RetrogeneDB ID:

retro_itri_1288

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393428.1:4103975..4104639(-)
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:ENSSTOG00000015587
Aliases:None
Description:keratin 18 [Source:HGNC Symbol;Acc:6430]


Retrocopy-Parental alignment summary:






>retro_itri_1288
CAGGAGGAACTGCTCTTCATGAAGAACCAAGAGGAGGAATTCAAAGGCCTTCAAGCCCAGATTGCCAGCTCTGGGTTGAC
AGTGCAGATAGATGCCCCCAAATCTTAGGATTTCAGCAAGATCCTGGCAGACATCTGGGCCCAGTATGATGAACTAGCTC
AGAAAAACCGAGAGGGACTGGACAAGTACTGATCCCAGCAAATTGAAGAGAGCACAGAGTGGGCACCTTGCAGCCAGCTG
AGATGGAAGCTGCTGAGATGATACTCACAGAACTGAGATGCACAGTCCAGTCCATGGAGATTAACCTGGACTTGATGAGA
AATCTGAAGATCAGCTTTGAGAACAGTCTGAAGGAAGTGGAGGCCTGCTACACCATGCAGATGGAGAAGTTCCATGGGGT
CCTGTTGCACCTGGAATCAAAGCTGTACAGACCCAGGCAGAGAGGCAGCTCCAGGCCTAGGACTATAAGGCCCTGCTGAA
CATCAGGGCCAAACTGGAGGCTGAGCTTGCCACTTACCGCCACCTGTTGGAAGACGGAGAGGACTTCAATCTCAATGATG
CCCTGGACAGCAGCAACTCAGTGCAAACCATCCAAAAGACCACCACCAGCAGGATTGTGGATGGCAAAATAGTGTCTGAG
ACCAATGACACCCAAGTGCTGAGG

ORF - retro_itri_1288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.33 %
Parental protein coverage: 53.22 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKEELLFMKKNHEEEVKGLQAQIANSGLTVEVDAPKSQDLSKIMADIRAQYDELAQKNREELDKYWSQQIE
.EELLFMK.N.EEE.KGLQAQIA.SGLTV..DAPKS.D.SKI.ADI.AQYDELAQKNRE.LDKY.SQQIE
RetrocopyQEELLFMK-NQEEEFKGLQAQIASSGLTVQIDAPKS*DFSKILADIWAQYDELAQKNREGLDKY*SQQIE
ParentalESTT-VVTSQTAEIGAAEITLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYSMQMEQLNGVLLHL
EST..V.T.Q.AE..AAE..LTELR.TVQS.EI.LD.MRNLK.S.ENSL.EVEA.Y.MQME...GVLLHL
RetrocopyESTE<VGTLQPAEMEAAEMILTELRCTVQSMEINLDLMRNLKISFENSLKEVEACYTMQMEKFHGVLLHL
ParentalESEL-AQTRAEGQRQTQDYEALLNIKVKLEAEIATYRRLLEDGEDFSLNDALDSSNSMQTIQKTTTRRIV
ES.L..QT.AE.Q.Q..DY.ALLNI..KLEAE.ATYR.LLEDGEDF.LNDALDSSNS.QTIQKTTT.RIV
RetrocopyESKL<VQTQAERQLQA*DYKALLNIRAKLEAELATYRHLLEDGEDFNLNDALDSSNSVQTIQKTTTSRIV
ParentalDGKIVSETNDTKVLR
DGKIVSETNDT.VLR
RetrocopyDGKIVSETNDTQVLR

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1288 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1288 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 17 parental genes, and 174 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,
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,
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,
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 ENSSTOG00000015587 3 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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