RetrogeneDB ID: retro_cjac_4001

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286972.1:2449..3092(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003706
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRT18
• Ensembl ID: ENSCJAG00000018165
• Aliases: None
• Description: None

Sequence

>retro_cjac_4001
CGTCTGCGAAGCCTGAGTCATGTCCTCTCACTCTCCTCCCCAGGCAGCATGAGCTTCACCACTCGCTCCTCCTTTTCCAC
CAACTACCGGTCCGTGGGCTCCGTCCGGGTGCCCAGCTATGGCGCCCGGCCGGTCAGCAGCGCGGCCAGCGTCTATGCAG
GCGCCGGGGGCTCTGGTTCCCGCGTCTCCGTGACGCGCTCCACCAGCGTCCGGAGCGGCATGGGGGTCAGGGGCCTGGCC
GTGGGGATGGCCAGGGGTCTGGCAGGAATGGGAGGCATCCAGAACGAGAAGGAGACCATGCAAATCCTGAACGACCGCCT
GGCCTCCTACCTGGACAGAGTCAGGAGCCTGGAGACCGAGAACCGGAAGCTGGAGAGCAAAATCCGGGAGCACCTGGAGA
AGAAGGGACCCCAGGTCAGAGACTGGGGCCATTACTTCAAGACCATCGAGGACCTGAGGGCTCAGATCTTCTCAAATACT
GTGAACAATGCCCGCATCGTTCTGCAGATTGACAATGCTCCTCTTGCTGCTGATGGCTTTAGCGTCAAGTATGAGACAGA
GCTGGCCATGCGCCAGTCTATGGAGAGCGACATCCATGGTCTCCCGCAATGTCATCGATGACACCAATGTCACTCGGCTG
CAG

Alignment

ORF - retro_cjac_4001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.88 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLRSLSPVLSLSSPGSMSFTTRSSFSTNYRSVGSVRVPSYGARPVSSAASVYAGAGGSGSRVSVTRSTSV
          RLRSLS.VLSLSSPGSMSFTTRSSFSTNYRSVGSVRVPSYGARPVSSAASVYAGAGGSGSRVSVTRSTSV
Retrocopy RLRSLSHVLSLSSPGSMSFTTRSSFSTNYRSVGSVRVPSYGARPVSSAASVYAGAGGSGSRVSVTRSTSV

Parental  RSGMGVGGLAAGMARGLAGMGGIQNEKETMQILNDRLASYLDRVRSLETENRKLEIKIREHLEKKGPQVR
          RSGMGV.GLA.GMARGLAGMGGIQNEKETMQILNDRLASYLDRVRSLETENRKLE.KIREHLEKKGPQVR
Retrocopy RSGMGVRGLAVGMARGLAGMGGIQNEKETMQILNDRLASYLDRVRSLETENRKLESKIREHLEKKGPQVR

Parental  DWGHYFKTIEDLRAQIFSNTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVESDIHGL-RKVIDDTN
          DWGHYFKTIEDLRAQIFSNTV.NARIVLQIDNA.LAAD.F.VKYETELAMRQS.ESDIHGL.R.VIDDTN
Retrocopy DWGHYFKTIEDLRAQIFSNTVNNARIVLQIDNAPLAADGFSVKYETELAMRQSMESDIHGL>RNVIDDTN

