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社区首页 >专栏 >特别栏目之新型冠状病毒(2019-nCoV)序列与人类基因相似性分析

特别栏目之新型冠状病毒(2019-nCoV)序列与人类基因相似性分析

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一粒沙
发布2020-02-25 13:26:08
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发布2020-02-25 13:26:08
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文章被收录于专栏:R语言交流中心
继上次的分析,我们发现序列的差异性,那么接下来我们看下26个样本中相似的序列30-29860bp。利用clustalx,我们进行位点的匹配分析,操作如下图:

接下来我们看下前面和最后差异的位置:

我们发现40216这个样本序列和其它的序列存在着完全的不重合位点。那么找到相似的序列后,我们对这段序列进行Blast分析,我们选择32-29860bp序列,具体的设置参数如下图:

然后,我们得到68个人类的基因和病毒的序列有相似的位点,当然匹配片段长度都集中在22-45bp。大体的结果如下:

同时,我们导出具体的68个基因,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

我大体对上面的基因在NCBI中进行了简单的检索,发现其中BAZ2B 可能与心脏猝死易感性有关;LRBA 有助于免疫效应分子的分泌或沉积;同时其中很多基因和线粒体功能、能量代谢相关。

接下来,那就是对真正有意义的匹配位点进行接下来的分析。是否这些和人类相关基因匹配的位点真正影响到人的相关表型,还需要进一步的实验分析,我们能做的也只有到目前的分析。

相关的数据见链接:

https://pan.baidu.com/s/1daF51k72D2qqFyPVtnCAQw提取码: aav7

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原始发表:2020-01-26,如有侵权请联系 cloudcommunity@tencent.com 删除

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