exonerate --bestn 1 --score 90 --exhaustive yes --forcegtag TRUE --model protein2genome /Pro_Hc_g3V-D3.fa Pro_Hc_g3V-D3.fa -
-ryo \nSugar block: %S\nCigar block: %C\nEquivalenced mismatches: %em\nEquivalenced similarity: %es(%ps)\nGene orientation: %g\nCDS region: %tcb-%tce\nAligned reginon: %tab-%tae\n>%ti(%tab-%tae
)\n%tcs\n --showtargetgff TRUE]
Query: Pro_Hc_g3V-D3
Target: Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 HiC_scaffold_14:46807373-46930452:+ len=123080
Model: protein2genome:local
Raw score: 3110
Query range: 0 -> 665
Target range: 11997 -> 111083
1 : ArgSerSerThrGlyHisGlnHisLeuLeuIleGluValAlaSerValProLeuTyrI : 20
!.!|||! ! !.!!|||||||||||||||:!!||||||||||||||||||||| !|
HisSerIleCysSerHisGlnHisLeuLeuLeuGluValAlaSerValProLeuProI
11998 : CATTCTATTTGCAGTCACCAGCACCTGCTGTTAGAAGTAGCTTCTGTTCCTCTGCCTA : 12055
21 : leSerGluThrHisGlnAspPheLysMetThrValLysGluLysGluAspLysValLe : 39
||||||||!:!|||!!.|||||||||||||||||||||||||||||||||:!!|||||
leSerGluSerHisHisAspPheLysMetThrValLysGluLysGluAspGlnValLe
12056 : TCTCTGAAAGCCATCACGATTTCAAGATGACCGTCAAAGAGAAGGAAGACCAAGTTTT : 12112
40 : uProLeuPheGluGlnLeuMetThrLeuThrLysLysGlnLeuProValAspGlnArg : 58
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
uProLeuPheGluGlnLeuMetThrLeuThrLysLysGlnLeuProValAspGlnArg
12113 : GCCACTGTTCGAGCAGTTGATGACCCTCACCAAAAAGCAGCTGCCTGTAGATCAAAGG : 12169
59 : AspPro***ArgLeuAlaHisPheGlyGluIleProArgGlyThrLeuPheAspCysP : 78
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||
AspPro---ArgLeuAlaHisPheGlyGluIleProArgGlyThrLeuPheAspCysP
12170 : GACCCA---AGACTCGCCCACTTCGGGGAAATTCCCAGAGGAACACTCTTCGACTGCT : 12226
79 : heHisGluValHisLeuHisGluAlaThrGluLeuPheLysValLeuTyr{A} >>> : 95
|||||||| !|||||||||||||||||||||||||||||||||||||||{|}
heHisGluLysHisLeuHisGluAlaThrGluLeuPheLysValLeuTyr{A}++
12227 : TCCACGAGAAACACCTTCATGAAGCAACCGAACTCTTTAAGGTTTTGTAT{G}gt... : 12280
96 : > Target Intron 1 >>>> {la}AlaAsnAspPheAspAspPheIleHisLeu : 105
75724 bp {||}||||||||||||||||||||||||||||||
++{la}AlaAsnAspPheAspAspPheIleHisLeu
=========
635 : ProPheAspArgProLeuThrAlaHisSerGluAlaGluLeuLeuThrAspAsnMetV : 654
|||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||
ProPheAspArgProMetThrAlaHisSerGluAlaGluLeuLeuThrAspAsnMetV
110989 : CCCTTCGACAGGCCCATGACAGCCCACAGCGAGGCAGAGCTCCTCACAGACAACATGG : 111048
655 : alPheThrAspValLysIleLysPheLeuAsp*** : 665
|||||||||||||||||||||||||||||||||||
alPheThrAspValLysIleLysPheLeuAsp***
111049 : TCTTCACCGACGTCAAAATCAAGTTCTTGGATTAA : 111083
# seqname source feature start end score strand frame attributes
#
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local gene 11998 111083 3110 + . gene_id 0 ; sequence DesPro_Hc_g3V-D3 ; gene_orientation +
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local cds 11998 12277 . + .
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local exon 11998 12277 . + . insertions 0 ; deletions 1
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local splice5 12278 12279 . + . intron_id 1 ; splice_site "GT"
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local intron 12278 88001 . + . intron_id 1
Pro_Hc_g3V-D3##HiC_scaffold_14##46807373##46930452 exonerate:protein2genome:local splice3 88000 88001 . + . intron_id 0 ; splice_site "AG"
HiC_scaffold_14##46807373##46930452(11997 -> 111083)的含义是在HiC_scaffold_14上的##46807373##46930452区间上，从第11997 开始匹配->到 第111083结束（Target range），中间会预测出外显子和内含子位置。那么这个基因实际上是从第（46807373+11997）位到第（46807373+111083）
这是一条预测正向转录的基因，程序设置了在原先比对的基础上延伸12000bp，当遇到可以补全的地方，则会选入预测结果，如这里的11997则是因为向前增加了3个碱基，如果没采纳应该默认是12000。
image.png
image.png
基因 DNA 分为编码区和非编码区，编码区包含外显子和内含子，一般非编码区具有基因表达的调控功能，如启动子在非编码区。编码区则转录为 mRNA 并最终翻译成蛋白质。
外显子和内含子都被转录到 mRNA 前体 hnRNA 中，当 hnRNA 进行剪接变为成熟的 mRNA 时，内含子被切除，而外显子保留。实际上真正编码蛋白质的是外显子，而内含子则无编码功能。
内含子存在于DNA 中，在转录的过程中，DNA 上的内含子也会被转录到前体 RNA 中，但前体 RNA 上的内含子会在 RNA 离开细胞核进行翻译前被切除。
