RetrogeneDB ID:

retro_lafr_514

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_2:86690996..86691571(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS7
Ensembl ID:ENSLAFG00000015087
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_514
TCAAGTGTGAAGACCGTGAGGCCCAATGGTGAAACGCTGGGTGAATTCAAGTCTGGCATTTCTCAAGGGCTGCTTGAACT
GGAGGTGACCTTGGACCTAAAGGCTCAGCTGAGGGAGCTGAATATAACCGCAGCCAAGGAAATTGAAGATGGTGGTGGAC
GGAAAATCTATTACAATCTTTGTTCCCTTTCCTCAGCTGAAGTCTTTCCAGAAAATTCAAGTCAGGCTAGTACATGAACT
GGAGAAAAAGTTCCATGGAAAGCACGTTGTCTTTATTGCTTAAAGGAGAATTCTGCCTAAACCAACTGGAAAAAGTCGTA
CAAAAAATAAGTAGAAGTCTCCCAGGAGCCGTCCTCTGACAGCCGTGCATGATGCAACCCTTGAAGACTTGGTCTTCCCC
AGTGAAATCGTGAGCAAGAGAGTCCATGTAAAACTGGATGGCAGCCAGCTTGGAAAAGTTCATGTGAACAACGCACAGCA
GAACAATGTGGAACACAAGATTGAATCTTTTTCTGGTGTGTTATGAGAAGCTCACGGGCAAGGACGTTAATTTTGAATTC
CCAGAGTTTCAACTG

ORF - retro_lafr_514 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.35 %
Parental protein coverage: 98.45 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRK-AIIIFVPVPQLKSF
SS.K.V.PNGE...EF.SGISQ.LLELE...DLKAQLRELNITAAKEIE.GGGRK..I.IFVP.PQLKSF
RetrocopySSVKTVRPNGETLGEFKSGISQGLLELEVTLDLKAQLRELNITAAKEIEDGGGRK>SITIFVPFPQLKSF
ParentalQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK
QKIQVRLV.ELEKKF.GKHVVFIA.RRILPKPT.KSRTKNK.K.PRSR.LTAVHDA.LEDLVFPSEIV.K
RetrocopyQKIQVRLVHELEKKFHGKHVVFIA*RRILPKPTGKSRTKNK*KSPRSRPLTAVHDATLEDLVFPSEIVSK
ParentalRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGV-YKKLTGKDVNFEFPEFQL
R..VKLDGS.L.KVH...AQQNNVEHK.E.FSGV.Y.KLTGKDVNFEFPEFQL
RetrocopyRVHVKLDGSQLGKVHVNNAQQNNVEHKIESFSGV>YEKLTGKDVNFEFPEFQL

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_514 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 22 parental genes, and 109 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184352 retrocopies
retro_amel_391, retro_amel_914,
Bos taurus ENSBTAG000000162245 retrocopies
retro_btau_1016, retro_btau_1046, retro_btau_1351, retro_btau_448, retro_btau_997,
Canis familiaris ENSCAFG000000032631 retrocopy
retro_cfam_1798,
Callithrix jacchus ENSCJAG000000164622 retrocopies
retro_cjac_16, retro_cjac_2287,
Cavia porcellus ENSCPOG000000097952 retrocopies
retro_cpor_1139, retro_cpor_773,
Dasypus novemcinctus ENSDNOG0000001328514 retrocopies
retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus ENSECAG000000202532 retrocopies
retro_ecab_276, retro_ecab_396,
Homo sapiens ENSG0000017186314 retrocopies
retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925, retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Loxodonta africana ENSLAFG00000015087 11 retrocopies
retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514 , retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus ENSMLUG000000061211 retrocopy
retro_mluc_1118,
Macaca mulatta ENSMMUG000000118707 retrocopies
retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Monodelphis domestica ENSMODG000000144952 retrocopies
retro_mdom_662, retro_mdom_810,
Mus musculus ENSMUSG000000614772 retrocopies
retro_mmus_271, retro_mmus_53,
Nomascus leucogenys ENSNLEG0000001540710 retrocopies
retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Oryctolagus cuniculus ENSOCUG000000085072 retrocopies
retro_ocun_203, retro_ocun_230,
Otolemur garnettii ENSOGAG000000281651 retrocopy
retro_ogar_133,
Pongo abelii ENSPPYG0000002587212 retrocopies
retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes ENSPTRG000000116153 retrocopies
retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Rattus norvegicus ENSRNOG000000085512 retrocopies
retro_rnor_39, retro_rnor_391,
Sus scrofa ENSSSCG000000273535 retrocopies
retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus ENSSTOG000000248303 retrocopies
retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus ENSTTRG000000016166 retrocopies
retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,


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