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


Retrocopy-Parental alignment summary:






>retro_itri_297
GGAATGCAAAAGAAAGCAAGGAAGTATGTGACCATGAAACGAATGCTTAGTCTTAGAGAAGAGAGGCTAAAAGAAAAGGA
TAAATCAAAACCTAAAAAGAAACAAAAGAACAATCCTAGTGCATCGAAGGAAAGAGAAGTTCCACAACACTCTTCCTGCT
TATTCTTCCATTACAATACACAACTGGGCCTACCTTATCATATCCTGGTTGATATCAATTTGATAAATTTTCCATTAAAG
CCAAACTGGACCTAGTGCAATCAATGATGGACTGTCTGTATGCCAAGTGTATCTCTTGTATAACTGATTGTGTAATGGCT
GAAATTGAAAAATTGGGGTAGAAGTATTGAGTAACTTTAAGGATTGCAAAGGATCCATGGTTTGAATCATTACCATGCAA
GCACAAAGGAATCTATGCAGATGACTGCTTAGTACAAAAAGTAACTCAGATCAAGTGTTAACATCATGGCCACAATTGAC
TGTGACCTTAAATGAAGACTCCAGAATATACCTGGAGTTCCTATCATGTACATTTCTAACCATAGATACAATATCAAGGG
TATGCTAGATAATTATGGAGCCCCTTGGTTC

ORF - retro_itri_297 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGKQKKTRKYATMKRMLSLRDERLKEKDRLKPKKKQKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILV
G.QKK.RKY.TMKRMLSLR.ER................PSA.KEREVPQH.SCLFF.YNTQLG.PYHILV
RetrocopyGMQKKARKYVTMKRMLSLREERXXXXXXXXXXXXXXNNPSASKEREVPQHSSCLFFHYNTQLGLPYHILV
ParentalDTNFIN-FSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTY
D.N.IN.FSIKAKLDLVQSMMDCLYAKCI.CITDCVMAEIEKLG.KY.V.LRIAKDP.FE.LPC.HKG.Y
RetrocopyDINLIN<FSIKAKLDLVQSMMDCLYAKCISCITDCVMAEIEKLG*KY*VTLRIAKDPWFESLPCKHKGIY
ParentalADDCLVQRVTQHKC-YIVATVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPRF
ADDCLVQ.VTQ.KC..I.AT.D.DLK.R...IPGVPIMYISNHRYNI..M.D.YGAP.F
RetrocopyADDCLVQKVTQIKC>NIMATIDCDLK*RLQNIPGVPIMYISNHRYNIKGMLDNYGAPWF

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_297 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_297 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 29 parental genes, and 164 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000182967 retrocopies
retro_amel_1447, retro_amel_1574, retro_amel_435, retro_amel_458, retro_amel_481, retro_amel_526, retro_amel_932,
Bos taurus ENSBTAG000000203811 retrocopy
retro_btau_446,
Canis familiaris ENSCAFG000000169713 retrocopies
retro_cfam_142, retro_cfam_205, retro_cfam_95,
Callithrix jacchus ENSCJAG000000205189 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 ENSCPOG000000011496 retrocopies
retro_cpor_1205, retro_cpor_212, retro_cpor_336, retro_cpor_351, retro_cpor_51, retro_cpor_634,
Equus caballus ENSECAG000000082611 retrocopy
retro_ecab_423,
Erinaceus europaeus ENSEEUG000000071731 retrocopy
retro_eeur_491,
Felis catus ENSFCAG000000227533 retrocopies
retro_fcat_1461, retro_fcat_523, retro_fcat_685,
Homo sapiens ENSG000001196166 retrocopies
retro_hsap_2686, retro_hsap_3040, retro_hsap_383, retro_hsap_3912, retro_hsap_4724, retro_hsap_535,
Gorilla gorilla ENSGGOG000000163183 retrocopies
retro_ggor_1872, retro_ggor_2507, retro_ggor_3080,
Latimeria chalumnae ENSLACG000000188791 retrocopy
retro_lcha_9,
Loxodonta africana ENSLAFG000000007241 retrocopy
retro_lafr_81,
Microcebus murinus ENSMICG000000060615 retrocopies
retro_mmur_1175, retro_mmur_832, retro_mmur_86, retro_mmur_906, retro_mmur_968,
Macaca mulatta ENSMMUG000000088878 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 ENSMODG000000061795 retrocopies
retro_mdom_1729, retro_mdom_622, retro_mdom_635, retro_mdom_820, retro_mdom_846,
Mustela putorius furoENSMPUG000000093217 retrocopies
retro_mputfur_1002, retro_mputfur_1131, retro_mputfur_1306, retro_mputfur_1315, retro_mputfur_1621, retro_mputfur_532, retro_mputfur_891,
Mus musculus ENSMUSG000000212433 retrocopies
retro_mmus_1575, retro_mmus_2358, retro_mmus_3268,
Nomascus leucogenys ENSNLEG000000163117 retrocopies
retro_nleu_1145, retro_nleu_1185, retro_nleu_1789, retro_nleu_1927, retro_nleu_1994, retro_nleu_686, retro_nleu_874,
Oryctolagus cuniculus ENSOCUG000000141201 retrocopy
retro_ocun_96,
Otolemur garnettii ENSOGAG0000000271119 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 ENSPPYG0000000599110 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 ENSPTRG000000065406 retrocopies
retro_ptro_1813, retro_ptro_1998, retro_ptro_2660, retro_ptro_297, retro_ptro_3142, retro_ptro_401,
Pteropus vampyrus ENSPVAG000000006573 retrocopies
retro_pvam_1169, retro_pvam_1272, retro_pvam_454,
Rattus norvegicus ENSRNOG000000047235 retrocopies
retro_rnor_2539, retro_rnor_2591, retro_rnor_2658, retro_rnor_771, retro_rnor_818,
Sorex araneus ENSSARG000000032703 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 ENSTBEG0000001355730 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 ENSTSYG000000063273 retrocopies
retro_tsyr_1016, retro_tsyr_1418, retro_tsyr_621,
Tursiops truncatus ENSTTRG000000024403 retrocopies
retro_ttru_1447, retro_ttru_1691, retro_ttru_584,


Copyright © RetrogeneDB 2014-2017