特別欄目之新型冠狀病毒（2019-nCoV）序列與人類基因相似性分析
- 2020 年 2 月 25 日
- 筆記
接下來我們看下前面和最後差異的位置：
我們發現40216這個樣本序列和其它的序列存在着完全的不重合位點。那麼找到相似的序列後，我們對這段序列進行Blast分析，我們選擇32-29860bp序列，具體的設置參數如下圖：
然後，我們得到68個人類的基因和病毒的序列有相似的位點，當然匹配片段長度都集中在22-45bp。大體的結果如下：
同時，我們導出具體的68個基因，列在下表：
|
Description |
Per. Ident |
Accession |
|---|---|---|
|
Homo sapiens OCRL inositol polyphosphate-5-phosphatase (OCRL), RefSeqGene on chromosome X |
0.8537 |
NG_008638.1 |
|
Homo sapiens thyroid hormone receptor interactor 11 (TRIP11), RefSeqGene on chromosome 14 |
0.8684 |
NG_016970.1 |
|
Homo sapiens BLM RecQ like helicase (BLM), RefSeqGene (LRG_20) on chromosome 15 |
0.807 |
NG_007272.1 |
|
Homo sapiens SIN3 transcription regulator family member A (SIN3A), RefSeqGene on chromosome 15 |
0.8077 |
NG_052855.1 |
|
Homo sapiens nucleotide binding protein like (NUBPL), RefSeqGene on chromosome 14 |
0.8298 |
NG_028349.1 |
|
Homo sapiens dedicator of cytokinesis 4 (DOCK4), RefSeqGene on chromosome 7 |
0.8684 |
NG_028060.2 |
|
Homo sapiens myosin XVIIIA (MYO18A), RefSeqGene on chromosome 17 |
0.8889 |
NG_051989.1 |
|
Homo sapiens diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2), RefSeqGene on chromosome 5 |
0.8718 |
NG_051568.1 |
|
Homo sapiens WD repeat domain 26 (WDR26), RefSeqGene on chromosome 1 |
0.9062 |
NG_047198.1 |
|
Homo sapiens bromodomain adjacent to zinc finger domain 2B (BAZ2B), RefSeqGene on chromosome 2 |
0.85 |
NG_051314.1 |
|
Homo sapiens adenosine deaminase 2 (ADA2), RefSeqGene (LRG_1217) on chromosome 22 |
0.9615 |
NG_033943.1 |
|
Homo sapiens inner mitochondrial membrane peptidase subunit 2 (IMMP2L), RefSeqGene on chromosome 7 |
0.8182 |
NG_030016.2 |
|
Homo sapiens solute carrier family 25 member 43 (SLC25A43), RefSeqGene on chromosome X |
0.8421 |
NG_016298.2 |
|
Homo sapiens parkin RBR E3 ubiquitin protein ligase (PRKN), RefSeqGene on chromosome 6 |
0.8222 |
NG_008289.2 |
|
Homo sapiens Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), RefSeqGene on chromosome 14 |
1 |
NG_051667.1 |
|
Homo sapiens synaptic vesicle glycoprotein 2B (SV2B), RefSeqGene on chromosome 15 |
0.8 |
NG_051558.1 |
|
Homo sapiens histone deacetylase 9 (HDAC9), RefSeqGene on chromosome 7 |
0.9286 |
NG_023250.3 |
|
Homo sapiens dystonin (DST), RefSeqGene on chromosome 6 |
0.8649 |
NG_029322.2 |
|
Homo sapiens sulfatase 1 (SULF1), RefSeqGene on chromosome 8 |
0.9286 |
NG_042849.1 |
|
Homo sapiens paired box 5 (PAX5), RefSeqGene (LRG_1384) on chromosome 9 |
0.9286 |
NG_033894.1 |
|
Homo sapiens WD repeat domain 72 (WDR72), RefSeqGene on chromosome 15 |
1 |
NG_017034.2 |
|
Homo sapiens TNNI3 interacting kinase (TNNI3K), RefSeqGene on chromosome 1 |
