RetrogeneDB ID: retro_itri_1609

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393571.1:1007869..1008581(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KRT18
• Ensembl ID: ENSSTOG00000015587
• Aliases: None
• Description: keratin 18 [Source:HGNC Symbol;Acc:6430]

Sequence

>retro_itri_1609
TCTGCACAGAGTGACATTTGTGGCCCCTACAGAGTCATTAATGACATCAATATCACTCAGCTACAGCTGGAAACAGGAAT
AGAAGCTCTCAAGGAAGAGCTGCTTGTTCATGAAGAAGAACCATGAGGAGAAAGGCAGAAGCTCAGAACCCCAGTCTGAC
AGCTCCTGGTTGATTGTGAAGATTGACGTCCCCAAATATCATGACCTGGTAGACAGGATCATGGTAGACATCAGGGGTTC
AGTATGAGGAGCTGGCTCATAAGATCCAAGATAATTTGGACAAGTATTAGCCCCAGAAGATTGAAGAGAGCACCACAGTG
GTCAGGTCATCATCTTCCTAGATTGGAACTGCCAAGGTAATGTTCATAGAGCTAAGGAACACAGCCTTGGTCCTTGGAGA
TCAACCTGGACTGTGGGTAAAATCTAAAGGCCAGCTTGGAGCATAGGCTAAGAAACATGGAGGCCTACTACTCCATGAAG
ATGGAGCAGTTCAGTGGGTCCTGATGCACTGGAGCCAGAGCTTGCAAAAATCAGGTCTGAAGATTAAAAGGCCCAAGATT
AAAAGACCCTGTTGAGCATCAAAGTCAAGTTATAGGCTGAGATGACCACCTACTGCTGTATGCTGAAGGGCTAAAAAGAC
CTCAGTCTCAATAACACCCTGGATAGCAGCACCTCCATGGGAACCACCCAAAAGATCACCACCACCAATGTT

Alignment

ORF - retro_itri_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.32 %
• Parental protein coverage: 56.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SVESDIHGLRKVIDDTNITRLQLETEIETLKEELL-FMKKNHEEEVKGLQAQIANSGLTVEVDAPKSQDL
          S..SDI.G...VI.D.NIT.LQLET.IE.LKEELL.FMKKNHEE.......Q...S.L.V..D.PK..DL
Retrocopy SAQSDICGPYRVINDINITQLQLETGIEALKEELL>FMKKNHEEKGRSSEPQSDSSWLIVKIDVPKYHDL

Parental  -SKIMADIRA-QYDELAQKNREELDKYWSQQIEESTTVVTSQTAEIGAAEITLTELRRTV-QSLEIDLDS
          ...IM.DIR..QY.ELA.K....LDKY..Q.IEESTTVV.S....IG.A.....ELR.T...SLEI.LD.
Retrocopy VDRIMVDIRG>QYEELAHKIQDNLDKY*PQKIEESTTVVRSSSS*IGTAKVMFIELRNTA>WSLEINLDC

Parental  MRNLKASLENSLREVEARYSMQMEQLNG-VLLH-LESELAQTRAEGQRQTQDYEALLNIKVKLEAEIATY
          ..NLKASLE..LR..EA.YSM.MEQ..G.VL.H.LE.ELA..R............L..IKVKL.AE..TY
Retrocopy G*NLKASLEHRLRNMEAYYSMKMEQFSG<VLMH<LEPELAKIRSXXXXXXXXXXXL-SIKVKL*AEMTTY

Parental  RRLLEDGEDFSLNDALDSSNSMQTIQKTTTRRI
          ...L....D.SLN..LDSS.SM.T.QK.TT...
Retrocopy CCMLKG*KDLSLNNTLDSSTSMGTTQKITTTNV

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1609 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1609 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 174 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,
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,
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,
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,