RetrogeneDB ID: retro_itri_297

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:6370426..6371017(+)
• Located in intron of: ENSSTOG00000004731

Retrocopy information

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

Parental gene information

• Parental gene symbol: FCF1
• Ensembl ID: ENSSTOG00000008083
• Aliases: None
• Description: FCF1 rRNA-processing protein [Source:HGNC Symbol;Acc:20220]

Sequence

>retro_itri_297
GGAATGCAAAAGAAAGCAAGGAAGTATGTGACCATGAAACGAATGCTTAGTCTTAGAGAAGAGAGGCTAAAAGAAAAGGA
TAAATCAAAACCTAAAAAGAAACAAAAGAACAATCCTAGTGCATCGAAGGAAAGAGAAGTTCCACAACACTCTTCCTGCT
TATTCTTCCATTACAATACACAACTGGGCCTACCTTATCATATCCTGGTTGATATCAATTTGATAAATTTTCCATTAAAG
CCAAACTGGACCTAGTGCAATCAATGATGGACTGTCTGTATGCCAAGTGTATCTCTTGTATAACTGATTGTGTAATGGCT
GAAATTGAAAAATTGGGGTAGAAGTATTGAGTAACTTTAAGGATTGCAAAGGATCCATGGTTTGAATCATTACCATGCAA
GCACAAAGGAATCTATGCAGATGACTGCTTAGTACAAAAAGTAACTCAGATCAAGTGTTAACATCATGGCCACAATTGAC
TGTGACCTTAAATGAAGACTCCAGAATATACCTGGAGTTCCTATCATGTACATTTCTAACCATAGATACAATATCAAGGG
TATGCTAGATAATTATGGAGCCCCTTGGTTC

Alignment

ORF - retro_itri_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKQKKTRKYATMKRMLSLRDERLKEKDRLKPKKKQKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILV
          G.QKK.RKY.TMKRMLSLR.ER................PSA.KEREVPQH.SCLFF.YNTQLG.PYHILV
Retrocopy GMQKKARKYVTMKRMLSLREERXXXXXXXXXXXXXXNNPSASKEREVPQHSSCLFFHYNTQLGLPYHILV

Parental  DTNFIN-FSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTY
          D.N.IN.FSIKAKLDLVQSMMDCLYAKCI.CITDCVMAEIEKLG.KY.V.LRIAKDP.FE.LPC.HKG.Y
Retrocopy DINLIN<FSIKAKLDLVQSMMDCLYAKCISCITDCVMAEIEKLG*KY*VTLRIAKDPWFESLPCKHKGIY

Parental  ADDCLVQRVTQHKC-YIVATVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPRF
          ADDCLVQ.VTQ.KC..I.AT.D.DLK.R...IPGVPIMYISNHRYNI..M.D.YGAP.F
Retrocopy ADDCLVQKVTQIKC>NIMATIDCDLK*RLQNIPGVPIMYISNHRYNIKGMLDNYGAPWF

