RetrogeneDB ID:

retro_ogar_1843

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873569.1:1542009..1542543(-)
Located in intron of:ENSOGAG00000011137
Retrocopy
information
Ensembl ID:ENSOGAG00000007217
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:B4USW9_OTOGA
Ensembl ID:ENSOGAG00000003205
Aliases:None
Description:High-mobility group box 1 (Predicted) [Source:UniProtKB/TrEMBL;Acc:B4USW9]


Retrocopy-Parental alignment summary:






>retro_ogar_1843
GTGGGCAAAGGAGACCGTAAGATGCCGAGAGGCAAAATGTCATCACACACATTCTTTGTGCAAACTAGTCGGGAGGAGCA
CAAGAAGCAGCACTCAGATGCTTCAGTCAACTTCTCAGAGTTGTCTAAGAAGCGCTCAGAGAGGAGGAAGACCACGTCTG
CTAAAGAGAAAGGAAAATTTGAAGACATGGCAAAGGCAGACAAGGCCCGTTATGAAAGAGAAATGAAAACCTATATCCCT
CCTAAAGGGGAAACCAAAAAGAAGTTCAAGGATCCCAATGCACCCAAGAGGCTTCCTTCGGCCTTTTCCTTGTTCTGTTC
TGAGTATCGCCCCCAAATCAAAGGAGAACATCCCGGCCTGTCCATTGGTGTTGTTCCAAAGAAGCTGGGAGAGATGTGGA
ATAACACTGCTGTGGATGACAAGCAGCCTCATGAAAAGACGGCTGCAAAGCTGAAGGAAAAATACGAAAAGGATATTGCT
GCATACCGAGCTAAAGGAAAGCCTGATGCAGCAAAAAAGGGAGTTGTCAAGGCT

ORF - retro_ogar_1843 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.76 %
Parental protein coverage: 84.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKAR
.GKGD.K.PRGKMSS..FFVQT.REEHKK.H.DASVNFSE.SKK.SER.KT.SAKEKGKFEDMAKADKAR
RetrocopyVGKGDRKMPRGKMSSHTFFVQTSREEHKKQHSDASVNFSELSKKRSERRKTTSAKEKGKFEDMAKADKAR
ParentalYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADD
YEREMKTYIPPKGETKKKFKDPNAPKR.PSAF.LFCSEYRP.IKGEHPGLSIG.V.KKLGEMWNNTA.DD
RetrocopyYEREMKTYIPPKGETKKKFKDPNAPKRLPSAFSLFCSEYRPQIKGEHPGLSIGVVPKKLGEMWNNTAVDD
ParentalKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKA
KQP.EK.AAKLKEKYEKDIAAYRAKGKPDAAKKGVVKA
RetrocopyKQPHEKTAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKA

