Red Sage Omics 丹参基因组信息平台
首页 基因查询 ID 对照表 功能注释 结构域预测 Pfam 基因组工具 蛋白互作 亚细胞定位 表达量 共表达 同源/共线性 GO/KEGG 注释 TF 结合位点 TF 靶基因 EMS 突变 JBrowse BLAST 下载 关于 帮助
数据资源
ID 对照表 功能注释 功能检索 次生代谢专题 文献证据 结构域预测 Pfam 同源/共线性
分析工具
基因组工具 引物设计 同源重组引物设计 核酸翻译 BLAST 蛋白互作 亚细胞定位 共表达 GO/KEGG 注释 功能检索
调控/突变
TF 结合位点 TF 靶基因 EMS 突变
帮助
关于 帮助 资源与版本
中文 EN

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。
示例

当前解析结果

SmilChr08G004420

染色体: Chr08 坐标: 53914670-53916806 链方向: + 类型: protein_coding

基本信息

统一新 Gene IDSmilChr08G004420
名称SmilChr08G004420
描述putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial
染色体 / SeqIDChr08 / NC_080394.1
坐标与链方向53914670 - 53916806 / +

ID 对照

NCBI Gene IDLOC130999139
GeneID130999139
locus_tag-
NCBI NameLOC130999139
原始查询SmilChr08G004420

查看完整 ID 对照表

功能注释

来源GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
描述putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial
产物putative pentatricopeptide repeat-containing protein At1g12700%2C mitochondrial
ArabidopsisAT1G12700 (RPF1)
RNA processing FACTOR [Source:NCBI gene (formerly Entrezgene);Acc:837825]
identity=35.5; qcov=0.876; evalue=1.46e-129; confidence=medium
RiceOs10g0497300 (PPR794)
-
identity=32.9; qcov=0.786; evalue=2.73e-90; confidence=low
GOGO:0005515 (protein binding)
KEGG-
PfamPF01535 (PPR); PF12854 (PPR_1); PF13041 (PPR_2); PF13812 (PPR_3); PF17177 (PPR_long); PF23276 (TPR_24)
InterPro-
eggNOG-
NRGeneID:130999139

打开注释模块

亚细胞定位 Top 5

Rank定位位置中文ScoreProtein ID
1 Mitochondrion 线粒体 1.00000 XP_057780621.1
2 Chloroplast 叶绿体 0.20000 XP_057780621.1
3 Nucleus 细胞核 0.00000 XP_057780621.1
4 Chromosome 染色体 0.00000 XP_057780621.1
5 Centromere 着丝粒 0.00000 XP_057780621.1

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
Chr8:53915006 G A EMS_canonical_SNV CDS_variant 4 B118,B37,C33,D7
Chr8:53915037 G GAA 2bp_insertion frameshift_variant 1 B131
Chr8:53915037 G GAA 2bp_insertion CDS_variant 1 B131
Chr8:53915038 G A EMS_canonical_SNV CDS_variant 1 A3
Chr8:53915039 ATT A 2bp_deletion frameshift_variant 1 B131
Chr8:53915039 ATT A 2bp_deletion CDS_variant 1 B131
Chr8:53915068 G A EMS_canonical_SNV CDS_variant 1 A3
Chr8:53915071 AAG A 2bp_deletion frameshift_variant 1 A3
Chr8:53915071 AAG A 2bp_deletion CDS_variant 1 A3
Chr8:53915074 C CTG 2bp_insertion frameshift_variant 1 A3
Chr8:53915074 C CTG 2bp_insertion CDS_variant 1 A3
Chr8:53915140 G A EMS_canonical_SNV CDS_variant 1 B13

