RetrogeneDB ID: retro_cjac_1546

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:28421825..28422340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB1
• Ensembl ID: ENSCJAG00000021615
• Aliases: LOC100392312, HMG-1, HMGB1
• Description: High mobility group protein B1 [Source:UniProtKB/Swiss-Prot;Acc:B0CM99]

Sequence

>retro_cjac_1546
GAGCACCCAAATGCTTCAGTCAGTTTCTCAGAGTTTTCTAAGAAGCACTCAGAGAAGTGGAAGACCCTCTCTGCTAAAGA
GATAGGAAAATTTAAATAAATGGCAATGACAGACAAAGCCTGTTGTGAAAAGGAAATGAAAACCTGTCTCCTTCCTAAAA
GGGGGAAAAAAAGTTCAAGTATCATATAATGCACCCAAGAGGCTACCTTCAGCCTTTTTCCTGTTCTGTTCTGAGTATTG
CCCCCAAATCAAAGGAGAACATTTCAGCCTATTCATTGGTGTAAAGAAATGGGGAGAGATAGGAAATACCACTGCTGCAG
ATGACAAGCAGCCTTACAAAAAGAAGGCCGTAAAACTGAAAGAATAATATGAAAAGGATATTGTTGCATACTGAGCTAAG
GAAAGCCTGATGCAGCAAAAAAGGCAGTCATTAAGGCTGAAAAAACAACAACAAGAAATAGAAGAAAGAGGAAGACCAGG
AAGATGAAAAGGATGAGGAGGAGAAAGATGAAAAA

Alignment

ORF - retro_cjac_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.85 %
• Parental protein coverage: 80.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP-KGETKKKFKDPNAPKRP
          .HP.ASV.FSEFSKK.SE.WKT.SAKE.GKF..MA..DKA..E.EMKT...P.KG..KK.....NAPKR.
Retrocopy EHPNASVSFSEFSKKHSEKWKTLSAKEIGKFK*MAMTDKACCEKEMKTCLLP>KGG-KKVQVSYNAPKRL

Parental  PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK-GK
          PSAFFLFCSEY.P.IKGEH..L.IG...KK.GE..N.TAADDKQPY.KKA.KLKE.YEKDI.AY.AK.GK
Retrocopy PSAFFLFCSEYCPQIKGEHFSLFIG--VKKWGEIGNTTAADDKQPYKKKAVKLKE*YEKDIVAY*AK<GK

Parental  PDAAKKGVVKAE-KSKKKK-EEEEDEEDEEDEEEEEDE
          PDAAKK.V.KAE.K...KK...EED.EDE.DEEE....
Retrocopy PDAAKKAVIKAE<KNNNKK*KKEEDQEDEKDEEEKDEK

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
SRP051959_colon	0.00 RPM	50.12 RPM
SRP051959_heart	0.05 RPM	41.15 RPM
SRP051959_kidney	0.00 RPM	49.70 RPM
SRP051959_liver	0.04 RPM	35.72 RPM
SRP051959_lung	0.00 RPM	50.20 RPM
SRP051959_lymph_node	0.00 RPM	40.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.38 RPM
SRP051959_spleen	0.04 RPM	49.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1546 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1546 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2858
Gorilla gorilla	retro_ggor_1977
Pongo abelii	retro_pabe_2362

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 342 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,
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	ENSCJAG00000003936	9 retrocopies	retro_cjac_1596, retro_cjac_1950, retro_cjac_2343, retro_cjac_2469, retro_cjac_2470, retro_cjac_2738, retro_cjac_2900, retro_cjac_688, retro_cjac_965,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555, retro_cjac_832,
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,
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,
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,
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,
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,
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,
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,