0.8788 |
NG_032939.2 |
|
Homo sapiens glutamate metabotropic receptor 7 (GRM7), RefSeqGene on chromosome 3 |
0.9286 |
NG_029781.1 |
|
Homo sapiens ubiquinol-cytochrome c reductase complex assembly factor 1 (UQCC1), RefSeqGene on chromosome 20 |
0.8462 |
NG_021421.1 |
|
Homo sapiens dihydrolipoamide dehydrogenase (DLD), RefSeqGene on chromosome 7 |
0.9286 |
NG_008045.1 |
|
Homo sapiens lipase maturation factor 1 (LMF1), RefSeqGene on chromosome 16 |
0.96 |
NG_021286.2 |
|
Homo sapiens cadherin 13 (CDH13), RefSeqGene on chromosome 16 |
0.9 |
NG_052819.1 |
|
Homo sapiens tau tubulin kinase 1 (TTBK1), RefSeqGene on chromosome 6 |
0.825 |
NG_051244.1 |
|
Homo sapiens pecanex 2 (PCNX2), RefSeqGene on chromosome 1 |
0.9 |
NG_050912.1 |
|
Homo sapiens mannose receptor C-type 1 (MRC1), RefSeqGene on chromosome 10 |
0.825 |
NG_047011.1 |
|
Homo sapiens potassium voltage-gated channel subfamily A member 4 (KCNA4), RefSeqGene on chromosome 11 |
0.96 |
NG_042309.1 |
|
Homo sapiens LPS responsive beige-like anchor protein (LRBA), RefSeqGene (LRG_1324) on chromosome 4 |
0.8611 |
NG_032855.1 |
|
Homo sapiens forkhead box O1 (FOXO1), RefSeqGene on chromosome 13 |
0.9062 |
NG_023244.1 |
|
Homo sapiens MCF.2 cell line derived transforming sequence (MCF2), RefSeqGene on chromosome X |
0.96 |
NG_016439.1 |
|
Homo sapiens adducin 1 (ADD1), RefSeqGene on chromosome 4 |
0.96 |
NG_012037.1 |
|
Homo sapiens glycine receptor alpha 1 (GLRA1), RefSeqGene on chromosome 5 |
0.9 |
NG_011764.1 |
|
Homo sapiens dentin sialophosphoprotein (DSPP), RefSeqGene (LRG_1242) on chromosome 4 |
0.825 |
NG_011595.1 |
|
Homo sapiens arylsulfatase B (ARSB), RefSeqGene on chromosome 5 |
0.7885 |
NG_007089.1 |
|
Homo sapiens NLR family pyrin domain containing 12 (NLRP12), RefSeqGene on chromosome 19 |
0.8378 |
NG_008651.2 |
|
Homo sapiens CDP-L-ribitol pyrophosphorylase A (CRPPA), RefSeqGene on chromosome 7 |
0.9259 |
NG_032690.2 |
|
Homo sapiens growth hormone receptor (GHR), RefSeqGene on chromosome 5 |
0.8293 |
NG_011688.2 |
|
Homo sapiens myosin light chain kinase family member 4 (MYLK4), RefSeqGene on chromosome 6 |
0.875 |
NG_052793.1 |
|
Homo sapiens BRISC and BRCA1 A complex member 2 (BABAM2), RefSeqGene on chromosome 2 |
0.9259 |
NG_051044.1 |
|
Homo sapiens contactin 5 (CNTN5), RefSeqGene on chromosome 11 |
0.9259 |
NG_047156.1 |
|
Homo sapiens G protein subunit beta 1 (GNB1), RefSeqGene on chromosome 1 |
0.9259 |
NG_047052.1 |
|
Homo sapiens HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 (HERC1), RefSeqGene on chromosome 15 |
0.875 |
NG_046958.1 |