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_297 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_297 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 29 parental genes, and 164 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018296	7 retrocopies	retro_amel_1447, retro_amel_1574, retro_amel_435, retro_amel_458, retro_amel_481, retro_amel_526, retro_amel_932,
Bos taurus	ENSBTAG00000020381	1 retrocopy	retro_btau_446,
Canis familiaris	ENSCAFG00000016971	3 retrocopies	retro_cfam_142, retro_cfam_205, retro_cfam_95,
Callithrix jacchus	ENSCJAG00000020518	9 retrocopies	retro_cjac_1432, retro_cjac_1615, retro_cjac_1711, retro_cjac_1926, retro_cjac_2158, retro_cjac_3094, retro_cjac_3125, retro_cjac_4092, retro_cjac_4148,
Cavia porcellus	ENSCPOG00000001149	6 retrocopies	retro_cpor_1205, retro_cpor_212, retro_cpor_336, retro_cpor_351, retro_cpor_51, retro_cpor_634,
Equus caballus	ENSECAG00000008261	1 retrocopy	retro_ecab_423,
Erinaceus europaeus	ENSEEUG00000007173	1 retrocopy	retro_eeur_491,
Felis catus	ENSFCAG00000022753	3 retrocopies	retro_fcat_1461, retro_fcat_523, retro_fcat_685,
Homo sapiens	ENSG00000119616	6 retrocopies	retro_hsap_2686, retro_hsap_3040, retro_hsap_383, retro_hsap_3912, retro_hsap_4724, retro_hsap_535,
Gorilla gorilla	ENSGGOG00000016318	3 retrocopies	retro_ggor_1872, retro_ggor_2507, retro_ggor_3080,
Latimeria chalumnae	ENSLACG00000018879	1 retrocopy	retro_lcha_9,
Loxodonta africana	ENSLAFG00000000724	1 retrocopy	retro_lafr_81,
Microcebus murinus	ENSMICG00000006061	5 retrocopies	retro_mmur_1175, retro_mmur_832, retro_mmur_86, retro_mmur_906, retro_mmur_968,
Macaca mulatta	ENSMMUG00000008887	8 retrocopies	retro_mmul_1306, retro_mmul_1422, retro_mmul_1704, retro_mmul_1737, retro_mmul_1891, retro_mmul_459, retro_mmul_492, retro_mmul_685,
Monodelphis domestica	ENSMODG00000006179	5 retrocopies	retro_mdom_1729, retro_mdom_622, retro_mdom_635, retro_mdom_820, retro_mdom_846,
Mustela putorius furo	ENSMPUG00000009321	7 retrocopies	retro_mputfur_1002, retro_mputfur_1131, retro_mputfur_1306, retro_mputfur_1315, retro_mputfur_1621, retro_mputfur_532, retro_mputfur_891,
Mus musculus	ENSMUSG00000021243	3 retrocopies	retro_mmus_1575, retro_mmus_2358, retro_mmus_3268,
Nomascus leucogenys	ENSNLEG00000016311	7 retrocopies	retro_nleu_1145, retro_nleu_1185, retro_nleu_1789, retro_nleu_1927, retro_nleu_1994, retro_nleu_686, retro_nleu_874,
Oryctolagus cuniculus	ENSOCUG00000014120	1 retrocopy	retro_ocun_96,
Otolemur garnettii	ENSOGAG00000002711	19 retrocopies	retro_ogar_1007, retro_ogar_1114, retro_ogar_1666, retro_ogar_1955, retro_ogar_2035, retro_ogar_2167, retro_ogar_2240, retro_ogar_2336, retro_ogar_2482, retro_ogar_2939, retro_ogar_3232, retro_ogar_3432, retro_ogar_3486, retro_ogar_3488, retro_ogar_503, retro_ogar_651, retro_ogar_739, retro_ogar_79, retro_ogar_972,
Pongo abelii	ENSPPYG00000005991	10 retrocopies	retro_pabe_1758, retro_pabe_214, retro_pabe_2295, retro_pabe_2437, retro_pabe_2613, retro_pabe_2685, retro_pabe_3188, retro_pabe_326, retro_pabe_3668, retro_pabe_3830,
Pan troglodytes	ENSPTRG00000006540	6 retrocopies	retro_ptro_1813, retro_ptro_1998, retro_ptro_2660, retro_ptro_297, retro_ptro_3142, retro_ptro_401,
Pteropus vampyrus	ENSPVAG00000000657	3 retrocopies	retro_pvam_1169, retro_pvam_1272, retro_pvam_454,
Rattus norvegicus	ENSRNOG00000004723	5 retrocopies	retro_rnor_2539, retro_rnor_2591, retro_rnor_2658, retro_rnor_771, retro_rnor_818,
Sorex araneus	ENSSARG00000003270	3 retrocopies	retro_sara_126, retro_sara_177, retro_sara_375,
Ictidomys tridecemlineatus	ENSSTOG00000008083	4 retrocopies	retro_itri_1149, retro_itri_297 , retro_itri_599, retro_itri_850,
Tupaia belangeri	ENSTBEG00000013557	30 retrocopies	retro_tbel_1190, retro_tbel_1261, retro_tbel_135, retro_tbel_1397, retro_tbel_1457, retro_tbel_1576, retro_tbel_182, retro_tbel_222, retro_tbel_2578, retro_tbel_2996, retro_tbel_3037, retro_tbel_3060, retro_tbel_3075, retro_tbel_3105, retro_tbel_3152, retro_tbel_3360, retro_tbel_342, retro_tbel_3564, retro_tbel_3568, retro_tbel_3661, retro_tbel_3694, retro_tbel_3797, retro_tbel_3923, retro_tbel_4463, retro_tbel_4506, retro_tbel_4571, retro_tbel_4645, retro_tbel_580, retro_tbel_776, retro_tbel_966,
Tarsius syrichta	ENSTSYG00000006327	3 retrocopies	retro_tsyr_1016, retro_tsyr_1418, retro_tsyr_621,
Tursiops truncatus	ENSTTRG00000002440	3 retrocopies	retro_ttru_1447, retro_ttru_1691, retro_ttru_584,