RetrogeneDB ID: retro_cjac_1548

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:33195823..33196413(+)
• Located in intron of: ENSCJAG00000001617

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008234
• Aliases: None
• Description: Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F7EMI9]

Sequence

>retro_cjac_1548
ATGGTGAAGGTGAAGGCCAGAGTAAATGGATTTGTCTCTGTTGGGCACTTGATCACCAGAGCTGCTTTTAACTCTAGCAA
AGTGGATACTGCTGCCATCAATGACCTCAACTACATGGTCTACATGTTTCAATATGATTCCACCAATGGCAAGTTCCACA
GTGCCATCAAGTCTGAGAATGAGAAGCTTGTCATCAATGGAAACCCCATAACCATCTTCCAGGAGTGAGATCCCACCCCA
ATCAAATGGGGTGATGCTGGCACTGATTATGTTATGGCACTGATTATGAAATTCACCAGTGTCTTAACTACCATGGAGAA
GACTGGGACTCATTTAGCCAAGGGAGCCAAAAGAGTCATTATCTCTGCACCCTCCGCTGATGCTGCCATGTTCATGATGG
ACGTAAATCATGAGAAATGTAAAAACAACTTCACAGTCATCAGCAATGCTTCCTGCACCACCAACTGCTTAGCCTCCCAG
CCAAGGTCATCCGTGACAACTTTAGCATTATAAAAGGACTTATGCCATCAATGCCACCTGGAAGAAAGTGGGTGGCCCCT
CCAGGAAACTGGGGTGTGATGACTGCAGGG

Alignment

ORF - retro_cjac_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.85 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKVKVGVNGFGRIGRLVTRAAFNSGKVDVVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVIN
          M.KVK..VNGF...G.L.TRAAFNS.KVD..AIN....DLNYMVYMFQYDST.GKFH...K.EN.KLVIN
Retrocopy MVKVKARVNGFVSVGHLITRAAFNSSKVDTAAIN----DLNYMVYMFQYDSTNGKFHSAIKSENEKLVIN

Parental  GNPITIFQERDPSKIKWGDAGAEY----VVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVN
          GNPITIFQE.DP..IKWGDAG..Y........T.V.TTMEK.G.HL..GAKRVIISAPSADA.MF.M.VN
Retrocopy GNPITIFQE*DPTPIKWGDAGTDYVMALIMKFTSVLTTMEKTGTHLAKGAKRVIISAPSADAAMFMMDVN

Parental  HEKYDNSLKIVSNASCTTNCLAPL-AKVIHDNFGIVEGLMNWLLPARTY--NPGGWGVLGTG
          HEK..N.....SNASCTTNCLA...AKVI.DNF.I..GLM....P.R.....PG.WGV...G
Retrocopy HEKCKNNFTVISNASCTTNCLASQ<AKVIRDNFSIIKGLMPSMPPGRKWVAPPGNWGVMTAG

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	121.41 RPM
SRP051959_heart	0.05 RPM	225.62 RPM
SRP051959_kidney	0.02 RPM	160.83 RPM
SRP051959_liver	0.00 RPM	306.95 RPM
SRP051959_lung	0.08 RPM	55.78 RPM
SRP051959_lymph_node	0.09 RPM	88.15 RPM
SRP051959_skeletal_muscle	0.04 RPM	743.56 RPM
SRP051959_spleen	0.13 RPM	63.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1548 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1548 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2852
Pan troglodytes	retro_ptro_1932
Pongo abelii	retro_pabe_2360
Macaca mulatta	retro_mmul_1469