|
Homo sapiens netrin G1 (NTNG1), RefSeqGene on chromosome 1 |
0.931 |
NG_042821.1 |
|
Homo sapiens hyperpolarization activated cyclic nucleotide gated potassium channel 1 (HCN1), RefSeqGene on chromosome 5 |
0.8462 |
NG_042183.1 |
|
Homo sapiens talin 2 (TLN2), RefSeqGene on chromosome 15 |
0.9259 |
NG_033932.1 |
|
Homo sapiens proteasome 20S subunit alpha 6 (PSMA6), RefSeqGene on chromosome 14 |
1 |
NG_011703.2 |
|
Homo sapiens calcium voltage-gated channel subunit alpha1 D (CACNA1D), RefSeqGene on chromosome 3 |
0.9259 |
NG_032999.1 |
|
Homo sapiens junction plakoglobin (JUP), RefSeqGene (LRG_401) on chromosome 17 |
0.875 |
NG_009090.2 |
|
Homo sapiens early growth response 2 (EGR2), RefSeqGene (LRG_239) on chromosome 10 |
0.9259 |
NG_008936.2 |
|
Homo sapiens transient receptor potential cation channel subfamily V member 1 (TRPV1), RefSeqGene on chromosome 17 |
0.8788 |
NG_029716.1 |
|
Homo sapiens phosphatidylinositol binding clathrin assembly protein (PICALM), RefSeqGene on chromosome 11 |
0.8378 |
NG_028942.1 |
|
Homo sapiens heparanase 2 (inactive) (HPSE2), RefSeqGene on chromosome 10 |
0.7917 |
NG_023416.1 |
|
Homo sapiens C-type lectin domain containing 16A (CLEC16A), RefSeqGene on chromosome 16 |
1 |
NG_016757.1 |
|
Homo sapiens glutamate ionotropic receptor kainate type subunit 2 (GRIK2), RefSeqGene on chromosome 6 |
0.8824 |
NG_009224.2 |
|
Homo sapiens dystrophin (DMD), RefSeqGene (LRG_199) on chromosome X |
0.9259 |
NG_012232.1 |
|
Homo sapiens thymocyte selection associated high mobility group box (TOX), RefSeqGene on chromosome 8 |
0.8824 |
NG_011993.1 |
|
Homo sapiens cadherin 2 (CDH2), RefSeqGene on chromosome 18 |
0.8378 |
NG_011959.1 |
|
Homo sapiens potassium voltage-gated channel subfamily Q member 1 (KCNQ1), RefSeqGene (LRG_287) on chromosome 11 |
0.875 |
NG_008935.1 |
|
Homo sapiens PKHD1 ciliary IPT domain containing fibrocystin/polyductin (PKHD1), RefSeqGene on chromosome 6 |
0.8462 |
NG_008753.1 |
|
Homo sapiens tyrosinase (TYR), RefSeqGene on chromosome 11 |
0.9259 |
NG_008748.1 |
|
Homo sapiens keratin 17 (KRT17), RefSeqGene on chromosome 17 |
0.875 |
NG_008625.1 |
|
Homo sapiens keratin 14 (KRT14), RefSeqGene on chromosome 17 |
0.875 |
NG_008624.1 |
|
Homo sapiens solute carrier family 12 member 6 (SLC12A6), RefSeqGene (LRG_270) on chromosome 15 |
0.8889 |
NG_007951.1 |
我大體對上面的基因在NCBI中進行了簡單的檢索，發現其中BAZ2B 可能與心臟猝死易感性有關；LRBA 有助於免疫效應分子的分泌或沉積；同時其中很多基因和線粒體功能、能量代謝相關。
接下來，那就是對真正有意義的匹配位點進行接下來的分析。是否這些和人類相關基因匹配的位點真正影響到人的相關表型，還需要進一步的實驗分析，我們能做的也只有到目前的分析。
相關的數據見鏈接：
https://pan.baidu.com/s/1daF51k72D2qqFyPVtnCAQw提取碼: aav7
歡迎交流學習！
