RetrogeneDB ID:

retro_lafr_178

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_1:20234283..20234858(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOA
Ensembl ID:ENSLAFG00000009726
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_178
ATGGCTGCCATCAAGAAGAAACTGGTGATTGTTGGTGATGAAGCCTATGGAAGACCTGCTTGCTCATAGTCTTCAGCAAG
GATCAGTTCCCCAAGGTGTATGTACCCACAGTGTTTGAGAACTATGTGGCAGATATTGAAGTGGATGGAAACCAGGTAGA
GTTGGCTTCGTGGGACACAGCCGGGCAGGAAGACTATGATCGTCTGAGGACCCTCTCCTATCCGGACACTGATGTTATGC
TGATGCTTTTCTCCATCGACACCCCAATAGTTTAGAAAACATCCCAGAAAAATAGACCCCAGAAATCAAGCATTTCTATC
CCAATGTGCCCATCATCTTGGTTGGGAACAAGAAGGATCTTCAGAATGATGAGCACACAGGTGGAACAAGCCAAGATGAA
GCAGGAGCTGGTAAAATCTGAAGAAGGCAGAGATATGGCAAACAGGATTGGTGCTTTTGGGTACATGGAGTGTTCAGCAA
AGACCAAAGATGGAGTGAGGGTGGTTTTTGAAATGGCCATGAGAACAGCTCTGCAAGCCAGACGTGGGAAGAAAAAATCT
GGGTGCAACATCTTG

ORF - retro_lafr_178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.12 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAAIRKKLVIVGDGACG-KTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRL
MAAI.KKLVIVGD.A.G.KTCLLIVFSKDQFP.VYVPTVFENYVADIEVDG.QVELA.WDTAGQEDYDRL
RetrocopyMAAIKKKLVIVGDEAYG<KTCLLIVFSKDQFPKVYVPTVFENYVADIEVDGNQVELASWDTAGQEDYDRL
ParentalRPLSYPDTDVILMCFSIDSP-DSLENIPEKWTPEVKHFCPNVPIIL-VGNKKDLRNDEHTRRELAKMKQE
R.LSYPDTDV.LM.FSID.P..SLENIPEK.TPE.KHF.PNVPIIL..G.....R....T..E.AKMKQE
RetrocopyRTLSYPDTDVMLMLFSIDTP<NSLENIPEK*TPEIKHFYPNVPIIL>LGTRRIFRMMS-TQVEQAKMKQE
ParentalPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
.VK.EEGRDMANRIGAFGYMECSAKTKDGVR.VFEMA.R.ALQARRGKKKSGC..L
RetrocopyLVKSEEGRDMANRIGAFGYMECSAKTKDGVRVVFEMAMRTALQARRGKKKSGCNIL

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_178 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 36 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082971 retrocopy
retro_acar_41,
Ailuropoda melanoleuca ENSAMEG000000125843 retrocopies
retro_amel_101, retro_amel_1515, retro_amel_615,
Anas platyrhynchos ENSAPLG000000146871 retrocopy
retro_apla_10,
Bos taurus ENSBTAG000000042792 retrocopies
retro_btau_206, retro_btau_540,
Canis familiaris ENSCAFG000000230662 retrocopies
retro_cfam_1652, retro_cfam_186,
Callithrix jacchus ENSCJAG000000039043 retrocopies
retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Dasypus novemcinctus ENSDNOG000000128256 retrocopies
retro_dnov_1012, retro_dnov_1814, retro_dnov_1904, retro_dnov_2090, retro_dnov_29, retro_dnov_326,
Dipodomys ordii ENSDORG000000033823 retrocopies
retro_dord_1, retro_dord_18, retro_dord_538,
Felis catus ENSFCAG000000274561 retrocopy
retro_fcat_29,
Gasterosteus aculeatus ENSGACG000000056701 retrocopy
retro_gacu_9,
Gallus gallus ENSGALG000000038061 retrocopy
retro_ggal_5,
Gorilla gorilla ENSGGOG000000128431 retrocopy
retro_ggor_2450,
Gadus morhua ENSGMOG000000081881 retrocopy
retro_gmor_18,
Latimeria chalumnae ENSLACG000000169411 retrocopy
retro_lcha_15,
Loxodonta africana ENSLAFG00000009726 8 retrocopies
retro_lafr_1196, retro_lafr_1197, retro_lafr_1198, retro_lafr_178 , retro_lafr_203, retro_lafr_261, retro_lafr_392, retro_lafr_82,
Meleagris gallopavo ENSMGAG000000022801 retrocopy
retro_mgal_2,
Myotis lucifugus ENSMLUG000000139116 retrocopies
retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta ENSMMUG000000129621 retrocopy
retro_mmul_977,
Monodelphis domestica ENSMODG000000129812 retrocopies
retro_mdom_19, retro_mdom_294,
Mus musculus ENSMUSG000000078159 retrocopies
retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Nomascus leucogenys ENSNLEG000000068394 retrocopies
retro_nleu_104, retro_nleu_2207, retro_nleu_377, retro_nleu_814,
Ornithorhynchus anatinus ENSOANG000000138071 retrocopy
retro_oana_7,
Oryctolagus cuniculus ENSOCUG000000133233 retrocopies
retro_ocun_1075, retro_ocun_726, retro_ocun_854,
Otolemur garnettii ENSOGAG000000284891 retrocopy
retro_ogar_2340,
Oreochromis niloticus ENSONIG000000188841 retrocopy
retro_onil_32,
Procavia capensis ENSPCAG000000096993 retrocopies
retro_pcap_191, retro_pcap_202, retro_pcap_98,
Pelodiscus sinensis ENSPSIG000000153281 retrocopy
retro_psin_7,
Pan troglodytes ENSPTRG000000149223 retrocopies
retro_ptro_10, retro_ptro_2456, retro_ptro_625,
Pteropus vampyrus ENSPVAG000000087381 retrocopy
retro_pvam_599,
Rattus norvegicus ENSRNOG000000505193 retrocopies
retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Sarcophilus harrisii ENSSHAG000000163082 retrocopies
retro_shar_60, retro_shar_96,
Sus scrofa ENSSSCG000000220801 retrocopy
retro_sscr_72,
Ictidomys tridecemlineatus ENSSTOG000000045612 retrocopies
retro_itri_39, retro_itri_96,
Takifugu rubripes ENSTRUG000000119441 retrocopy
retro_trub_19,
Tarsius syrichta ENSTSYG000000082203 retrocopies
retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,
Vicugna pacos ENSVPAG000000109313 retrocopies
retro_vpac_130, retro_vpac_24, retro_vpac_492,


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