RetrogeneDB ID: retro_hsap_1129

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:65812504..65813769(-)
• Located in intron of: ENSG00000174099

Retrocopy information

• Ensembl ID: ENSG00000215208
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRT18
• Ensembl ID: ENSG00000111057
• Aliases: KRT18, CYK18, K18
• Description: keratin 18 [Source:HGNC Symbol;Acc:6430]

Sequence

>retro_hsap_1129
ACTACCTACCCATCCCTGGGCTCCATCCAGGTGCCCAGCTATGGCACCTGGCTGGTCAGCAGCACAACCAACGTCTATGC
AGGCACTGGGGGCTCTGGTTCCCGGATCTCCATGTCCTGCTCCACCAGCTTCCGGGGCTGCTTGGGGTCCAGGGGCCTGG
CCGGAGGGATGGCTAGGGGTCTGGCAGGAATGGGAGGCATCCAGAATGAGAAGGAGACCATGCAAAGCCTGAAGACCGCC
TGGCCTACTACCTGGACAGAGTGAGGAGCCCAGAGACCAAGAACTGGAAGGTGGAGAGTAAAATCTGGGAGCACCTGGAG
AAGACAGGACCCCAGGTCAGAGACTGGGTCCATTATTTCAAGACCATCGAGGACCTGAGGGCTCATATCTTCACAAATAC
TGTGGACAATGTCCACATTGTTCTGCAGATCGACAATGCCCATCTTGCTGCTGATGCCTTTAGAGTCAAGTATGACACAG
AGCTGGCCATGCGCCAGTCTGTGGAGAGCGACATCTATGGGCTCTGCAAGGTCATTGATGACACCAGTGTCACTCAGCTG
CAGCTGAAGACAGAGATCGAGACTCTCAAGGAGGAGCTGCTCTTAATGAAGAAGAACCATGAAGAGGAAGTAAAAGGCCT
ACAAGCCCAGATTGTCAGCTCTGGTTTGATCTTGGAGGTAGATGCCCCCAAATCTCAGGACCTTGCCAAGATCATGGCAG
ACATCTGGGCCCAATATGACGAGCTGGCTCGGAAGAACTGAGAAGGGCTGGACAAATACTGGTCTCAGCAGATTAAGGAG
AGTACCACAGTGGTCACCATGCAGTTGGCCAAGGTTGGAGCTGTTGAGATGATGCTCTCAACAGATGAGCTGTAACATAC
AGCCCAGTCCTCGGAGACTGACCTGGACTCCATGAGAAATCTGAAGGCCAGCTTGGAGAACAGCCTGAGGGAGGTGGAGG
CCTGGTACACCCTGCAGATGGAGCAACTCAACGGGATCCTGCTGCACCTGGAGTTGGAGTTGACACAGACCCGGGCAGAG
GGGCAGCACCAGGCCCAGGAGTAGGAGGCCCTGCTGAACATTAAGGTCAAGCTGGAGGCTGAGATTGCCATGTATCACTG
CCTGCCAGAAGACATCAAGGACTTCAGTCTTGGTGATGCCTTGGACAGCAGTAACTCCATGCAAACCATCCAAAAGACCA
CCACCCGCCAGACAGTGGATGGCAAAGTGGTGTCTGAGATCAATGACACCAAAGTTCTGAGACAT

Alignment

ORF - retro_hsap_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.14 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGGLAGMGGIQNE
          T.Y.SLGS.Q.PSYG...VSS...VYAG.GGSGSRIS.S.STSFRG..GS.GLA.G.A.GLAGMGGIQNE
Retrocopy TTYPSLGSIQVPSYGTWLVSSTTNVYAGTGGSGSRISMSCSTSFRGCLGSRGLAGGMARGLAGMGGIQNE

Parental  KETMQSLN-DRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQIFANTVDNAR
          KETMQSL..DRLA.YLDRVRS.ET.N...ESKI.EHLEK.GPQVRDW.HYFK.IEDLRA.IF.NTVDN..
Retrocopy KETMQSLK<DRLAYYLDRVRSPETKNWKVESKIWEHLEKTGPQVRDWVHYFKTIEDLRAHIFTNTVDNVH

Parental  IVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNITRLQLETEIEALKEELLFMKKNHEE
          IVLQIDNA.LAAD.FRVKY.TELAMRQSVE.DI.GL.KVIDDT..T.LQL.TEIE.LKEELL.MKKNHEE
Retrocopy IVLQIDNAHLAADAFRVKYDTELAMRQSVESDIYGLCKVIDDTSVTQLQLKTEIETLKEELLLMKKNHEE

Parental  EVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTTVVTTQSAEV
          EVKGLQAQI.SSGL..EVDAPKSQDLAKIMADI.AQYDELARKN.E.LDKYWSQQI.ESTTVVT.Q.A.V
Retrocopy EVKGLQAQIVSSGLILEVDAPKSQDLAKIMADIWAQYDELARKN*EGLDKYWSQQIKESTTVVTMQLAKV

Parental  GAAETTLT--ELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESELAQTRAEGQ
          GA.E..L...EL..T.QS.E.DLDSMRNLKASLENSLREVEA.Y.LQMEQLNGILLHLE.EL.QTRAEGQ
Retrocopy GAVEMMLSTDEL*HTAQSSETDLDSMRNLKASLENSLREVEAWYTLQMEQLNGILLHLELELTQTRAEGQ

Parental  RQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTTRRIVDGKVVSETNDTKV
          .QAQE.EALLNIKVKLEAEIA.Y..L.ED..DF.LGDALDSSNSMQTIQKTTTR..VDGKVVSE.NDTKV
Retrocopy HQAQE*EALLNIKVKLEAEIAMYHCLPEDIKDFSLGDALDSSNSMQTIQKTTTRQTVDGKVVSEINDTKV

Parental  LRH
          LRH
Retrocopy LRH

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
bodymap2_adipose	0.00 RPM	8.95 RPM
bodymap2_adrenal	0.08 RPM	10.71 RPM
bodymap2_brain	0.02 RPM	1.24 RPM
bodymap2_breast	0.06 RPM	37.70 RPM
bodymap2_colon	0.00 RPM	68.51 RPM
bodymap2_heart	0.17 RPM	3.58 RPM
bodymap2_kidney	0.00 RPM	132.71 RPM
bodymap2_liver	0.00 RPM	164.76 RPM
bodymap2_lung	0.00 RPM	169.64 RPM
bodymap2_lymph_node	0.09 RPM	13.65 RPM
bodymap2_ovary	0.00 RPM	43.55 RPM
bodymap2_prostate	0.00 RPM	60.43 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.78 RPM
bodymap2_testis	0.04 RPM	31.33 RPM
bodymap2_thyroid	0.00 RPM	148.47 RPM
bodymap2_white_blood_cells	0.00 RPM	1.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1129 was not detected

EST

No EST(s) were mapped for retro_hsap_1129 retrocopy.

TSS

No TSS is located nearby retro_hsap_1129 retrocopy 5' end.

Lab

retro_hsap_1129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1129 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_677
Gorilla gorilla	retro_ggor_881
Pongo abelii	retro_pabe_934

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 325 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,
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,
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,
Rattus norvegicus	ENSRNOG00000047393	3 retrocopies	retro_rnor_1513, retro_rnor_2529, retro_rnor_581,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).