RetrogeneDB ID:

retro_ogar_842

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873529.1:14508449..14508859(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000032544
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3A
Ensembl ID:ENSOGAG00000024312
Aliases:None
Description:H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]


Retrocopy-Parental alignment summary:






>retro_ogar_842
ATGGCTGATACAAAGTAGACGGCCCGCAAATCCCCCCGGTGGTAAAGCAGCCGGGAAGCAACTGGCTGCAAAAGCTGCTG
GCAAGAGTGCGCCCTCTGCTGGAGGGGAGACGAAACCTCTTCGCTACAGGCCTGGGAACTGTGGCACTTGGTGAAATTAG
GCATTATCAGAAGTCCCCTGAACTTCTGATTCGCAAACTTCCTCTCCAGCGTCTGGTGCGAAAAATTGCTCAGGACTTTA
AGACAGATCTGTGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGCAGACAAGTGAGGCCTATCTGATTGGCCTTTTTGAA
GATAACAACCTGTGTGCTATCCAGGCCTCACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCACGCCGCATAGGCAA
AGATCGGGCT

ORF - retro_ogar_842 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKST-GGKAPRKQLATKAARKSAPSTGGVKKPHRYRPG-TVALREIRRYQKSTELLIRKLPF
MA.TK.TARKS..GGKA..KQLA.KAA.KSAPS.GG..KP.RYRPG.TVAL.EIR.YQKS.ELLIRKLP.
RetrocopyMADTK*TARKSP>GGKAAGKQLAAKAAGKSAPSAGGETKPLRYRPG>TVALGEIRHYQKSPELLIRKLPL
ParentalQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
QRLVR.IAQDFKTDL.FQSAAIGALQ..SEAYL.GLFED.NLCAI.A.RVTIMPKDIQLARRI...RA
RetrocopyQRLVRKIAQDFKTDLCFQSAAIGALQQTSEAYLIGLFEDNNLCAIQASRVTIMPKDIQLARRIGKDRA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_842 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 27 parental genes, and 174 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000145887 retrocopies
retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Bos taurus ENSBTAG000000245613 retrocopies
retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris ENSCAFG000000049162 retrocopies
retro_cfam_1117, retro_cfam_622,
Canis familiaris ENSCAFG000000161194 retrocopies
retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Dipodomys ordii ENSDORG000000081329 retrocopies
retro_dord_238, retro_dord_283, retro_dord_43, retro_dord_589, retro_dord_678, retro_dord_685, retro_dord_719, retro_dord_765, retro_dord_774,
Erinaceus europaeus ENSEEUG000000137961 retrocopy
retro_eeur_2,
Felis catus ENSFCAG000000036174 retrocopies
retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus ENSFCAG000000304245 retrocopies
retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Homo sapiens ENSG000001630415 retrocopies
retro_hsap_2825, retro_hsap_2889, retro_hsap_3102, retro_hsap_3214, retro_hsap_4800,
Gorilla gorilla ENSGGOG0000002252611 retrocopies
retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gadus morhua ENSGMOG000000143061 retrocopy
retro_gmor_9,
Macropus eugenii ENSMEUG000000040905 retrocopies
retro_meug_1041, retro_meug_1065, retro_meug_1819, retro_meug_281, retro_meug_573,
Macaca mulatta ENSMMUG000000314839 retrocopies
retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Monodelphis domestica ENSMODG000000059833 retrocopies
retro_mdom_1037, retro_mdom_1132, retro_mdom_175,
Mustela putorius furoENSMPUG000000138113 retrocopies
retro_mputfur_1159, retro_mputfur_787, retro_mputfur_881,
Mus musculus ENSMUSG0000001655918 retrocopies
retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972, retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Nomascus leucogenys ENSNLEG000000015772 retrocopies
retro_nleu_25, retro_nleu_35,
Otolemur garnettii ENSOGAG00000024312 11 retrocopies
retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842 , retro_ogar_955,
Otolemur garnettii ENSOGAG0000002593314 retrocopies
retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Oreochromis niloticus ENSONIG000000158057 retrocopies
retro_onil_45, retro_onil_47, retro_onil_51, retro_onil_54, retro_onil_61, retro_onil_65, retro_onil_69,
Pongo abelii ENSPPYG0000000016814 retrocopies
retro_pabe_1285, retro_pabe_2151, retro_pabe_2204, retro_pabe_2252, retro_pabe_2391, retro_pabe_2679, retro_pabe_2722, retro_pabe_2805, retro_pabe_2938, retro_pabe_3078, retro_pabe_323, retro_pabe_3420, retro_pabe_3637, retro_pabe_3697,
Pongo abelii ENSPPYG000000086361 retrocopy
retro_pabe_2662,
Pan troglodytes ENSPTRG0000000204520 retrocopies
retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098, retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pteropus vampyrus ENSPVAG000000084592 retrocopies
retro_pvam_218, retro_pvam_52,
Rattus norvegicus ENSRNOG000000032204 retrocopies
retro_rnor_121, retro_rnor_191, retro_rnor_336, retro_rnor_44,
Sus scrofa ENSSSCG000000239712 retrocopies
retro_sscr_31, retro_sscr_712,
Tursiops truncatus ENSTTRG000000158897 retrocopies
retro_ttru_1094, retro_ttru_1306, retro_ttru_18, retro_ttru_451, retro_ttru_738, retro_ttru_814, retro_ttru_92,


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