RetrogeneDB ID:

retro_nleu_1165

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397283.1:11054129..11054710(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB1
Ensembl ID:ENSNLEG00000000720
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1165
ATGGGCAAAGGAGATCCAAGGAAGCTGAGACGTAAAATGTGATATGCATTCTTTGTCCACACTTGTTGGGAGGAGCACAA
GAAGAAGCACCCAGATGCTCAGTCAACTCAAGAGTTTTCTAAGAAATGCTCACAGAGGTGCAAGACCATGTCTGCTAAAG
AGAAAGGGAGATTTGAAGACATGGCAAAGGTGGACAAGACCCGTTATGAAAGAGAAATGAAAACCTATATCCCTCCTAAA
TGAGAGACAAAAAAAGAAGTTCGAGGATCCCAATGTACCCAAGAGGCCTCCTATGGCCTTTTTCTTGTTCTATTATGAGT
GTCGCCCAAAAATCAAAGGAGAACATCCTGGCCTACCATTGGTGAGCTGTAAAGAAATTGGGAGAGATGTGGAAGGGCAC
TGCCTCAGATGATAAGCAGCCTTATGAAAAGAAGGCTGTGAAGCTGAAGGAAAAACATGAAAAAGATATTGCTGCATAGT
GAGCTAAAGGAAAGCCTGATGCAGCAAAAAAGCGAGTTGTCAAGGCTGAAAAAAGCAAGAAAAAGAAGGAAGAGGAGGAA
GATGAAGATGATGATGATGAA

ORF - retro_nleu_1165 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.39 %
Parental protein coverage: 91.16 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKAR
MGKGDP.K.R.KM..YAFFV.TC.EEHKKKHPDA.....EFSKKCS.R.KTMSAKEKG.FEDMAK.DK.R
RetrocopyMGKGDPRKLRRKM*-YAFFVHTCWEEHKKKHPDAQ-STQEFSKKCSQRCKTMSAKEKGRFEDMAKVDKTR
ParentalYEREMKTYIPPKGETKK-KFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDV-AKKLGEMWNNTA
YEREMKTYIPPK.ETKK.KF.DPN.PKRPP.AFFLF..E.RPKIKGEHPGL..IG....KKLGEMW..TA
RetrocopyYEREMKTYIPPK*ETKK>KFEDPNVPKRPPMAFFLFYYECRPKIKGEHPGL<TIGEL<VKKLGEMWKGTA
ParentalADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEED
.DDKQPYEKKA.KLKEK.EKDIAA..AKGKPDAAKK.VVKAEKSKKKKEEEEDE.D...
RetrocopySDDKQPYEKKAVKLKEKHEKDIAA**AKGKPDAAKKRVVKAEKSKKKKEEEEDEDDDDE

