RetrogeneDB ID:

retro_lafr_576

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_22:28950915..28951345(-)
Located in intron of:ENSLAFG00000014889
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSLAFG00000016213
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_576
ATGGCTAAGGGGCAGGTCCTGAAGCTCAATGGTGAGGCCATCTCCTGAGCCACCTGGCAGCCATCTGGCCAAGCAAGGAC
TCTGGGAGGGAAGGCAGTGATTGTGTACTGTGAGGGCATCAACACTTCCAGCAACTTTTACAGAAACCAAGTTGAAGTAC
CTGGCCTCCCCCCTCAAGTGCATGAACACCAACTCACCCCATGGGCTTCTACCACTTCCAGGTGCCGAGTCACGTCTTTT
GGCTGACCATGTGATGCATGCTGCCCCAAAAGGCGAAATGTGACCAGACCACCCTGGGTCACCTCAAGGAGTTCATTGGA
ATCCCCTCTTGGATAAGAAAAAGCAGATGGCGGTTCCTGCTGCCCTCAAGGTTACGAACCTGAAGCCCACTTGCAAGTTT
ATCTGCCTGGGGTGCCTGGCTGGGAAGGTT

ORF - retro_lafr_576 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.6 %
Parental protein coverage: 71.43 %
Number of stop codons detected: 1
Number of frameshifts detected: 6


Retrocopy - Parental Gene Alignment:

ParentalMAEGQVLVLDGR-GHLLGRLAAI-VAKQVL-LGRKVVVVRCEGINISGNFYRN-KLKYLAFLRKRMNTNP
MA.GQVL.L.G..GHLL..LAAI..AKQ.L.LG.K.V.V.CEGIN.S.NFYRN.KLKYLA...K.MNTN.
RetrocopyMAKGQVLKLNGE<GHLLSHLAAI<LAKQGL<LGGKAVIVYCEGINTSSNFYRN>KLKYLASPLKCMNTNS
ParentalSRGP-YHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKR-MVVPAALKVVRLKPTRK
..G..YHF..PS..FW.T...MLP.K.K..Q..L..LK.F.GI.P....K.R.M.VPAALKV..LKPT.K
RetrocopyPHGL>YHFQVPSHVFWLTM*CMLPQKAKCDQTTLGHLKEFIGI-PSWIRKSR<MAVPAALKVTNLKPTCK
ParentalFAYLGRLAHEV
F..LG.LA..V
RetrocopyFICLGCLAGKV

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_576 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 23 parental genes, and 156 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000140272 retrocopies
retro_amel_1332, retro_amel_1720,
Bos taurus ENSBTAG000000052963 retrocopies
retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris ENSCAFG000000298923 retrocopies
retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus ENSCJAG0000000007216 retrocopies
retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Equus caballus ENSECAG000000158323 retrocopies
retro_ecab_388, retro_ecab_653, retro_ecab_773,
Echinops telfairi ENSETEG000000170762 retrocopies
retro_etel_46, retro_etel_853,
Homo sapiens ENSG0000014254122 retrocopies
retro_hsap_1072, retro_hsap_1100, retro_hsap_1111, retro_hsap_1268, retro_hsap_1410, retro_hsap_2200, retro_hsap_2500, retro_hsap_293, retro_hsap_298, retro_hsap_3173, retro_hsap_3350, retro_hsap_3444, retro_hsap_3652, retro_hsap_3752, retro_hsap_3772, retro_hsap_397, retro_hsap_436, retro_hsap_615, retro_hsap_671, retro_hsap_730, retro_hsap_753, retro_hsap_967,
Gorilla gorilla ENSGGOG0000000293211 retrocopies
retro_ggor_12, retro_ggor_1739, retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Loxodonta africana ENSLAFG00000016213 3 retrocopies
retro_lafr_1160, retro_lafr_576 , retro_lafr_810,
Microcebus murinus ENSMICG000000093186 retrocopies
retro_mmur_240, retro_mmur_283, retro_mmur_311, retro_mmur_359, retro_mmur_65, retro_mmur_736,
Macaca mulatta ENSMMUG0000000755114 retrocopies
retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mustela putorius furoENSMPUG000000026043 retrocopies
retro_mputfur_1418, retro_mputfur_853, retro_mputfur_935,
Mus musculus ENSMUSG000000741293 retrocopies
retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Nomascus leucogenys ENSNLEG0000000521123 retrocopies
retro_nleu_1173, retro_nleu_1429, retro_nleu_1568, retro_nleu_159, retro_nleu_1823, retro_nleu_1873, retro_nleu_1892, retro_nleu_1897, retro_nleu_2047, retro_nleu_228, retro_nleu_2398, retro_nleu_2415, retro_nleu_2463, retro_nleu_2614, retro_nleu_2789, retro_nleu_2928, retro_nleu_330, retro_nleu_392, retro_nleu_441, retro_nleu_475, retro_nleu_513, retro_nleu_744, retro_nleu_760,
Oryctolagus cuniculus ENSOCUG000000252589 retrocopies
retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Otolemur garnettii ENSOGAG000000046257 retrocopies
retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Procavia capensis ENSPCAG000000040864 retrocopies
retro_pcap_163, retro_pcap_290, retro_pcap_415, retro_pcap_416,
Pongo abelii ENSPPYG000000102511 retrocopy
retro_pabe_148,
Pan troglodytes ENSPTRG000000112981 retrocopy
retro_ptro_31,
Pteropus vampyrus ENSPVAG000000109583 retrocopies
retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus ENSRNOG0000002061810 retrocopies
retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa ENSSSCG000000031664 retrocopies
retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,
Tupaia belangeri ENSTBEG000000165793 retrocopies
retro_tbel_2417, retro_tbel_4071, retro_tbel_958,


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