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_057780621.1
646 aa
N
1
323
646
PPR_2
PPR
PPR_3
PPR_1
TPR_24
PPR_2
PPR
PPR_3
PPR_1
PPR_2
PPR
PPR_3
PPR_1
PPR_2
PPR
PPR_3
PPR_1
PPR_2
PPR
PPR_1
PPR_2
PPR
PPR_1
PPR_3
PPR_2
PPR
PPR_long
PPR_1
PPR_2
PPR
PPR_3
PPR_1
PPR
PPR_2
TPR_24
PPR_3
PPR_1
PPR_2
PPR
PPR_1
PPR_2
PPR
C
PF13041 PPR_2 187-237 aa PF01535 PPR 227-253 aa PF13812 PPR_3 255-305 aa PF12854 PPR_1 258-286 aa PF23276 TPR_24 258-353 aa PF13041 PPR_2 261-309 aa PF01535 PPR 263-293 aa PF13812 PPR_3 290-339 aa PF12854 PPR_1 291-323 aa PF13041 PPR_2 295-344 aa PF01535 PPR 298-326 aa PF13812 PPR_3 319-370 aa PF12854 PPR_1 328-359 aa PF13041 PPR_2 330-368 aa PF01535 PPR 333-361 aa PF13812 PPR_3 357-413 aa PF12854 PPR_1 363-391 aa PF13041 PPR_2 365-414 aa PF01535 PPR 369-398 aa PF12854 PPR_1 397-425 aa PF13041 PPR_2 400-447 aa PF01535 PPR 404-425 aa PF12854 PPR_1 433-464 aa PF13812 PPR_3 433-480 aa PF13041 PPR_2 435-483 aa PF01535 PPR 438-465 aa PF17177 PPR_long 441-560 aa PF12854 PPR_1 468-497 aa PF13041 PPR_2 470-519 aa PF01535 PPR 474-502 aa PF13812 PPR_3 494-552 aa PF12854 PPR_1 501-532 aa PF01535 PPR 508-537 aa PF13041 PPR_2 510-553 aa PF23276 TPR_24 528-625 aa PF13812 PPR_3 529-583 aa PF12854 PPR_1 536-569 aa PF13041 PPR_2 540-589 aa PF01535 PPR 543-573 aa PF12854 PPR_1 571-603 aa PF13041 PPR_2 575-620 aa PF01535 PPR 578-608 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_057780621.1 Pfam PF13041 PPR_2 Repeat 187 237 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 227 253 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 255 305 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 258 286 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF23276 TPR_24 Repeat 258 353 7.8e-32 110.7 Pentatricopeptide repeat-containing protein
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 261 309 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 263 293 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 290 339 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 291 323 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 295 344 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 298 326 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 319 370 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 328 359 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 330 368 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 333 361 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 357 413 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 363 391 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 365 414 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 369 398 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 397 425 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 400 447 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 404 425 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 433 464 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 433 480 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 435 483 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 438 465 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF17177 PPR_long Repeat 441 560 3.2e-26 92.7 Pentacotripeptide-repeat region of PRORP
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 468 497 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 470 519 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 474 502 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 494 552 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 501 532 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF01535 PPR Repeat 508 537 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 510 553 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF23276 TPR_24 Repeat 528 625 7.8e-32 110.7 Pentatricopeptide repeat-containing protein
XP_057780621.1 Pfam PF13812 PPR_3 Repeat 529 583 8.1e-58 193.1 Pentatricopeptide repeat domain
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 536 569 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 540 589 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 543 573 2.2e-85 275.9 PPR repeat
XP_057780621.1 Pfam PF12854 PPR_1 Repeat 571 603 6.1e-122 397.7 PPR repeat
XP_057780621.1 Pfam PF13041 PPR_2 Repeat 575 620 2.5e-148 482.9 PPR repeat family
XP_057780621.1 Pfam PF01535 PPR Repeat 578 608 2.2e-85 275.9 PPR repeat

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_057924638.1
CTTACCTGCTTTTGCACTTAGCAATCTCTCAAAAAAGAGTGCGAATGAGTCGGAATCACGCTGCCATGATTTTGGGAAGAATTATCTCCAATTCTTCTTTCAATTCATCCACTCTCCCCTTTGCTTCTCTACACTCGTTTCTTGTCAAACCCAAATTCAATTTTGATAATCTCACCCACCAAATTAGATACTTCTACGCCAAACCCAGATTCAATCTTGATAATCTCAGCCACCAAATTAGATCCTTCTCCTCCTATCCC...

CDS

1 records

下载 CDS FASTA
LOC130999139
ATGAGTCGGAATCACGCTGCCATGATTTTGGGAAGAATTATCTCCAATTCTTCTTTCAATTCATCCACTCTCCCCTTTGCTTCTCTACACTCGTTTCTTGTCAAACCCAAATTCAATTTTGATAATCTCACCCACCAAATTAGATACTTCTACGCCAAACCCAGATTCAATCTTGATAATCTCAGCCACCAAATTAGATCCTTCTCCTCCTATCCCAGATTTAATCTTGATAATCTCACCCACCAAATTAGATACTTCTC...

Protein

1 records

下载 Protein FASTA
XP_057780621.1
MSRNHAAMILGRIISNSSFNSSTLPFASLHSFLVKPKFNFDNLTHQIRYFYAKPRFNLDNLSHQIRSFSSYPRFNLDNLTHQIRYFSAYHRFDFESIREPNDAVALFRDLMRTEPLPSVKLFSKLLSAVVKMRQYSLALHLIDEMLQRDVPVDHYILSIAIDCYCRLKKPDFGFAILGIFFKRGYEPTVVTFTILIKGLLLVGRIPEAAKVLWKLSVYQLCEPNERTYSTMIDGICKAVGTLKALELLCLLEKEKGICKL...

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

跳转到基因组浏览器