Parental  VTRLQ
          VTRLQ
Retrocopy VTRLQ

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	101.02 RPM
SRP051959_heart	0.04 RPM	1.18 RPM
SRP051959_kidney	0.00 RPM	16.24 RPM
SRP051959_liver	0.00 RPM	37.95 RPM
SRP051959_lung	0.02 RPM	14.41 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.04 RPM
SRP051959_spleen	0.04 RPM	1.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4001 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4001 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 338 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011981	2 retrocopies	retro_amel_1366, retro_amel_1896,
Canis familiaris	ENSCAFG00000007154	10 retrocopies	retro_cfam_1045, retro_cfam_1205, retro_cfam_1393, retro_cfam_1413, retro_cfam_1672, retro_cfam_2124, retro_cfam_2170, retro_cfam_611, retro_cfam_698, retro_cfam_883,
Callithrix jacchus	ENSCJAG00000018165	29 retrocopies	retro_cjac_1323, retro_cjac_1457, retro_cjac_1638, retro_cjac_1847, retro_cjac_1857, retro_cjac_1885, retro_cjac_1915, retro_cjac_2074, retro_cjac_2087, retro_cjac_2179, retro_cjac_2232, retro_cjac_2252, retro_cjac_2349, retro_cjac_2614, retro_cjac_2689, retro_cjac_2842, retro_cjac_3036, retro_cjac_3145, retro_cjac_3995, retro_cjac_4001 , retro_cjac_4065, retro_cjac_4120, retro_cjac_4138, retro_cjac_4158, retro_cjac_4200, retro_cjac_626, retro_cjac_794, retro_cjac_878, retro_cjac_955,
Cavia porcellus	ENSCPOG00000002618	1 retrocopy	retro_cpor_111,
Echinops telfairi	ENSETEG00000008130	1 retrocopy	retro_etel_1177,
Homo sapiens	ENSG00000111057	60 retrocopies	retro_hsap_1129, retro_hsap_1153, retro_hsap_1226, retro_hsap_1404, retro_hsap_1650, retro_hsap_1774, retro_hsap_1818, retro_hsap_1907, retro_hsap_1981, retro_hsap_2115, retro_hsap_2174, retro_hsap_2242, retro_hsap_2276, retro_hsap_2353, retro_hsap_2361, retro_hsap_2433, retro_hsap_2461, retro_hsap_2517, retro_hsap_2543, retro_hsap_2565, retro_hsap_2571, retro_hsap_2626, retro_hsap_2752, retro_hsap_2848, retro_hsap_2869, retro_hsap_2877, retro_hsap_2915, retro_hsap_2922, retro_hsap_2973, retro_hsap_306, retro_hsap_3098, retro_hsap_3161, retro_hsap_3203, retro_hsap_3227, retro_hsap_3236, retro_hsap_327, retro_hsap_3400, retro_hsap_3452, retro_hsap_3492, retro_hsap_3498, retro_hsap_3567, retro_hsap_3645, retro_hsap_3651, retro_hsap_3948, retro_hsap_4145, retro_hsap_4201, retro_hsap_4215, retro_hsap_4238, retro_hsap_4277, retro_hsap_434, retro_hsap_4681, retro_hsap_4727, retro_hsap_4736, retro_hsap_4756, retro_hsap_483, retro_hsap_4915, retro_hsap_4919, retro_hsap_832, retro_hsap_846, retro_hsap_866,
Gorilla gorilla	ENSGGOG00000010157	28 retrocopies	retro_ggor_1246, retro_ggor_1513, retro_ggor_1606, retro_ggor_1641, retro_ggor_1692, retro_ggor_1725, retro_ggor_1838, retro_ggor_1914, retro_ggor_2024, retro_ggor_2062, retro_ggor_2128, retro_ggor_2201, retro_ggor_2301, retro_ggor_2360, retro_ggor_2407, retro_ggor_2462, retro_ggor_2468, retro_ggor_2653, retro_ggor_2815, retro_ggor_2823, retro_ggor_2903, retro_ggor_2941, retro_ggor_3069, retro_ggor_455, retro_ggor_685, retro_ggor_692, retro_ggor_881, retro_ggor_898,
Macropus eugenii	ENSMEUG00000012262	14 retrocopies	retro_meug_1392, retro_meug_1430, retro_meug_1461, retro_meug_1467, retro_meug_1631, retro_meug_1651, retro_meug_1810, retro_meug_2024, retro_meug_2082, retro_meug_2132, retro_meug_323, retro_meug_425, retro_meug_575, retro_meug_771,
Myotis lucifugus	ENSMLUG00000022439	8 retrocopies	retro_mluc_1247, retro_mluc_1248, retro_mluc_1758, retro_mluc_1876, retro_mluc_2179, retro_mluc_2234, retro_mluc_2420, retro_mluc_549,
Macaca mulatta	ENSMMUG00000031911	4 retrocopies	retro_mmul_1601, retro_mmul_279, retro_mmul_91, retro_mmul_948,