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 539 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006675	5 retrocopies	retro_amel_1189, retro_amel_146, retro_amel_1792, retro_amel_1826, retro_amel_549,
Ailuropoda melanoleuca	ENSAMEG00000014329	35 retrocopies	retro_amel_1050, retro_amel_1082, retro_amel_1134, retro_amel_1174, retro_amel_1229, retro_amel_1235, retro_amel_1253, retro_amel_1308, retro_amel_1538, retro_amel_1550, retro_amel_1598, retro_amel_1605, retro_amel_1614, retro_amel_1658, retro_amel_1776, retro_amel_1801, retro_amel_1802, retro_amel_187, retro_amel_1900, retro_amel_1904, retro_amel_268, retro_amel_294, retro_amel_387, retro_amel_443, retro_amel_471, retro_amel_601, retro_amel_605, retro_amel_641, retro_amel_738, retro_amel_750, retro_amel_762, retro_amel_852, retro_amel_899, retro_amel_961, retro_amel_992,
Bos taurus	ENSBTAG00000014731	4 retrocopies	retro_btau_1175, retro_btau_1417, retro_btau_834, retro_btau_887,
Canis familiaris	ENSCAFG00000015077	4 retrocopies	retro_cfam_122, retro_cfam_214, retro_cfam_3, retro_cfam_7,
Callithrix jacchus	ENSCJAG00000008234	1 retrocopy	retro_cjac_1548 ,
Cavia porcellus	ENSCPOG00000026350	1 retrocopy	retro_cpor_125,
Equus caballus	ENSECAG00000022051	11 retrocopies	retro_ecab_1006, retro_ecab_1067, retro_ecab_1086, retro_ecab_1125, retro_ecab_143, retro_ecab_191, retro_ecab_225, retro_ecab_333, retro_ecab_546, retro_ecab_854, retro_ecab_907,
Erinaceus europaeus	ENSEEUG00000011444	3 retrocopies	retro_eeur_427, retro_eeur_569, retro_eeur_677,
Echinops telfairi	ENSETEG00000013749	118 retrocopies	retro_etel_1011, retro_etel_1037, retro_etel_1070, retro_etel_1117, retro_etel_1132, retro_etel_1153, retro_etel_1171, retro_etel_1183, retro_etel_1214, retro_etel_1215, retro_etel_1247, retro_etel_1249, retro_etel_1255, retro_etel_1257, retro_etel_1258, retro_etel_1266, retro_etel_127, retro_etel_1320, retro_etel_1349, retro_etel_1352, retro_etel_1381, retro_etel_1386, retro_etel_1389, retro_etel_1408, retro_etel_1419, retro_etel_1422, retro_etel_1431, retro_etel_1437, retro_etel_1470, retro_etel_1473, retro_etel_1490, retro_etel_150, retro_etel_1511, retro_etel_1538, retro_etel_1550, retro_etel_1563, retro_etel_1570, retro_etel_1588, retro_etel_1601, retro_etel_1608, retro_etel_1620, retro_etel_163, retro_etel_1635, retro_etel_1641, retro_etel_1674, retro_etel_1679, retro_etel_1702, retro_etel_1738, retro_etel_1746, retro_etel_1759, retro_etel_1769, retro_etel_1776, retro_etel_1780, retro_etel_180, retro_etel_184, retro_etel_1840, retro_etel_1869, retro_etel_1895, retro_etel_1897, retro_etel_1949, retro_etel_1970, retro_etel_1976, retro_etel_1982, retro_etel_1989, retro_etel_2033, retro_etel_2076, retro_etel_209, retro_etel_212, retro_etel_213, retro_etel_2152, retro_etel_2161, retro_etel_2173, retro_etel_2198, retro_etel_2202, retro_etel_2210, retro_etel_243, retro_etel_290, retro_etel_330, retro_etel_339, retro_etel_340, retro_etel_365, retro_etel_397, retro_etel_432, retro_etel_440, retro_etel_463, retro_etel_489, retro_etel_495, retro_etel_504, retro_etel_536, retro_etel_557, retro_etel_586, retro_etel_589, retro_etel_600, retro_etel_611, retro_etel_618, retro_etel_621, retro_etel_624, retro_etel_649, retro_etel_653, retro_etel_69, retro_etel_770, retro_etel_780, retro_etel_790, retro_etel_792, retro_etel_798, retro_etel_802, retro_etel_810, retro_etel_874, retro_etel_895, retro_etel_899, retro_etel_90, retro_etel_906, retro_etel_931, retro_etel_934, retro_etel_935, retro_etel_968, retro_etel_969, retro_etel_987,
Felis catus	ENSFCAG00000006874	17 retrocopies	retro_fcat_1038, retro_fcat_1147, retro_fcat_1166, retro_fcat_1337, retro_fcat_1781, retro_fcat_1858, retro_fcat_1870, retro_fcat_1881, retro_fcat_2005, retro_fcat_2007, retro_fcat_411, retro_fcat_582, retro_fcat_719, retro_fcat_726, retro_fcat_731, retro_fcat_806, retro_fcat_847,
Loxodonta africana	ENSLAFG00000002780	3 retrocopies	retro_lafr_421, retro_lafr_46, retro_lafr_954,
