RetrogeneDB ID:

retro_itri_1090

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393374.1:960400..961079(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000002964
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1090
ATGGTGGGTTACTACAAAGACCTAAGCATGCAGAGACATGGCTCACCAGATGATATCAAAAAGGCATACCAGAAACTGGC
TCTAAAGAGGCATCTAGAAGCTCTGAGAATAAAAAAGAAGCAGAGAGAAAATTCAAACAAGTAGCTGAAGCATATGAAGC
ATCATCAGATGCTTAAAAAAATAGGACATCTATGACAACTTTGTCAAAGAAAGATTAGATTGTGGAGGAGGAGGTGCTGG
TCATTTTGATGGTCCATGTGAGTTTGGCTTCACATTCCAGAACCCAGATGATGTCTTCAGGGAATTTTTTGGTGGAAAGG
ACTCACTTTAATTTGACTTCTTTGAAGACCCTTCTGAAGACTTTTTTGGGACCTGAAAGGGTTCCTGAGGAAGCAGAAAC
CAAGGTACAAGTTTGGTTTTCTCTGCTTTTAGTGGATTTCCATAATCTGGAAGTGATTTTTATTCATTTAATACAGGATT
TACTTCATTTGAGTCACTAAGTCACAGTGACATCACTTCATTCTCTTCTGCATCATTTGGTAGCAGCTGGATAGGCAATT
TCAAATGTTTATCACCTTCTACCAAAATAGTAAAAAGCAGAAAAAATCACTACTAAGAGAACTATTGAGAATGGTGAAAA
GAAGTAGAAGTTGAAGAAGACAGCTAGTCAAAGTCCTTA

ORF - retro_itri_1090 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.36 %
Parental protein coverage: 69.42 %
Number of stop codons detected: 6
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMVDYYEVLGVQRHASPEDIKKAYRKLALRWHPD-KNPENKEEAERKFKQVAEAYEVLSDA-KKR-DIYDK
MV.YY..L..QRH.SP.DIKKAY.KLAL..H........KE.AERKFKQVAEAYE..SDA.K.R.DIYD.
RetrocopyMVGYYKDLSMQRHGSPDDIKKAYQKLALKRHLE<SSENKKE-AERKFKQVAEAYEASSDA*KNR<DIYDN
ParentalYGKEGLNGGGGGGSHFDSPFEFGFTFRNPDDVFRDFFGGRDPFSFDFFEDTFDDFFGNRRGPRGSRNRGA
..KE.L..GGGG..HFD.P.EFGFTF.NPDDVFR.FFGG.D...FDFFED...DFFG...G..GSRN.G.
RetrocopyFVKERLDCGGGGAGHFDGPCEFGFTFQNPDDVFREFFGGKDSL*FDFFEDPSEDFFGT*KGS*GSRNQGT
ParentalGSFFSAFSGFPTFGGGFSAFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGSFKSISTSTKIVNGR-KITTK
...FSAFSGFP..G..F..F.TGFTSF.SL.H...TSFSS.SFG.S..G.FK..S.STKIV..R.KITTK
RetrocopySLVFSAFSGFP*SGSDFYSFNTGFTSFESLSHSDITSFSSASFGSSWIGNFKCLSPSTKIVKSR>KITTK
ParentalRIVENGQER-VEVEEDGQLKSL
R..ENG....VEVEED...KSL
RetrocopyRTIENGEKK<VEVEEDS*SKSL

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_1090 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1090 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 26 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013323 retrocopies
retro_amel_127, retro_amel_685, retro_amel_95,
Bos taurus ENSBTAG000000007713 retrocopies
retro_btau_163, retro_btau_222, retro_btau_248,
Canis familiaris ENSCAFG000000051746 retrocopies
retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Callithrix jacchus ENSCJAG000000052887 retrocopies
retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Cavia porcellus ENSCPOG0000001395317 retrocopies
retro_cpor_1035, retro_cpor_1074, retro_cpor_1147, retro_cpor_1352, retro_cpor_1360, retro_cpor_1364, retro_cpor_259, retro_cpor_325, retro_cpor_38, retro_cpor_40, retro_cpor_538, retro_cpor_610, retro_cpor_720, retro_cpor_793, retro_cpor_814, retro_cpor_840, retro_cpor_952,
Equus caballus ENSECAG000000090052 retrocopies
retro_ecab_105, retro_ecab_22,
Felis catus ENSFCAG000000156542 retrocopies
retro_fcat_1072, retro_fcat_91,
Homo sapiens ENSG000001059939 retrocopies
retro_hsap_103, retro_hsap_166, retro_hsap_2399, retro_hsap_2400, retro_hsap_4031, retro_hsap_519, retro_hsap_54, retro_hsap_889, retro_hsap_939,
Gorilla gorilla ENSGGOG000000047036 retrocopies
retro_ggor_1819, retro_ggor_201, retro_ggor_210, retro_ggor_251, retro_ggor_478, retro_ggor_719,
Loxodonta africana ENSLAFG000000133844 retrocopies
retro_lafr_105, retro_lafr_107, retro_lafr_260, retro_lafr_468,
Microcebus murinus ENSMICG000000097601 retrocopy
retro_mmur_474,
Myotis lucifugus ENSMLUG000000091234 retrocopies
retro_mluc_1371, retro_mluc_147, retro_mluc_304, retro_mluc_333,
Macaca mulatta ENSMMUG000000031766 retrocopies
retro_mmul_1050, retro_mmul_165, retro_mmul_2326, retro_mmul_243, retro_mmul_379, retro_mmul_970,
Mustela putorius furoENSMPUG000000097974 retrocopies
retro_mputfur_1084, retro_mputfur_11, retro_mputfur_1199, retro_mputfur_70,
Mus musculus ENSMUSG000000291316 retrocopies
retro_mmus_113, retro_mmus_171, retro_mmus_2023, retro_mmus_3273, retro_mmus_435, retro_mmus_870,
Nomascus leucogenys ENSNLEG000000013805 retrocopies
retro_nleu_1524, retro_nleu_2, retro_nleu_2063, retro_nleu_2820, retro_nleu_52,
Oryctolagus cuniculus ENSOCUG000000000642 retrocopies
retro_ocun_240, retro_ocun_83,
Otolemur garnettii ENSOGAG000000106402 retrocopies
retro_ogar_248, retro_ogar_3412,
Pongo abelii ENSPPYG000000182284 retrocopies
retro_pabe_100, retro_pabe_2165, retro_pabe_226, retro_pabe_669,
Pelodiscus sinensis ENSPSIG000000181021 retrocopy
retro_psin_19,
Pteropus vampyrus ENSPVAG000000001551 retrocopy
retro_pvam_24,
Rattus norvegicus ENSRNOG000000103536 retrocopies
retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Ictidomys tridecemlineatus ENSSTOG00000002964 7 retrocopies
retro_itri_1090 , retro_itri_1143, retro_itri_169, retro_itri_54, retro_itri_74, retro_itri_832, retro_itri_85,
Tupaia belangeri ENSTBEG000000095867 retrocopies
retro_tbel_1521, retro_tbel_1533, retro_tbel_1571, retro_tbel_1978, retro_tbel_3918, retro_tbel_4142, retro_tbel_67,
Tarsius syrichta ENSTSYG000000054484 retrocopies
retro_tsyr_1358, retro_tsyr_297, retro_tsyr_360, retro_tsyr_491,
Tursiops truncatus ENSTTRG000000139292 retrocopies
retro_ttru_1864, retro_ttru_637,


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