RetrogeneDB ID:

retro_pabe_3400

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:30946517..30947799(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT18
Ensembl ID:ENSPPYG00000004563
Aliases:None
Description:keratin 18 [Source:HGNC Symbol;Acc:6430]


Retrocopy-Parental alignment summary:






>retro_pabe_3400
ATGAGCTTCACCACTTGCTCCACCTTCTCCACCAACTACGCGTCCCTGGGCTCTGTCCAGGTGCCCCGCTACGGCGCCCA
GCCGCAAGCAGCGTGGCCAGCGTCTATGCAGGCGAGGTCTCTGGTTTCTAGATCTCCGTGTCCTGCTCCACCAGCTTCCC
GGGCAGCATGGGGTCCAGGGGCCTGGCTGCGGGGATGGCCAGGGGTCTGGCAGGAATGGGAGGCATCCAGAACAAGAAGG
AGACCATGCACGACTTGAACGACGGTCTGGCCGCCTATCTGGACAGAGTGAGGAGCCTGGAGACCGACAACAGGAAGCTG
GAGAGCAAAATCCGGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAGAGACTAGAGCCATTACTTCAAGACCATTCAGGA
CCTGAGGGCTCAGATCTTTGCAAATACTGTAGACAATGTCCCCATCGTTCTGCAGATCGACAATGCCGGACTTGCTGCTG
ATTACTTTAGAGTCAAGTATGAGACAGAGCTGGTCTTGCGCCAGTCTATGGAGAACGACATCCATGGGCTCCTCAAGGTC
ATGGATGGCACCAATGTCACTCGGCTGCAGCTGGAGACACAGATCGAGGCTCTCAAGGAGGAGCTGCTCTTCATGAAGAA
GAACCATGAAGAGAAAGTGAAATGCCTGCAAGCCCAGATTGCAGCTCTGGGTCAACTGTGGAGGCAGACGCCCCCAAATC
TCAGGACCTTGCCAAGATCATGGCAGACATCCAGGCCAAATATGACCAGCTGGCTCGGAAGAACCGATAGGAGCTAGACA
AGTACTGGTCTCGGCTGATTGAGGAGAGCACCACAGTGCTCCCCACCCAGTCCGCTGAGGTTGGACCTGCTGAGGTGACA
CTCACGGAGCTGCTACGTATAGTCGAGTCCTTGTAGGTAGACCTGGACTCGATGAGAAATCTGAAGGCCAGCTTGGAGAA
CAGCCTGAGGGAGGTGGAAGCCCACTACACCCTGCAAATGGAACAGCTCAACGGCATCCTGCTGCACCAGGAGTCAGAGC
TGGCACAGACCTGGGGAGAGAGGTAGCGCTAGGCGCAAGAGTACGAGTCCCTGCTGAACATCAAGGTCAAGCTGGAGGCT
GAGATCGCCACCTACCACCGCCTGCTGGAAGATGGCGAGGACTTCAGTCTTGGTGACTGCCTGGACAGCAGCAACTCCAT
GCAAACCATACAAAACACCACCAGCCAGATAGTGAATGGCAAAGTGGTGTCTGAGACCAACACCACCAAAGTTCGGAGAC
AT

ORF - retro_pabe_3400 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.25 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMNFTTRSTFSTNYRSLGSVQAPSYGARP-VSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAG
M.FTT.STFSTNY.SLGSVQ.P.YGA.P..SS.ASVYAG...SG..ISVS.STSF.G.MGS.GLA.G.A.
RetrocopyMSFTTCSTFSTNYASLGSVQVPRYGAQP<ASSVASVYAGEV-SGF*ISVSCSTSFPGSMGSRGLAAGMAR
ParentalGLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQ
GLAGMGGIQN.KETM..LND.LA.YLDRVRSLET.NR.LESKIREHLEKKGPQVRD.SHYFK.I.DLRAQ
RetrocopyGLAGMGGIQNKKETMHDLNDGLAAYLDRVRSLETDNRKLESKIREHLEKKGPQVRD*SHYFKTIQDLRAQ
ParentalIFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNVTRLQLETEIEALKEE
IFANTVDN..IVLQIDNA.LAAD.FRVKYETEL..RQS.ENDIHGL.KV.D.TNVTRLQLET.IEALKEE
RetrocopyIFANTVDNVPIVLQIDNAGLAADYFRVKYETELVLRQSMENDIHGLLKVMDGTNVTRLQLETQIEALKEE
ParentalLLFMKKNHEEEVKGLQAQIA-SSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEES
LLFMKKNHEE.VK.LQAQIA.SSG.TVE.DAPKSQDLAKIMADI.A.YD.LARKNR.ELDKYWS..IEES
RetrocopyLLFMKKNHEEKVKCLQAQIA<SSGSTVEADAPKSQDLAKIMADIQAKYDQLARKNR*ELDKYWSRLIEES
ParentalTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESE
TTV..TQSAEVG.AE.TLTEL.R.V.SL..DLDSMRNLKASLENSLREVEA.Y.LQMEQLNGILLH.ESE
RetrocopyTTVLPTQSAEVGPAEVTLTELLRIVESL*VDLDSMRNLKASLENSLREVEAHYTLQMEQLNGILLHQESE
ParentalLAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTTRRIVDGKV
LAQT..E..R.AQEYE.LLNIKVKLEAEIATY.RLLEDGEDF.LGD.LDSSNSMQTIQ.TT...IV.GKV
RetrocopyLAQTWGER*R*AQEYESLLNIKVKLEAEIATYHRLLEDGEDFSLGDCLDSSNSMQTIQNTTS-QIVNGKV
ParentalVSETNDTKVLRH
VSETN.TKV.RH
RetrocopyVSETNTTKVRRH

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 2 .05 RPM
SRP007412_cerebellum 0 .00 RPM 6 .20 RPM
SRP007412_heart 0 .00 RPM 1 .29 RPM
SRP007412_kidney 0 .00 RPM 50 .15 RPM
SRP007412_liver 0 .00 RPM 198 .51 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3400 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3400 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3400 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4238
Pan troglodytes retro_ptro_2881
Parental genes homology:
Parental genes homology involve 21 parental genes, and 338 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,
Echinops telfairi ENSETEG000000081301 retrocopy
retro_etel_1177,
Homo sapiens ENSG0000011105760 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,
Mus musculus ENSMUSG000000230432 retrocopies
retro_mmus_1152, retro_mmus_479,
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 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 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,
Pteropus vampyrus ENSPVAG000000093612 retrocopies
retro_pvam_140, retro_pvam_557,
Rattus norvegicus ENSRNOG000000473933 retrocopies
retro_rnor_1513, retro_rnor_2529, retro_rnor_581,
Ictidomys tridecemlineatus ENSSTOG000000155873 retrocopies
retro_itri_1288, retro_itri_1517, retro_itri_1609,
Tursiops truncatus ENSTTRG000000129772 retrocopies
retro_ttru_1273, retro_ttru_463,
Vicugna pacos ENSVPAG000000074213 retrocopies
retro_vpac_287, retro_vpac_390, retro_vpac_53,


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