Gene Card 基因详情

支持统一新 ID、NCBI Gene ID、GeneID、locus_tag、Transcript ID、Protein ID，以及已人工核对的文献基因名查询。页面会先解析到丹参统一基因，再整合坐标、序列、注释、亚细胞定位、EMS 突变和下载入口。

当前解析结果

`SmilChr01G001160`

染色体: Chr01 坐标: 23565007-23582155 链方向: + 类型: protein_coding

基本信息

统一新 Gene ID	`SmilChr01G001160`
名称	SmilChr01G001160
描述	DNA ligase 4
染色体 / SeqID	Chr01 / NC_080387.1
坐标与链方向	23565007 - 23582155 / `+`

ID 对照

NCBI Gene ID	`LOC131007079`
GeneID	`131007079`
locus_tag	`-`
NCBI Name	`LOC131007079`
原始查询	`SmilChr01G001160`

查看完整 ID 对照表

功能注释

来源	GFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
描述	DNA ligase 4
产物	DNA ligase 4
Arabidopsis	`AT5G57160` (ATLIG4) DNA ligase IV [Source:NCBI gene (formerly Entrezgene);Acc:835822] identity=57.8; qcov=1.03; evalue=0; confidence=high
Rice	`Os10g0489200` - identity=26.1; qcov=0.244; evalue=3.53e-26; confidence=weak
GO	GO:0003677 (DNA binding); GO:0003910 (DNA ligase (ATP) activity); GO:0005524 (ATP binding); GO:0006297 (nucleotide-excision repair, DNA gap filling); GO:0006303 (double-strand break repair via nonhomologous end joining); GO:0006310 (DNA recombination); GO:0032807 (DNA ligase IV complex); GO:0051103 (GO:0051103); GO:0071897 (DNA biosynthetic process)
KEGG	smil03450 (Non-homologous end-joining - Salvia miltiorrhiza (redroot sage))
Pfam	PF00533 (BRCT); PF01068 (DNA_ligase_A_M); PF04675 (DNA_ligase_A_N); PF04679 (DNA_ligase_A_C); PF09414 (RNA_ligase); PF11411 (DNA_ligase_IV); PF12738 (PTCB-BRCT); PF16589 (BRCT_2)
InterPro	-
eggNOG	-
NR	GeneID:131007079

打开注释模块

亚细胞定位 Top 5

Rank	定位位置	中文	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057790203.1`
2	Nucleoplasm	核质	0.80000	`XP_057790203.1`
3	Nuclear body	核内小体	0.40000	`XP_057790203.1`
4	Chromosome	染色体	0.00000	`XP_057790203.1`
5	Centromere	着丝粒	0.00000	`XP_057790203.1`

进入亚细胞定位查询

EMS 诱变突变

下表显示该基因在丹参 EMS 材料中的前 12 个候选突变；完整结果可进入 EMS 突变库继续筛选或下载。

位置	REF	ALT	类型	影响	携带材料数	材料
`Chr1:23565163`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B48,D2
`Chr1:23565221`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B101,B104,C16,D11
`Chr1:23565271`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B26,C19
`Chr1:23565272`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	A21,D10
`Chr1:23565284`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C79
`Chr1:23565286`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B66
`Chr1:23565290`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C32,C68
`Chr1:23565321`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B140
`Chr1:23565455`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	C32,C68,D4
`Chr1:23565483`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	B121,B135,B33,C61
`Chr1:23566829`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	A18,B12,B24,C85,C86
`Chr1:23570725`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B124,B8

进入 EMS 突变库

预测功能结构域

结构域结果来自 Pfam-A HMM 数据库和 HMMER hmmscan；位置为对应蛋白序列上的氨基酸坐标。

XP_057790203.1

1211 aa

606

1211

DNA_ligase_A_N

DNA_ligase_A_M

RNA_ligase

DNA_ligase_A_C

BRCT

BRCT_2

PTCB-BRCT

DNA_ligase_IV

PF04675 DNA_ligase_A_N 5-188 aa PF01068 DNA_ligase_A_M 228-443 aa PF09414 RNA_ligase 247-439 aa PF04679 DNA_ligase_A_C 468-586 aa PF00533 BRCT 654-725 aa PF16589 BRCT_2 655-736 aa PF12738 PTCB-BRCT 672-714 aa PF11411 DNA_ligase_IV 746-779 aa

