RetrogeneDB ID:

retro_hsap_3651

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:116778488..116779768(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218153
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT18
Ensembl ID:ENSG00000111057
Aliases:KRT18, CYK18, K18
Description:keratin 18 [Source:HGNC Symbol;Acc:6430]


Retrocopy-Parental alignment summary:






>retro_hsap_3651
ATGAGCTTCACCACTTGCTCCACCTTCTCCACCAACTACCATTCCCTGGGCTCTGTCCAGACACCCAGCTTCATCGCCCA
GCTGGTCAGCAGTGCAGCCAGTGTCTATGCAGGCACCCAGGACTCTGGTTCCCGGATCTCTGTGTCCCGCTCCACCAGCT
TCTGGGGCGGCATGGGATCCGGGGGCCTGGCTGCAGGGATGGCCAGGGGTCTGGCAGGGATAGCAGGCATCCAGAATGAG
AAGGAGACCATGCAAAGCCTGAACGACTGTCTGGCCTCCTACCTGGACAGAGTGAGGAGCCTGGAGACCGAGAACTGGAA
GCTGGAGAGCAAAATCCGGGAGCACCTGGGGAAGAAGGGACCCCAGGCCAGAGACTGGAGCCATTACTTCATGACCATCA
GGACCTGAGGGCTCAGATCTTCACAAATACTGTGGACAATGCCCGCATCGTTCTGCAAATCAATGCCTGTTTTGCTGCTG
ATGACTTCAGTGTCAAGTATGAGACAGAGCTGCCCATGTGCCAGTCTGTGGAGAGCGACATCCATGGGGTCCACAAGGTC
ATTGATGACACCAATGTCACTCGGCTGCAGCTGGAGACAGAGATCGAGGCTCTCAAAAAGCAGCTGCTCTTCATGAAGAA
CCATGAAGAGGAAGTAAAGGCCTACAAGCCCAGACTGCCAGCTCTGGGCTGACCGTGGAGGTAGATGCCCCCAAATCTCA
GGACCTTGCCAAGATCATGGAAGACATCTGGGCCCAATATGACGAGCTGGCTCGGAAGAACTAAGAGGAGCTGGACAAGT
ACTGGTCTCAGCAGATTGAGGTGAGCACCACAGTGGCCACCACTCAGTCCACCGAGGTTGGAGCTGCTGAGATGACGCTC
ACAGAGCTGAGATGTACAATCCATTCCTTGGAGATCGACCTGGACTCCATGAGAAATCTGAAGGCCGCTTGGAAAGCAGC
CTGAGGGAGGTGGAGGCCTGCTATGCCCTGCAGATGGAACAGCTCAATGGGATCCTGCTGCACCTGGAGTCAGAGCTGGC
ACAGACCCAGGCAGAGGGACAGCACTAGGCCCAGCAGTACGAGGCCCTGCTGGACATCAAAGTCAAGCTGGAGACTCAGA
TTGCCACCTACCAATGCCTGCTGGAAGATGGCGAGGACTTCAATCTTGGTGATGCCCTGGACAACAGCAACTCCATGCAA
ACCATCCAAAAGACACCACCCGCCCAATAGTGGATGGCGAAGTGGTGTCTGAGACCAATGACACCAAAGTTCTGAGACAT

