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[求助] NCBI中某個(gè)基因的mRNA序列是如何得到的？？已有1人參與

NCBI數(shù)據(jù)庫(kù)中可以查一個(gè)基因的信息，包括全長(zhǎng)mRNA序列和蛋白序列。我想問(wèn)下，1. 一個(gè)基因的mRNA序列是如何確定的？ 2. mRNA序列中還會(huì)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(gè)堿基往后找，第一個(gè)ATG就是CDS開(kāi)始位置，但是不是這樣，查詢NCBI數(shù)據(jù)庫(kù)時(shí)發(fā)現(xiàn)很多基因給出的CDS區(qū)域之前也有好幾個(gè)ATG。

請(qǐng)生物信息學(xué)的同學(xué)或懂行的同學(xué)不吝賜教，謝謝！

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1樓 2015-06-02 16:45:20

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【答案】應(yīng)助回帖

感謝參與，應(yīng)助指數(shù) +1

應(yīng)該是分人工注釋和機(jī)器注釋兩種方法得到的。人工注釋是研究人員根據(jù)實(shí)驗(yàn)數(shù)據(jù)來(lái)確定開(kāi)放閱讀框，這種方法準(zhǔn)確度高但是獲得的數(shù)據(jù)很少、速度很慢，無(wú)法跟上高通量測(cè)序短時(shí)間內(nèi)獲得大量序列的要求；機(jī)器注釋是人們根據(jù)目前已知的基因特征，比如同源相似等，開(kāi)發(fā)一系列的自動(dòng)注釋程序，然后讓計(jì)算機(jī)分析，目前大部分基因都是用這種方法注釋的。NCBI的頁(yè)面里應(yīng)該有描述。

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2樓2015-06-02 17:13:41

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引用回帖:

2樓: Originally posted by liuderong at 2015-06-02 17:13:41
應(yīng)該是分人工注釋和機(jī)器注釋兩種方法得到的。人工注釋是研究人員根據(jù)實(shí)驗(yàn)數(shù)據(jù)來(lái)確定開(kāi)放閱讀框，這種方法準(zhǔn)確度高但是獲得的數(shù)據(jù)很少、速度很慢，無(wú)法跟上高通量測(cè)序短時(shí)間內(nèi)獲得大量序列的要求；機(jī)器注釋是人們根據(jù) ...

也就是說(shuō)機(jī)器注釋的mRNA序列并不代表就是真實(shí)的序列，對(duì)吧？只有來(lái)自實(shí)驗(yàn)數(shù)據(jù)，如5‘ RACE ,3' RACE等鑒定出一個(gè)mRNA的全長(zhǎng)序列還是其真實(shí)序列。是不是這樣

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3樓2015-06-02 19:24:31

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引用回帖:

這里有一個(gè)基因的NCBI給出的mRNA序列頁(yè)面，能告訴我怎么看是機(jī)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
//

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4樓2015-06-02 19:38:50

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有好幾篇參考文獻(xiàn)了，說(shuō)明有實(shí)驗(yàn)數(shù)據(jù)支持，即使最開(kāi)始是機(jī)器注釋的，那到現(xiàn)在這個(gè)階段也算是人工驗(yàn)證了。

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5樓2015-06-02 21:07:39

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liuderong

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3樓: Originally posted by 89509306 at 2015-06-02 19:24:31
也就是說(shuō)機(jī)器注釋的mRNA序列并不代表就是真實(shí)的序列，對(duì)吧？只有來(lái)自實(shí)驗(yàn)數(shù)據(jù)，如5‘ RACE ,3' RACE等鑒定出一個(gè)mRNA的全長(zhǎng)序列還是其真實(shí)序列。是不是這樣...

機(jī)器注釋的確僅僅是一個(gè)參考，不過(guò)目前的算法還算成熟，很多預(yù)測(cè)的都是實(shí)際存在的。如果有確切的實(shí)驗(yàn)數(shù)據(jù)說(shuō)明機(jī)器注釋的有問(wèn)題，那就應(yīng)該以實(shí)驗(yàn)為準(zhǔn)。

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6樓2015-06-02 21:11:36

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