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_1843 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 24 parental genes, and 354 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088807 retrocopies
retro_amel_1130, retro_amel_1216, retro_amel_1299, retro_amel_1389, retro_amel_1545, retro_amel_1629, retro_amel_1767,
Bos taurus ENSBTAG000000181032 retrocopies
retro_btau_1551, retro_btau_224,
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,
Choloepus hoffmanni ENSCHOG0000000242316 retrocopies
retro_chof_108, retro_chof_1130, retro_chof_1214, retro_chof_148, retro_chof_164, retro_chof_1708, retro_chof_1741, retro_chof_1764, retro_chof_1797, retro_chof_2155, retro_chof_2484, retro_chof_443, retro_chof_538, retro_chof_591, retro_chof_720, retro_chof_795,
Callithrix jacchus ENSCJAG0000002161511 retrocopies
retro_cjac_1042, retro_cjac_1546, retro_cjac_1819, retro_cjac_1842, retro_cjac_1934, retro_cjac_2269, retro_cjac_2901, retro_cjac_2934, retro_cjac_3090, retro_cjac_718, retro_cjac_895,
Cavia porcellus ENSCPOG000000039851 retrocopy
retro_cpor_69,
Echinops telfairi ENSETEG0000000404818 retrocopies
retro_etel_1092, retro_etel_111, retro_etel_1146, retro_etel_1290, retro_etel_1293, retro_etel_146, retro_etel_1481, retro_etel_1587, retro_etel_1892, retro_etel_1943, retro_etel_2015, retro_etel_453, retro_etel_498, retro_etel_508, retro_etel_577, retro_etel_826, retro_etel_827, retro_etel_871,
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,
Loxodonta africana ENSLAFG000000002694 retrocopies
retro_lafr_349, retro_lafr_512, retro_lafr_607, retro_lafr_685,
Macropus eugenii ENSMEUG000000013802 retrocopies
retro_meug_1591, retro_meug_825,
Myotis lucifugus ENSMLUG0000002597917 retrocopies
retro_mluc_1062, retro_mluc_1103, retro_mluc_1446, retro_mluc_1584, retro_mluc_1591, retro_mluc_1608, retro_mluc_1615, retro_mluc_1773, retro_mluc_1798, retro_mluc_2013, retro_mluc_2201, retro_mluc_2460, retro_mluc_506, retro_mluc_551, retro_mluc_800, retro_mluc_809, retro_mluc_953,
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,
Oryctolagus cuniculus ENSOCUG0000002133516 retrocopies
retro_ocun_1039, retro_ocun_1112, retro_ocun_1368, retro_ocun_1407, retro_ocun_1554, retro_ocun_1658, retro_ocun_1739, retro_ocun_1882, retro_ocun_1937, retro_ocun_285, retro_ocun_36, retro_ocun_471, retro_ocun_616, retro_ocun_633, retro_ocun_737, retro_ocun_825,
Otolemur garnettii ENSOGAG0000000177319 retrocopies
retro_ogar_1318, retro_ogar_1647, retro_ogar_1728, retro_ogar_187, retro_ogar_1930, retro_ogar_204, retro_ogar_2076, retro_ogar_2530, retro_ogar_2591, retro_ogar_2678, retro_ogar_2743, retro_ogar_2983, retro_ogar_3127, retro_ogar_3371, retro_ogar_343, retro_ogar_3433, retro_ogar_3479, retro_ogar_3513, retro_ogar_65,
Otolemur garnettii ENSOGAG00000003205 104 retrocopies
retro_ogar_1008, retro_ogar_1043, retro_ogar_106, retro_ogar_1133, retro_ogar_123, retro_ogar_1232, retro_ogar_1296, retro_ogar_1299, retro_ogar_1330, retro_ogar_1386, retro_ogar_1398, retro_ogar_1399, retro_ogar_1421, retro_ogar_1423, retro_ogar_1424, retro_ogar_1431, retro_ogar_1461, retro_ogar_1560, retro_ogar_1571, retro_ogar_1585, retro_ogar_1597, retro_ogar_1600, retro_ogar_1607, retro_ogar_1628, retro_ogar_163, retro_ogar_1664, retro_ogar_1698, retro_ogar_17, retro_ogar_172, retro_ogar_1738, retro_ogar_1758, retro_ogar_1781, retro_ogar_1843 , retro_ogar_1844, retro_ogar_1861, retro_ogar_1867, retro_ogar_1878, retro_ogar_1894, retro_ogar_1896, retro_ogar_198, retro_ogar_1991, retro_ogar_2136, retro_ogar_2165, retro_ogar_219, retro_ogar_2282, retro_ogar_2318, retro_ogar_2319, retro_ogar_2352, retro_ogar_2385, retro_ogar_2403, retro_ogar_2429, retro_ogar_2436, retro_ogar_2458, retro_ogar_250, retro_ogar_2559, retro_ogar_2598, retro_ogar_2615, retro_ogar_2618, retro_ogar_2730, retro_ogar_2777, retro_ogar_2778, retro_ogar_2814, retro_ogar_2824, retro_ogar_2836, retro_ogar_284, retro_ogar_2845, retro_ogar_2891, retro_ogar_2894, retro_ogar_2906, retro_ogar_2961, retro_ogar_3008, retro_ogar_3018, retro_ogar_3028, retro_ogar_304, retro_ogar_311, retro_ogar_3136, retro_ogar_317, retro_ogar_320, retro_ogar_3208, retro_ogar_3230, retro_ogar_3325, retro_ogar_3330, retro_ogar_3355, retro_ogar_3374, retro_ogar_3500, retro_ogar_422, retro_ogar_435, retro_ogar_511, retro_ogar_542, retro_ogar_547, retro_ogar_634, retro_ogar_663, retro_ogar_698, retro_ogar_716, retro_ogar_772, retro_ogar_778, retro_ogar_8, retro_ogar_835, retro_ogar_890, retro_ogar_904, retro_ogar_912, retro_ogar_918, retro_ogar_92, retro_ogar_933,
Otolemur garnettii ENSOGAG000000171493 retrocopies
retro_ogar_3117, retro_ogar_3323, retro_ogar_3336,
Otolemur garnettii ENSOGAG000000321471 retrocopy
retro_ogar_1712,
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,
Sarcophilus harrisii ENSSHAG000000140342 retrocopies
retro_shar_136, retro_shar_634,
Ictidomys tridecemlineatus ENSSTOG0000000044319 retrocopies
retro_itri_1060, retro_itri_1220, retro_itri_127, retro_itri_1489, retro_itri_1531, retro_itri_1580, retro_itri_1644, retro_itri_1852, retro_itri_233, retro_itri_238, retro_itri_444, retro_itri_518, retro_itri_553, retro_itri_584, retro_itri_712, retro_itri_754, retro_itri_792, retro_itri_825, retro_itri_991,
Tarsius syrichta ENSTSYG000000063287 retrocopies
retro_tsyr_1405, retro_tsyr_1621, retro_tsyr_1744, retro_tsyr_1937, retro_tsyr_1945, retro_tsyr_632, retro_tsyr_76,


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