RetrogeneDB ID: retro_sscr_1222

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: Y:1068562..1069020(+)
• Located in intron of: ENSSSCG00000025253

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB1
• Ensembl ID: ENSSSCG00000009327
• Aliases: None
• Description: high mobility group box 1 [Source:HGNC Symbol;Acc:4983]

Sequence

>retro_sscr_1222
CATTCATTCTTTGTGCAAACTTGCTGGGAGGAACATAAGAAGAATCACCCAGATGCTTCTGTCAGTTTCTCAGAGTTTTA
TAAGAAGCGCTGAGGGAGGTGGAAGACCATGTCTGCTAAGGAGAAAGGAAAATTTGGAGACATAGCAAAGGCGGACAAGG
CCTGTTATAAAAGATAAATAAAAATTTACATACCTCCTAAAGGGAAGACAAAAAAAAGTTCAAGAATTCCAATGCACCCA
AGAAGATTCCTTCTGGATTTTTCTTATTTTCTTCTGAGTATCATCCAAAAATGAAAGAACATCCTGGCCTATCCATCAGT
GATATTGCAAAGAAACAGGGAAAGATGTAGAATAACACTGCTGCAGATATCAAGCAGCCTTATGAAAAAAAGGACGCTAA
CCTGAAGGAAAAGTACAAAAAGAATATTACTGCATACCAAGCTAAAGGAAAGCCTGAT

Alignment

ORF - retro_sscr_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKG-E
          ..FFVQTC.EEHKK.HPDASV.FSEF.KK...RWKTMSAKEKGKF.D.AKADKA.Y.R..K.YIPPKG.E
Retrocopy HSFFVQTCWEEHKKNHPDASVSFSEFYKKR*GRWKTMSAKEKGKFGDIAKADKACYKR*IKIYIPPKG<E

Parental  TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK
          ....FK..NAPK..PS.FFLF.SEY.PK.K.EHPGLSI.D.AKK.G.M.NNTAAD.KQPYEKK.A.LKEK
Retrocopy DXXXFKNSNAPKKIPSGFFLFSSEYHPKMK-EHPGLSISDIAKKQGKM*NNTAADIKQPYEKKDANLKEK

Parental  YEKDIAAYRAKGKPD
          Y.K.I.AY.AKGKPD
Retrocopy YKKNITAYQAKGKPD

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
SRP014902_placenta	0.00 RPM	55.35 RPM
SRP014902_testis	0.00 RPM	227.30 RPM
SRP018288_heart	0.00 RPM	302.56 RPM
SRP018288_kidney	0.00 RPM	329.11 RPM
SRP018288_liver	0.00 RPM	231.23 RPM
SRP018288_lung	0.00 RPM	355.27 RPM
SRP018856_adipose	0.00 RPM	214.38 RPM
SRP035408_brain	0.00 RPM	1105.87 RPM
SRP035408_liver	0.00 RPM	695.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1222 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1222 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 302 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Equus caballus	ENSECAG00000008439	2 retrocopies	retro_ecab_101, retro_ecab_64,
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,
Macropus eugenii	ENSMEUG00000001380	2 retrocopies	retro_meug_1591, retro_meug_825,
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,
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,
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,
Sus scrofa	ENSSSCG00000009327	3 retrocopies	retro_sscr_1222 , retro_sscr_304, retro_sscr_649,
Sus scrofa	ENSSSCG00000012745	3 retrocopies	retro_sscr_1094, retro_sscr_466, retro_sscr_467,
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,