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[求助]
NCBI中某個基因的mRNA序列是如何得到的？？ 已有1人參與
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NCBI數(shù)據(jù)庫中可以查一個基因的信息，包括全長mRNA序列和蛋白序列。 我想問下，1. 一個基因的mRNA序列是如何確定的？ 2. mRNA序列中還會給出哪部分是CDS區(qū)，那CDS區(qū)又是如何確定的？ 一直以為是從mRNA第一個堿基往后找，第一個ATG就是CDS開始位置，但是不是這樣，查詢NCBI數(shù)據(jù)庫時發(fā)現(xiàn)很多基因給出的CDS區(qū)域之前也有好幾個ATG。 請生物信息學的同學或懂行的同學不吝賜教，謝謝！ |
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liuderong
鐵桿木蟲 (正式寫手)
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2樓2015-06-02 17:13:41
3樓2015-06-02 19:24:31
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這里有一個基因的NCBI給出的mRNA序列頁面，能告訴我怎么看是機器注釋還是人工注釋呢？ 謝謝了~~ http://www.ncbi.nlm.nih.gov/nuccore/NM_000600.3 Homo sapiens interleukin 6 (IL6), mRNA NCBI Reference Sequence: NM_000600.3 FASTA Graphics Go to: LOCUS NM_000600 1201 bp mRNA linear PRI 15-MAR-2015 DEFINITION Homo sapiens interleukin 6 (IL6), mRNA. ACCESSION NM_000600 VERSION NM_000600.3 GI:224831235 KEYWORDS RefSeq. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1201) AUTHORS Schulz I, Engel C, Niestroj AJ, Kehlen A, Rahfeld JU, Kleinschmidt M, Lehmann K, Rossner S and Demuth HU. TITLE A non-canonical function of eukaryotic elongation factor 1A1: regulation of interleukin-6 expression JOURNAL Biochim. Biophys. Acta 1843 (5), 965-975 (2014) PUBMED 24487064 REMARK GeneRIF: eukaryotic elongation factor 1A1 (eEF1A1) was verified as the relevant target of HAK bioactivity. eEF1A1 forms complexes with STAT3 and PKCdelta, which are crucial for STAT3(S727) phosphorylation and for NF-kappaB/STAT3-enhanced interleukin-6 expression REFERENCE 2 (bases 1 to 1201) AUTHORS Yang X, Feng L, Li C and Li Y. TITLE Association of IL-6-174G > C and -572C > G polymorphisms with risk of young ischemic stroke patients JOURNAL Gene 539 (2), 258-262 (2014) PUBMED 24486505 REMARK GeneRIF: IL-6-174G > C and -572C > G polymorphisms are associated with the risk of ischemic stroke. REFERENCE 3 (bases 1 to 1201) AUTHORS Wada TT, Araki Y, Sato K, Aizaki Y, Yokota K, Kim YT, Oda H, Kurokawa R and Mimura T. TITLE Aberrant histone acetylation contributes to elevated interleukin-6 production in rheumatoid arthritis synovial fibroblasts JOURNAL Biochem. Biophys. Res. Commun. 444 (4), 682-686 (2014) PUBMED 24513290 REMARK GeneRIF: IL-6 production is elevated in rheumatoid arthritis synovial fibroblasts. Histone H3 acetylation is increased in the IL-6 promoter. REFERENCE 4 (bases 1 to 1201) AUTHORS Mitchell AM, Possel P, Sjogren E and Kristenson M. TITLE Hopelessness the 'active ingredient'? Associations of hopelessness and depressive symptoms with interleukin-6 JOURNAL Int J Psychiatry Med 46 (1), 109-117 (2013) PUBMED 24547612 REMARK GeneRIF: Depressive symptoms and hopelessness are not independent predictors of IL-6 levels. REFERENCE 5 (bases 1 to 1201) AUTHORS Kikkert R, de Groot ER and Aarden LA. TITLE Cytokine induction by pyrogens: comparison of whole blood, mononuclear cells, and TLR-transfectants JOURNAL J. Immunol. Methods 336 (1), 45-55 (2008) PUBMED 18456276 REFERENCE 6 (bases 1 to 1201) AUTHORS Dinarello CA. TITLE Infection, fever, and exogenous and endogenous pyrogens: some concepts have changed JOURNAL J. Endotoxin Res. 10 (4), 201-222 (2004) PUBMED 15373964 REMARK Review article REFERENCE 7 (bases 1 to 1201) AUTHORS Chen QY. TITLE [Stable and efficient expression of human interleukin-6 cDNA in mammalian cells after gene transfer] JOURNAL Zhonghua Zhong Liu Za Zhi 14 (5), 340-344 (1992) PUBMED 1291290 REFERENCE 8 (bases 1 to 1201) AUTHORS May LT and Sehgal PB. TITLE Phosphorylation of interleukin-6 at serine54: an early event in the secretory pathway in human fibroblasts JOURNAL Biochem. Biophys. Res. Commun. 185 (2), 524-530 (1992) PUBMED 1610348 REFERENCE 9 (bases 1 to 1201) AUTHORS May LT, Shaw JE, Khanna AK, Zabriskie JB and Sehgal PB. TITLE Marked cell-type-specific differences in glycosylation of human interleukin-6 JOURNAL Cytokine 3 (3), 204-211 (1991) PUBMED 1883960 REFERENCE 10 (bases 1 to 1201) AUTHORS Sandler,N.H. TITLE A case of meningitis admitted as schizophrenia JOURNAL J Ky Med Assoc 73 (1), 25-26 (1975) PUBMED 1113021 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from AK301141.1, BC015511.1 and AA721478.1. This sequence is a reference standard in the RefSeqGene project. On Mar 11, 2009 this sequence version replaced gi:155369258. Summary: This gene encodes a cytokine that functions in inflammation and the maturation of B cells. In addition, the encoded protein has been shown to be an endogenous pyrogen capable of inducing fever in people with autoimmune diseases or infections. The protein is primarily produced at sites of acute and chronic inflammation, where it is secreted into the serum and induces a transcriptional inflammatory response through interleukin 6 receptor, alpha. The functioning of this gene is implicated in a wide variety of inflammation-associated disease states, including suspectibility to diabetes mellitus and systemic juvenile rheumatoid arthritis. [provided by RefSeq, Jun 2011]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: X04430.1, BC015511.