
Bos taurus ENSBTAG000000022753 retrocopies
retro_btau_1051, retro_btau_1186, retro_btau_859,
Canis familiaris ENSCAFG000000024903 retrocopies
retro_cfam_1832, retro_cfam_206, retro_cfam_593,
Callithrix jacchus ENSCJAG000000017433 retrocopies
retro_cjac_2812, retro_cjac_4144, retro_cjac_910,
Cavia porcellus ENSCPOG000000257595 retrocopies
retro_cpor_1137, retro_cpor_1233, retro_cpor_1392, retro_cpor_552, retro_cpor_58,
Dasypus novemcinctus ENSDNOG000000185074 retrocopies
retro_dnov_1850, retro_dnov_278, retro_dnov_692, retro_dnov_996,
Dipodomys ordii ENSDORG000000099606 retrocopies
retro_dord_148, retro_dord_244, retro_dord_355, retro_dord_375, retro_dord_696, retro_dord_92,
Equus caballus ENSECAG000000224836 retrocopies
retro_ecab_10, retro_ecab_1075, retro_ecab_20, retro_ecab_425, retro_ecab_783, retro_ecab_869,
Erinaceus europaeus ENSEEUG000000064773 retrocopies
retro_eeur_227, retro_eeur_626, retro_eeur_687,
Echinops telfairi ENSETEG000000081836 retrocopies
retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Felis catus ENSFCAG000000011993 retrocopies
retro_fcat_1439, retro_fcat_335, retro_fcat_969,
Homo sapiens ENSG000001122455 retrocopies
retro_hsap_2171, retro_hsap_3212, retro_hsap_479, retro_hsap_4798, retro_hsap_807,
Gorilla gorilla ENSGGOG000000225217 retrocopies
retro_ggor_1723, retro_ggor_2180, retro_ggor_2251, retro_ggor_2986, retro_ggor_452, retro_ggor_662, retro_ggor_763,
Latimeria chalumnae ENSLACG000000071831 retrocopy
retro_lcha_90,
Loxodonta africana ENSLAFG00000006572 8 retrocopies
retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328 , retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus ENSMLUG000000011621 retrocopy
retro_mluc_264,
Macaca mulatta ENSMMUG000000027771 retrocopy
retro_mmul_1720,
Monodelphis domestica ENSMODG000000187015 retrocopies
retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Mustela putorius furoENSMPUG000000031181 retrocopy
retro_mputfur_17,
Mus musculus ENSMUSG0000002606410 retrocopies
retro_mmus_1192, retro_mmus_1830, retro_mmus_1874, retro_mmus_1891, retro_mmus_2138, retro_mmus_2876, retro_mmus_2985, retro_mmus_3053, retro_mmus_3527, retro_mmus_575,
Nomascus leucogenys ENSNLEG000000004406 retrocopies
retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Ochotona princeps ENSOPRG000000049384 retrocopies
retro_opri_246, retro_opri_511, retro_opri_692, retro_opri_973,
Pongo abelii ENSPPYG000000167435 retrocopies
retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Pan troglodytes ENSPTRG000000183144 retrocopies
retro_ptro_1657, retro_ptro_2239, retro_ptro_3190, retro_ptro_360,
Pteropus vampyrus ENSPVAG000000152252 retrocopies
retro_pvam_487, retro_pvam_848,
Rattus norvegicus ENSRNOG000000117714 retrocopies
retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus ENSRNOG000000463704 retrocopies
retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri ENSTBEG0000000995614 retrocopies
retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tarsius syrichta ENSTSYG000000046322 retrocopies
retro_tsyr_1011, retro_tsyr_1152,
Tursiops truncatus ENSTTRG000000041296 retrocopies
retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,
Vicugna pacos ENSVPAG000000042779 retrocopies
retro_vpac_167, retro_vpac_201, retro_vpac_275, retro_vpac_427, retro_vpac_476, retro_vpac_496, retro_vpac_535, retro_vpac_560, retro_vpac_583,


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