Macropus eugenii	ENSMEUG00000015273	67 retrocopies	retro_meug_1057, retro_meug_1066, retro_meug_1080, retro_meug_1086, retro_meug_1197, retro_meug_1206, retro_meug_1249, retro_meug_1286, retro_meug_1310, retro_meug_1319, retro_meug_1352, retro_meug_1369, retro_meug_1377, retro_meug_1390, retro_meug_1423, retro_meug_1429, retro_meug_1542, retro_meug_1595, retro_meug_1646, retro_meug_165, retro_meug_1686, retro_meug_1759, retro_meug_1776, retro_meug_180, retro_meug_185, retro_meug_1870, retro_meug_1884, retro_meug_1889, retro_meug_2039, retro_meug_2046, retro_meug_2047, retro_meug_2085, retro_meug_2088, retro_meug_2113, retro_meug_2141, retro_meug_2178, retro_meug_239, retro_meug_374, retro_meug_382, retro_meug_383, retro_meug_393, retro_meug_416, retro_meug_421, retro_meug_450, retro_meug_453, retro_meug_460, retro_meug_50, retro_meug_595, retro_meug_602, retro_meug_630, retro_meug_643, retro_meug_661, retro_meug_678, retro_meug_680, retro_meug_70, retro_meug_720, retro_meug_731, retro_meug_739, retro_meug_758, retro_meug_761, retro_meug_777, retro_meug_79, retro_meug_834, retro_meug_844, retro_meug_866, retro_meug_879, retro_meug_890,
Microcebus murinus	ENSMICG00000006546	16 retrocopies	retro_mmur_1049, retro_mmur_1064, retro_mmur_1084, retro_mmur_1255, retro_mmur_1431, retro_mmur_1446, retro_mmur_145, retro_mmur_1463, retro_mmur_1553, retro_mmur_1567, retro_mmur_329, retro_mmur_429, retro_mmur_464, retro_mmur_670, retro_mmur_780, retro_mmur_873,
Myotis lucifugus	ENSMLUG00000014320	18 retrocopies	retro_mluc_1073, retro_mluc_1102, retro_mluc_1352, retro_mluc_1487, retro_mluc_1577, retro_mluc_1772, retro_mluc_1886, retro_mluc_2039, retro_mluc_2222, retro_mluc_2292, retro_mluc_2518, retro_mluc_569, retro_mluc_584, retro_mluc_657, retro_mluc_848, retro_mluc_898, retro_mluc_957, retro_mluc_976,
Monodelphis domestica	ENSMODG00000018066	41 retrocopies	retro_mdom_1060, retro_mdom_1089, retro_mdom_1104, retro_mdom_1137, retro_mdom_1161, retro_mdom_1184, retro_mdom_1233, retro_mdom_1241, retro_mdom_1317, retro_mdom_1358, retro_mdom_1384, retro_mdom_142, retro_mdom_1494, retro_mdom_1544, retro_mdom_1610, retro_mdom_1631, retro_mdom_1661, retro_mdom_1691, retro_mdom_1698, retro_mdom_1743, retro_mdom_1810, retro_mdom_1908, retro_mdom_2022, retro_mdom_275, retro_mdom_310, retro_mdom_354, retro_mdom_382, retro_mdom_497, retro_mdom_531, retro_mdom_552, retro_mdom_584, retro_mdom_590, retro_mdom_591, retro_mdom_628, retro_mdom_678, retro_mdom_766, retro_mdom_816, retro_mdom_828, retro_mdom_832, retro_mdom_835, retro_mdom_863,
Mustela putorius furo	ENSMPUG00000016891	28 retrocopies	retro_mputfur_1027, retro_mputfur_105, retro_mputfur_1051, retro_mputfur_1091, retro_mputfur_1152, retro_mputfur_1197, retro_mputfur_1198, retro_mputfur_1229, retro_mputfur_1278, retro_mputfur_1422, retro_mputfur_1461, retro_mputfur_1483, retro_mputfur_1630, retro_mputfur_244, retro_mputfur_300, retro_mputfur_31, retro_mputfur_317, retro_mputfur_380, retro_mputfur_481, retro_mputfur_513, retro_mputfur_555, retro_mputfur_612, retro_mputfur_717, retro_mputfur_789, retro_mputfur_817, retro_mputfur_842, retro_mputfur_88, retro_mputfur_925,
Mus musculus	ENSMUSG00000057666	109 retrocopies	retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Ornithorhynchus anatinus	ENSOANG00000004492	1 retrocopy	retro_oana_81,
Ochotona princeps	ENSOPRG00000012514	10 retrocopies	retro_opri_1113, retro_opri_128, retro_opri_147, retro_opri_371, retro_opri_414, retro_opri_420, retro_opri_47, retro_opri_557, retro_opri_832, retro_opri_988,
Procavia capensis	ENSPCAG00000006928	9 retrocopies	retro_pcap_199, retro_pcap_210, retro_pcap_267, retro_pcap_365, retro_pcap_369, retro_pcap_440, retro_pcap_446, retro_pcap_68, retro_pcap_93,
Pteropus vampyrus	ENSPVAG00000012570	14 retrocopies	retro_pvam_1250, retro_pvam_1292, retro_pvam_1303, retro_pvam_160, retro_pvam_199, retro_pvam_280, retro_pvam_284, retro_pvam_31, retro_pvam_387, retro_pvam_451, retro_pvam_581, retro_pvam_680, retro_pvam_845, retro_pvam_976,
Rattus norvegicus	ENSRNOG00000018630	4 retrocopies	retro_rnor_107, retro_rnor_335, retro_rnor_407, retro_rnor_91,
Rattus norvegicus	ENSRNOG00000030638	2 retrocopies	retro_rnor_1571, retro_rnor_1777,
Sarcophilus harrisii	ENSSHAG00000014953	4 retrocopies	retro_shar_178, retro_shar_330, retro_shar_40, retro_shar_533,
Sus scrofa	ENSSSCG00000000694	2 retrocopies	retro_sscr_1213, retro_sscr_572,
Ictidomys tridecemlineatus	ENSSTOG00000007538	9 retrocopies	retro_itri_1069, retro_itri_1308, retro_itri_1472, retro_itri_1679, retro_itri_1802, retro_itri_419, retro_itri_540, retro_itri_752, retro_itri_979,
Tursiops truncatus	ENSTTRG00000016094	2 retrocopies	retro_ttru_654, retro_ttru_707,
Xenopus tropicalis	ENSXETG00000033975	1 retrocopy	retro_xtro_70,