RetrogeneDB ID: retro_cfam_467

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:51413038..51413541(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HMGB1
• Ensembl ID: ENSCAFG00000006597
• Aliases: HMGB1, HMG1
• Description: Canis lupus familiaris high mobility group box 1 (HMGB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001002937]

Sequence

>retro_cfam_467
ATGGGCAAAGGAGATCCTAAGAAGACGAGAGGCAAAATATCATCATATGCATTTTGTGCAAACTTGCCGAGAGGAACACA
AGAAGAAGCACCCAGATGCTCCAGTCAACTTCTCAGAGTTTTCTAAGAAGTGCTCAGAAAGGTGGAAGACCATGTCTACT
AAAGAGAAAGGAAAATTTGAAGACATGACTAAGGTGGACAAGGCCCGTTATGAAAGAGAAATGAAACTTCCTCCCCAAAG
GGGAAACAAAAAAGAAGTTTAAGGATCCCAATGTACCCAAGAGGCCTCCCTTGGCCTTTTTCTTGTTTTGTTCTGAGTAT
TGCCCAAAAATCAAAGGAGAACATCCCGCCCTATCCATTGGTGATGTTGCAAAGAAACTGGGAGAGATGTGGAATAACAC
TGCTGCAGATGACAAGCAGCCTTATGAAAAGAAGGCTGCTAAGCTGAAGGAAAAATATGAAAAGGATATTGCTGCATACC
GAGCTAAAGGAAAGCCTGATGCG

Alignment

ORF - retro_cfam_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.63 %
• Parental protein coverage: 79.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPKKPRGKMSSYAFFVQTCR-EEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA
          MGKGDPKK.RGK.SSYAF.....R.E..K.KHPDA.VNFSEFSKKCSERWKTMS.KEKGKFEDM.K.DKA
Retrocopy MGKGDPKKTRGKISSYAFCANLPR>EHKK-KHPDAPVNFSEFSKKCSERWKTMSTKEKGKFEDMTKVDKA

Parental  RYEREMKTYIPP-KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA
          RYEREMK...PP.KGETKKKFKDPN.PKRPP.AFFLFCSEY.PKIKGEHP.LSIGDVAKKLGEMWNNTAA
Retrocopy RYEREMK--LPP>KGETKKKFKDPNVPKRPPLAFFLFCSEYCPKIKGEHPALSIGDVAKKLGEMWNNTAA

Parental  DDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDA
          DDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDA
Retrocopy DDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDA

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.04 RPM	398.69 RPM
SRP017611_brain	0.00 RPM	186.89 RPM
SRP017611_kidney	0.00 RPM	264.61 RPM
SRP017611_liver	0.07 RPM	83.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_467 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_467 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 35 parental genes, and 577 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008880	7 retrocopies	retro_amel_1130, retro_amel_1216, retro_amel_1299, retro_amel_1389, retro_amel_1545, retro_amel_1629, retro_amel_1767,
Bos taurus	ENSBTAG00000018103	2 retrocopies	retro_btau_1551, retro_btau_224,
Canis familiaris	ENSCAFG00000006597	13 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,
Canis familiaris	ENSCAFG00000028715	1 retrocopy	retro_cfam_1537,
Choloepus hoffmanni	ENSCHOG00000002423	16 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	ENSCJAG00000021615	11 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	ENSCPOG00000003985	1 retrocopy	retro_cpor_69,
Equus caballus	ENSECAG00000008439	2 retrocopies	retro_ecab_101, retro_ecab_64,
Echinops telfairi	ENSETEG00000004048	18 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,
Felis catus	ENSFCAG00000000200	10 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	ENSG00000189403	37 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	ENSGGOG00000026764	23 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	ENSLAFG00000000269	4 retrocopies	retro_lafr_349, retro_lafr_512, retro_lafr_607, retro_lafr_685,
Macropus eugenii	ENSMEUG00000001380	2 retrocopies	retro_meug_1591, retro_meug_825,
Microcebus murinus	ENSMICG00000000573	1 retrocopy	retro_mmur_1529,
Microcebus murinus	ENSMICG00000007144	7 retrocopies	retro_mmur_11, retro_mmur_1452, retro_mmur_154, retro_mmur_182, retro_mmur_40, retro_mmur_428, retro_mmur_664,
Myotis lucifugus	ENSMLUG00000025979	17 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	ENSMMUG00000023399	3 retrocopies	retro_mmul_2079, retro_mmul_320, retro_mmul_385,
Monodelphis domestica	ENSMODG00000009238	14 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	ENSMUSG00000066551	129 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,
Oryctolagus cuniculus	ENSOCUG00000021335	16 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	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	ENSOGAG00000032147	1 retrocopy	retro_ogar_1712,
Ochotona princeps	ENSOPRG00000003507	8 retrocopies	retro_opri_1030, retro_opri_1150, retro_opri_1209, retro_opri_140, retro_opri_279, retro_opri_42, retro_opri_553, retro_opri_706,
Procavia capensis	ENSPCAG00000002201	2 retrocopies	retro_pcap_256, retro_pcap_432,
Pongo abelii	ENSPPYG00000005546	35 retrocopies	retro_pabe_1023, retro_pabe_1125, retro_pabe_1254, retro_pabe_1334, retro_pabe_1500, retro_pabe_159, retro_pabe_1724, retro_pabe_1831, retro_pabe_1973, retro_pabe_1997, retro_pabe_2070, retro_pabe_2089, retro_pabe_2194, retro_pabe_222, retro_pabe_2313, retro_pabe_2362, retro_pabe_2406, retro_pabe_2444, retro_pabe_264, retro_pabe_2732, retro_pabe_2751, retro_pabe_2752, retro_pabe_2777, retro_pabe_2953, retro_pabe_2966, retro_pabe_3008, retro_pabe_3365, retro_pabe_3523, retro_pabe_3684, retro_pabe_3757, retro_pabe_452, retro_pabe_511, retro_pabe_522, retro_pabe_761, retro_pabe_762,
Pteropus vampyrus	ENSPVAG00000001431	6 retrocopies	retro_pvam_1156, retro_pvam_154, retro_pvam_429, retro_pvam_508, retro_pvam_774, retro_pvam_960,
Rattus norvegicus	ENSRNOG00000029813	1 retrocopy	retro_rnor_421,
Sorex araneus	ENSSARG00000004470	14 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	ENSSHAG00000014034	2 retrocopies	retro_shar_136, retro_shar_634,
Sus scrofa	ENSSSCG00000009327	3 retrocopies	retro_sscr_1222, retro_sscr_304, retro_sscr_649,
Ictidomys tridecemlineatus	ENSSTOG00000000443	19 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	ENSTSYG00000006328	7 retrocopies	retro_tsyr_1405, retro_tsyr_1621, retro_tsyr_1744, retro_tsyr_1937, retro_tsyr_1945, retro_tsyr_632, retro_tsyr_76,
Tursiops truncatus	ENSTTRG00000010327	8 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,