Mustela putorius furo	ENSMPUG00000006369	2 retrocopies	retro_mputfur_1591, retro_mputfur_171,
Mus musculus	ENSMUSG00000023043	2 retrocopies	retro_mmus_1152, retro_mmus_479,
Nomascus leucogenys	ENSNLEG00000017732	45 retrocopies	retro_nleu_1234, retro_nleu_1238, retro_nleu_1252, retro_nleu_1346, retro_nleu_1397, retro_nleu_1421, retro_nleu_1454, retro_nleu_1500, retro_nleu_1547, retro_nleu_1563, retro_nleu_1683, retro_nleu_1801, retro_nleu_1872, retro_nleu_1953, retro_nleu_1960, retro_nleu_2023, retro_nleu_2173, retro_nleu_2293, retro_nleu_2308, retro_nleu_2310, retro_nleu_241, retro_nleu_2494, retro_nleu_2551, retro_nleu_264, retro_nleu_2721, retro_nleu_2807, retro_nleu_2901, retro_nleu_2935, retro_nleu_3008, retro_nleu_3061, retro_nleu_353, retro_nleu_357, retro_nleu_364, retro_nleu_415, retro_nleu_427, retro_nleu_505, retro_nleu_512, retro_nleu_613, retro_nleu_639, retro_nleu_699, retro_nleu_785, retro_nleu_791, retro_nleu_824, retro_nleu_832, retro_nleu_924,
Oryctolagus cuniculus	ENSOCUG00000027691	1 retrocopy	retro_ocun_58,
Pongo abelii	ENSPPYG00000004563	60 retrocopies	retro_pabe_1020, retro_pabe_1130, retro_pabe_1161, retro_pabe_1399, retro_pabe_1486, retro_pabe_1487, retro_pabe_1522, retro_pabe_1552, retro_pabe_1628, retro_pabe_1751, retro_pabe_1809, retro_pabe_1852, retro_pabe_1870, retro_pabe_1890, retro_pabe_1893, retro_pabe_1942, retro_pabe_1966, retro_pabe_1991, retro_pabe_2060, retro_pabe_2128, retro_pabe_2134, retro_pabe_2145, retro_pabe_2174, retro_pabe_2278, retro_pabe_2335, retro_pabe_2359, retro_pabe_2376, retro_pabe_2381, retro_pabe_2427, retro_pabe_2431, retro_pabe_2465, retro_pabe_250, retro_pabe_2564, retro_pabe_2628, retro_pabe_2655, retro_pabe_2675, retro_pabe_2682, retro_pabe_2797, retro_pabe_2822, retro_pabe_2855, retro_pabe_2884, retro_pabe_2890, retro_pabe_290, retro_pabe_2992, retro_pabe_2998, retro_pabe_3252, retro_pabe_3400, retro_pabe_3401, retro_pabe_3437, retro_pabe_3448, retro_pabe_3464, retro_pabe_3488, retro_pabe_362, retro_pabe_3636, retro_pabe_3681, retro_pabe_3702, retro_pabe_374, retro_pabe_3824, retro_pabe_934, retro_pabe_956,
Pan troglodytes	ENSPTRG00000004996	58 retrocopies	retro_ptro_1121, retro_ptro_1172, retro_ptro_1188, retro_ptro_1251, retro_ptro_1321, retro_ptro_1405, retro_ptro_1420, retro_ptro_1462, retro_ptro_1482, retro_ptro_1496, retro_ptro_1501, retro_ptro_1586, retro_ptro_1610, retro_ptro_1659, retro_ptro_1721, retro_ptro_1725, retro_ptro_1737, retro_ptro_1772, retro_ptro_1860, retro_ptro_193, retro_ptro_1941, retro_ptro_1946, retro_ptro_1971, retro_ptro_1977, retro_ptro_2010, retro_ptro_2094, retro_ptro_2188, retro_ptro_2244, retro_ptro_2277, retro_ptro_2310, retro_ptro_2341, retro_ptro_2366, retro_ptro_2371, retro_ptro_247, retro_ptro_2470, retro_ptro_2476, retro_ptro_264, retro_ptro_2679, retro_ptro_2817, retro_ptro_2852, retro_ptro_2861, retro_ptro_2881, retro_ptro_2900, retro_ptro_2956, retro_ptro_3079, retro_ptro_3110, retro_ptro_3144, retro_ptro_3150, retro_ptro_3169, retro_ptro_3277, retro_ptro_364, retro_ptro_581, retro_ptro_587, retro_ptro_600, retro_ptro_677, retro_ptro_787, retro_ptro_841, retro_ptro_962,
Pteropus vampyrus	ENSPVAG00000009361	2 retrocopies	retro_pvam_140, retro_pvam_557,
Rattus norvegicus	ENSRNOG00000047393	3 retrocopies	retro_rnor_1513, retro_rnor_2529, retro_rnor_581,
Ictidomys tridecemlineatus	ENSSTOG00000015587	3 retrocopies	retro_itri_1288, retro_itri_1517, retro_itri_1609,
Tursiops truncatus	ENSTTRG00000012977	2 retrocopies	retro_ttru_1273, retro_ttru_463,
Vicugna pacos	ENSVPAG00000007421	3 retrocopies	retro_vpac_287, retro_vpac_390, retro_vpac_53,