ORF - retro_hsap_3651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMSFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGG
MSFTT.STFSTNY.SLGSVQ.PS..A..VSSAASVYAG...SGSRISVSRSTSF.GGMGSGGLA.G.A.G
RetrocopyMSFTTCSTFSTNYHSLGSVQTPSFIAQLVSSAASVYAGTQDSGSRISVSRSTSFWGGMGSGGLAAGMARG
ParentalLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKII-EDLRAQ
LAG..GIQNEKETMQSLND.LASYLDRVRSLETEN..LESKIREHL.KKGPQ.RDWSHYF..I..DLRAQ
RetrocopyLAGIAGIQNEKETMQSLNDCLASYLDRVRSLETENWKLESKIREHLGKKGPQARDWSHYFMTI<QDLRAQ
ParentalIFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNITRLQLETEIEALKEE
IF.NTVDNARIVLQI.NA..AADDF.VKYETEL.M.QSVE.DIHG..KVIDDTN.TRLQLETEIEALK..
RetrocopyIFTNTVDNARIVLQI-NACFAADDFSVKYETELPMCQSVESDIHGVHKVIDDTNVTRLQLETEIEALKKQ
ParentalLLFMKKNHEEEV-KGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEES
LLFM.KNHEEEV.KGLQAQ.ASSGLTVEVDAPKSQDLAKIM.DI.AQYDELARKN.EELDKYWSQQIE.S
RetrocopyLLFM-KNHEEEV<KGLQAQTASSGLTVEVDAPKSQDLAKIMEDIWAQYDELARKN*EELDKYWSQQIEVS
ParentalTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKAS-LENSLREVEARYALQMEQLNGILLHLES
TTV.TTQS.EVGAAE.TLTELR.T..SLEIDLDSMRNLKA..LE.SLREVEA.YALQMEQLNGILLHLES
RetrocopyTTVATTQSTEVGAAEMTLTELRCTIHSLEIDLDSMRNLKAA<LESSLREVEACYALQMEQLNGILLHLES
ParentalELAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKT-TTRRIVDG
ELAQT.AEGQ..AQ.YEALL.IKVKLE..IATY..LLEDGEDFNLGDALD.SNSMQTIQKT.TTR.IVDG
RetrocopyELAQTQAEGQH*AQQYEALLDIKVKLETQIATYQCLLEDGEDFNLGDALDNSNSMQTIQKT<TTRPIVDG
ParentalKVVSETNDTKVLRH
.VVSETNDTKVLRH
RetrocopyEVVSETNDTKVLRH

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .02 RPM 8 .95 RPM
bodymap2_adrenal 0 .04 RPM 10 .71 RPM
bodymap2_brain 0 .00 RPM 1 .24 RPM
bodymap2_breast 0 .00 RPM 37 .70 RPM
bodymap2_colon 0 .00 RPM 68 .51 RPM
bodymap2_heart 0 .00 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 .00 RPM 13 .65 RPM
bodymap2_ovary 0 .10 RPM 43 .55 RPM
bodymap2_prostate 0 .00 RPM 60 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .78 RPM
bodymap2_testis 0 .02 RPM 31 .33 RPM
bodymap2_thyroid 0 .00 RPM 148 .47 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3651 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_3651 retrocopy
EST ID Start End Identity Match Mis-match Score
DA225742 116778550 116779084 100 534 0 534

TSS - click to see more details

No TSS is located nearby retro_hsap_3651 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3651 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3651 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2476
Gorilla gorilla retro_ggor_2468
Pongo abelii retro_pabe_2998
Parental genes homology:
Parental genes homology involve 15 parental genes, and 325 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119812 retrocopies
retro_amel_1366, retro_amel_1896,
Canis familiaris ENSCAFG0000000715410 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 ENSCJAG0000001816529 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 ENSCPOG000000026181 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 ENSGGOG0000001015728 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 ENSMEUG0000001226214 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 ENSMLUG000000224398 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 ENSMMUG000000319114 retrocopies
retro_mmul_1601, retro_mmul_279, retro_mmul_91, retro_mmul_948,
Mustela putorius furoENSMPUG000000063692 retrocopies
retro_mputfur_1591, retro_mputfur_171,
Nomascus leucogenys ENSNLEG0000001773245 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 ENSOCUG000000276911 retrocopy
retro_ocun_58,
Pongo abelii ENSPPYG0000000456360 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 ENSPTRG0000000499658 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 ENSRNOG000000473933 retrocopies
retro_rnor_1513, retro_rnor_2529, retro_rnor_581,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 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 .00 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 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

Indel association:

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





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