Protein ID	来源	结构域编号	结构域名称	类型	起始 aa	终止 aa	E-value	Score	说明
`XP_057790203.1`	Pfam	`PF04675`	DNA_ligase_A_N	Family	5	188	1.4e-36	127.0	DNA ligase N terminus
`XP_057790203.1`	Pfam	`PF01068`	DNA_ligase_A_M	Domain	228	443	1.2e-42	146.7	ATP dependent DNA ligase domain
`XP_057790203.1`	Pfam	`PF09414`	RNA_ligase	Family	247	439	9.2e-07	29.9	RNA ligase
`XP_057790203.1`	Pfam	`PF04679`	DNA_ligase_A_C	Domain	468	586	9.2e-11	42.7	ATP dependent DNA ligase C terminal region
`XP_057790203.1`	Pfam	`PF00533`	BRCT	Domain	654	725	4.9e-12	46.6	BRCA1 C Terminus (BRCT) domain
`XP_057790203.1`	Pfam	`PF16589`	BRCT_2	Domain	655	736	3.9e-17	63.1	BRCT domain
`XP_057790203.1`	Pfam	`PF12738`	PTCB-BRCT	Domain	672	714	1.3e-08	35.5	twin BRCT domain
`XP_057790203.1`	Pfam	`PF11411`	DNA_ligase_IV	Family	746	779	1.9e-05	25.3	DNA ligase IV

cDNA / CDS / Protein 序列

下载基因组 DNA（仅基因区域）

每个公开基因均提供参考注释对应的转录本序列；蛋白编码基因另提供 CDS 和蛋白序列。非编码 RNA 不适用 CDS 或蛋白下载。真实 accession 的版本后缀予以保留。

cDNA

1 records

下载 cDNA FASTA

XM_057934220.1
GTTTTGGTTCTAGAAATTTTATACTCCACTTGTAAAGAGTAGTAGATACGTTTTCTCTCTCGAAAATAGTATATCAGTTGATTTCCCCCCAAATCCAATTCCAATACCCAAACATAAAAAAGCAAGCAGATAGCTTCTTTCTGCCGGCAATAATGTCGGAAACCAAGTTCAGTGTAATGGTGAGCCTCTTCAACTGGATGCAGAAGAGCAAGTCGTCGTCTCTTAAGCGTTCCAAATTCCGCAAGTTTCTCGACACCTTC...

CDS

1 records

下载 CDS FASTA

LOC131007079
ATGTCGGAAACCAAGTTCAGTGTAATGGTGAGCCTCTTCAACTGGATGCAGAAGAGCAAGTCGTCGTCTCTTAAGCGTTCCAAATTCCGCAAGTTTCTCGACACCTTCTGCCGCCCCCGAAACGGCGCCGACTACTTCGCCGCCATCCGCCTCATCCTCCCCGCCCTCGACCGCGAGCGCGGCTCCTATGGCCTTCGCGAGCACGTCCTCGCTACCTGTATCATCGACGCCCTCGGCATCTCTCGCGACTCCCCCGACTC...

Protein

1 records

下载 Protein FASTA

XP_057790203.1
MSETKFSVMVSLFNWMQKSKSSSLKRSKFRKFLDTFCRPRNGADYFAAIRLILPALDRERGSYGLREHVLATCIIDALGISRDSPDSQRLINWRKGGAKSGAFAGNFALVAAEVLQRRQGMSSGDLTIVELNELLDRLATSDNRSEKISVLSELIRKTNVQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLRDRSQRHKRQDIEVGKPVRPQLALRVSNAAAAWKKLHGKEVVVECKFDGDRI...

上下游序列下载

upstream/downstream 最大各 10000 bp。负链基因会自动反向互补，使最终 FASTA 为转录方向 5′→3′。

下载 upstream 下载 downstream 下载 upstream + gene + downstream

JBrowse

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