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: complete on the 3' end. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-67 AK301141.1 1-67 68-1180 BC015511.1 1-1113 1181-1201 AA721478.1 1-21 c FEATURES Location/Qualifiers source 1..1201 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="7" /map="7p21" gene 1..1201 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /note="interleukin 6" /db_xref="GeneID:3569" /db_xref="HGNC:HGNC:6018" /db_xref="HPRD:00970" /db_xref="MIM:147620" exon 1..135 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /inference="alignment:Splign:1.39.8" misc_feature 30..32 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /note="upstream in-frame stop codon" CDS 117..755 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /note="hybridoma growth factor; interleukin BSF-2; B-cell differentiation factor; CTL differentiation factor; CDF; IFN-beta-2; interferon beta-2; B-cell stimulatory factor 2; interferon, beta 2" /codon_start=1 /product="interleukin-6 precursor" /protein_id="NP_000591.1" /db_xref="GI:10834984" /db_xref="CCDS:CCDS5375.1" /db_xref="GeneID:3569" /db_xref="HGNC:HGNC:6018" /db_xref="HPRD:00970" /db_xref="MIM:147620" /translation="MNSFSTSAFGPVAFSLGLLLVLPAAFPAPVPPGEDSKDVAAPHR QPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCF QSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKN LDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM" sig_peptide 117..203 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" mat_peptide 204..752 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /product="interleukin-6" exon 136..326 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /inference="alignment:Splign:1.39.8" exon 327..440 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /inference="alignment:Splign:1.39.8" exon 441..587 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /inference="alignment:Splign:1.39.8" exon 588..1184 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /inference="alignment:Splign:1.39.8" STS 789..1035 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /standard_name="D7S2743" /db_xref="UniSTS:20883" STS 819..1078 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" /standard_name="STS-M14584" /db_xref="UniSTS:73733" regulatory 1156..1161 /regulatory_class="polyA_signal_sequence" /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" polyA_site 1184 /gene="IL6" /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6" ORIGIN 1 aatattagag tctcaacccc caataaatat aggactggag atgtctgagg ctcattctgc 61 cctcgagccc accgggaacg aaagagaagc tctatctccc ctccaggagc ccagctatga 121 actccttctc cacaagcgcc ttcggtccag ttgccttctc cctggggctg ctcctggtgt 181 tgcctgctgc cttccctgcc ccagtacccc caggagaaga ttccaaagat gtagccgccc 241 cacacagaca gccactcacc tcttcagaac gaattgacaa acaaattcgg tacatcctcg 301 acggcatctc agccctgaga aaggagacat gtaacaagag taacatgtgt gaaagcagca 361 aagaggcact ggcagaaaac aacctgaacc ttccaaagat ggctgaaaaa gatggatgct 421 tccaatctgg attcaatgag gagacttgcc tggtgaaaat catcactggt cttttggagt 481 ttgaggtata cctagagtac ctccagaaca gatttgagag tagtgaggaa caagccagag 541 ctgtgcagat gagtacaaaa gtcctgatcc agttcctgca gaaaaaggca aagaatctag 601 atgcaataac cacccctgac ccaaccacaa atgccagcct gctgacgaag ctgcaggcac 661 agaaccagtg gctgcaggac atgacaactc atctcattct gcgcagcttt aaggagttcc 721 tgcagtccag cctgagggct cttcggcaaa tgtagcatgg gcacctcaga ttgttgttgt 781 taatgggcat tccttcttct ggtcagaaac ctgtccactg ggcacagaac ttatgttgtt 841 ctctatggag aactaaaagt atgagcgtta ggacactatt ttaattattt ttaatttatt 901 aatatttaaa tatgtgaagc tgagttaatt tatgtaagtc atatttatat ttttaagaag 961 taccacttga aacattttat gtattagttt tgaaataata atggaaagtg gctatgcagt 1021 ttgaatatcc tttgtttcag agccagatca tttcttggaa agtgtaggct tacctcaaat 1081 aaatggctaa cttatacata tttttaaaga aatatttata ttgtatttat ataatgtata 1141 aatggttttt ataccaataa atggcatttt aaaaaattca gcaaaaaaaa aaaaaaaaaa 1201 a // |
4樓2015-06-02 19:38:50
liuderong
鐵桿木蟲 (正式寫手)
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5樓2015-06-02 21:07:39
liuderong
鐵桿木蟲 (正式寫手)
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6樓2015-06-02 21:11:36
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