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






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_1165 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 16 parental genes, and 302 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000659713 retrocopies
retro_cfam_1088, retro_cfam_1102, retro_cfam_1387, retro_cfam_1628, retro_cfam_1765, retro_cfam_1831, retro_cfam_1980, retro_cfam_242, retro_cfam_280, retro_cfam_467, retro_cfam_495, retro_cfam_521, retro_cfam_528,
Equus caballus ENSECAG000000084392 retrocopies
retro_ecab_101, retro_ecab_64,
Felis catus ENSFCAG0000000020010 retrocopies
retro_fcat_1046, retro_fcat_1271, retro_fcat_1306, retro_fcat_1330, retro_fcat_1759, retro_fcat_693, retro_fcat_728, retro_fcat_762, retro_fcat_770, retro_fcat_821,
Homo sapiens ENSG0000018940337 retrocopies
retro_hsap_1230, retro_hsap_1357, retro_hsap_1504, retro_hsap_1589, retro_hsap_1608, retro_hsap_176, retro_hsap_1832, retro_hsap_1954, retro_hsap_2103, retro_hsap_2192, retro_hsap_2219, retro_hsap_2228, retro_hsap_2340, retro_hsap_2490, retro_hsap_2552, retro_hsap_2613, retro_hsap_2660, retro_hsap_2858, retro_hsap_2947, retro_hsap_3317, retro_hsap_3340, retro_hsap_3592, retro_hsap_3615, retro_hsap_3666, retro_hsap_382, retro_hsap_3942, retro_hsap_4003, retro_hsap_4109, retro_hsap_4309, retro_hsap_4669, retro_hsap_470, retro_hsap_4738, retro_hsap_4832, retro_hsap_525, retro_hsap_554, retro_hsap_758, retro_hsap_933,
Gorilla gorilla ENSGGOG0000002676423 retrocopies
retro_ggor_1057, retro_ggor_1212, retro_ggor_1421, retro_ggor_1596, retro_ggor_1637, retro_ggor_1662, retro_ggor_1735, retro_ggor_1777, retro_ggor_1856, retro_ggor_1951, retro_ggor_1977, retro_ggor_213, retro_ggor_2422, retro_ggor_2441, retro_ggor_2478, retro_ggor_259, retro_ggor_2897, retro_ggor_3013, retro_ggor_388, retro_ggor_448, retro_ggor_483, retro_ggor_753, retro_ggor_964,
Macropus eugenii ENSMEUG000000013802 retrocopies
retro_meug_1591, retro_meug_825,
Microcebus murinus ENSMICG000000071447 retrocopies
retro_mmur_11, retro_mmur_1452, retro_mmur_154, retro_mmur_182, retro_mmur_40, retro_mmur_428, retro_mmur_664,
Macaca mulatta ENSMMUG000000233993 retrocopies
retro_mmul_2079, retro_mmul_320, retro_mmul_385,
Monodelphis domestica ENSMODG0000000923814 retrocopies
retro_mdom_1088, retro_mdom_1144, retro_mdom_1228, retro_mdom_1689, retro_mdom_1727, retro_mdom_1819, retro_mdom_2007, retro_mdom_2024, retro_mdom_3, retro_mdom_434, retro_mdom_548, retro_mdom_72, retro_mdom_760, retro_mdom_958,
Mus musculus ENSMUSG00000066551129 retrocopies
retro_mmus_1025, retro_mmus_1037, retro_mmus_1047, retro_mmus_1065, retro_mmus_1094, retro_mmus_1112, retro_mmus_1113, retro_mmus_1114, retro_mmus_1115, retro_mmus_1128, retro_mmus_1135, retro_mmus_1140, retro_mmus_1178, retro_mmus_1181, retro_mmus_1209, retro_mmus_1284, retro_mmus_1302, retro_mmus_1351, retro_mmus_1407, retro_mmus_1423, retro_mmus_1508, retro_mmus_1553, retro_mmus_1554, retro_mmus_1584, retro_mmus_1672, retro_mmus_1705, retro_mmus_1706, retro_mmus_1712, retro_mmus_1716, retro_mmus_1725, retro_mmus_1775, retro_mmus_1794, retro_mmus_1800, retro_mmus_1822, retro_mmus_1845, retro_mmus_1871, retro_mmus_1989, retro_mmus_2015, retro_mmus_2077, retro_mmus_2080, retro_mmus_2096, retro_mmus_2191, retro_mmus_2194, retro_mmus_2199, retro_mmus_2209, retro_mmus_2224, retro_mmus_2229, retro_mmus_2280, retro_mmus_2300, retro_mmus_2324, retro_mmus_2404, retro_mmus_2407, retro_mmus_2409, retro_mmus_2414, retro_mmus_2420, retro_mmus_2425, retro_mmus_2467, retro_mmus_2469, retro_mmus_2524, retro_mmus_2532, retro_mmus_2627, retro_mmus_2670, retro_mmus_2682, retro_mmus_2702, retro_mmus_2719, retro_mmus_2754, retro_mmus_2789, retro_mmus_2815, retro_mmus_2823, retro_mmus_2866, retro_mmus_2877, retro_mmus_2886, retro_mmus_292, retro_mmus_2923, retro_mmus_2936, retro_mmus_2940, retro_mmus_2954, retro_mmus_2965, retro_mmus_2977, retro_mmus_303, retro_mmus_3046, retro_mmus_3056, retro_mmus_3059, retro_mmus_3067, retro_mmus_3070, retro_mmus_3075, retro_mmus_3102, retro_mmus_3106, retro_mmus_3121, retro_mmus_3169, retro_mmus_3175, retro_mmus_319, retro_mmus_3190, retro_mmus_3199, retro_mmus_3207, retro_mmus_3239, retro_mmus_3289, retro_mmus_3322, retro_mmus_3353, retro_mmus_3375, retro_mmus_3476, retro_mmus_3494, retro_mmus_3533, retro_mmus_359, retro_mmus_3612, retro_mmus_3676, retro_mmus_3692, retro_mmus_3715, retro_mmus_418, retro_mmus_515, retro_mmus_530, retro_mmus_574, retro_mmus_599, retro_mmus_618, retro_mmus_623, retro_mmus_624, retro_mmus_634, retro_mmus_704, retro_mmus_705, retro_mmus_785, retro_mmus_813, retro_mmus_839, retro_mmus_855, retro_mmus_881, retro_mmus_903, retro_mmus_906, retro_mmus_930, retro_mmus_965, retro_mmus_981,
Nomascus leucogenys ENSNLEG00000000720 33 retrocopies
retro_nleu_1148, retro_nleu_1165 , retro_nleu_1241, retro_nleu_1271, retro_nleu_1393, retro_nleu_1461, retro_nleu_1633, retro_nleu_1746, retro_nleu_1932, retro_nleu_2160, retro_nleu_2210, retro_nleu_2377, retro_nleu_2512, retro_nleu_2517, retro_nleu_2637, retro_nleu_2681, retro_nleu_2708, retro_nleu_2752, retro_nleu_278, retro_nleu_2798, retro_nleu_2859, retro_nleu_292, retro_nleu_301, retro_nleu_322, retro_nleu_345, retro_nleu_393, retro_nleu_520, retro_nleu_576, retro_nleu_602, retro_nleu_875, retro_nleu_885, retro_nleu_968, retro_nleu_984,
Nomascus leucogenys ENSNLEG000000066623 retrocopies
retro_nleu_113, retro_nleu_517, retro_nleu_550,
Rattus norvegicus ENSRNOG000000298131 retrocopy
retro_rnor_421,
Sorex araneus ENSSARG0000000447014 retrocopies
retro_sara_131, retro_sara_182, retro_sara_259, retro_sara_293, retro_sara_302, retro_sara_342, retro_sara_378, retro_sara_402, retro_sara_47, retro_sara_564, retro_sara_576, retro_sara_613, retro_sara_655, retro_sara_765,
Sus scrofa ENSSSCG000000093273 retrocopies
retro_sscr_1222, retro_sscr_304, retro_sscr_649,
Tursiops truncatus ENSTTRG000000103278 retrocopies
retro_ttru_102, retro_ttru_1143, retro_ttru_119, retro_ttru_1382, retro_ttru_256, retro_ttru_723, retro_ttru_757, retro_ttru_956,


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