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2024-04-26 21:43:20, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_002128 3428 bp mRNA linear PRI 07-JUL-2013
DEFINITION Homo sapiens high mobility group box 1 (HMGB1), mRNA.
ACCESSION NM_002128
VERSION NM_002128.4 GI:118918424
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 3428)
AUTHORS Zandarashvili,L., Sahu,D., Lee,K., Lee,Y.S., Singh,P.,
Rajarathnam,K. and Iwahara,J.
TITLE Real-time kinetics of high-mobility group box 1 (HMGB1) oxidation
in extracellular fluids studied by in situ protein NMR spectroscopy
JOURNAL J. Biol. Chem. 288 (17), 11621-11627 (2013)
PUBMED 23447529
REMARK GeneRIF: Real-time kinetics of high-mobility group box 1 (HMGB1)
oxidation in extracellular fluids studied by in situ protein NMR
spectroscopy.
REFERENCE 2 (bases 1 to 3428)
AUTHORS Arrigo,T., Chirico,V., Salpietro,V., Munafo,C., Ferrau,V.,
Gitto,E., Lacquaniti,A. and Salpietro,C.
TITLE High-mobility group protein B1: a new biomarker of metabolic
syndrome in obese children
JOURNAL Eur. J. Endocrinol. 168 (4), 631-638 (2013)
PUBMED 23384711
REMARK GeneRIF: HMGB1 serum levels were statistically higher in obese
children compared to controls.
Publication Status: Online-Only
REFERENCE 3 (bases 1 to 3428)
AUTHORS Little,A.J., Corbett,E., Ortega,F. and Schatz,D.G.
TITLE Cooperative recruitment of HMGB1 during V(D)J recombination through
interactions with RAG1 and DNA
JOURNAL Nucleic Acids Res. 41 (5), 3289-3301 (2013)
PUBMED 23325855
REMARK GeneRIF: HMGB1 binds more tightly to a RAG1-DNA complex over RAG1
or DNA alone.
REFERENCE 4 (bases 1 to 3428)
AUTHORS Moreno,J.A., Sastre,C., Madrigal-Matute,J., Munoz-Garcia,B.,
Ortega,L., Burkly,L.C., Egido,J., Martin-Ventura,J.L. and
Blanco-Colio,L.M.
TITLE HMGB1 expression and secretion are increased via TWEAK-Fn14
interaction in atherosclerotic plaques and cultured monocytes
JOURNAL Arterioscler. Thromb. Vasc. Biol. 33 (3), 612-620 (2013)
PUBMED 23288170
REMARK GeneRIF: TWEAK/Fn14 can regulate expression and secretion of HMGB1
in monocytes/macrophages, participating in the inflammatory
response associated with atherosclerotic plaque development.
REFERENCE 5 (bases 1 to 3428)
AUTHORS Mao,X.J., Wang,G.F., Chen,Z.J., Wang,L.N., Zhang,J.B. and Wang,H.L.
TITLE Expression of HMGB1 and its clinical significance in T-cell
lymphoma
JOURNAL Asian Pac. J. Cancer Prev. 13 (11), 5569-5571 (2012)
PUBMED 23317219
REMARK GeneRIF: High expression of HMGB1 is associated with T-cell
lymphoma.
REFERENCE 6 (bases 1 to 3428)
AUTHORS Ge,H. and Roeder,R.G.
TITLE The high mobility group protein HMG1 can reversibly inhibit class
II gene transcription by interaction with the TATA-binding protein
JOURNAL J. Biol. Chem. 269 (25), 17136-17140 (1994)
PUBMED 8006019
REFERENCE 7 (bases 1 to 3428)
AUTHORS Paull,T.T., Haykinson,M.J. and Johnson,R.C.
TITLE The nonspecific DNA-binding and -bending proteins HMG1 and HMG2
promote the assembly of complex nucleoprotein structures
JOURNAL Genes Dev. 7 (8), 1521-1534 (1993)
PUBMED 8339930
REFERENCE 8 (bases 1 to 3428)
AUTHORS Parkkinen,J. and Rauvala,H.
TITLE Interactions of plasminogen and tissue plasminogen activator (t-PA)
with amphoterin. Enhancement of t-PA-catalyzed plasminogen
activation by amphoterin
JOURNAL J. Biol. Chem. 266 (25), 16730-16735 (1991)
PUBMED 1909331
REFERENCE 9 (bases 1 to 3428)
AUTHORS Wen,L., Huang,J.K., Johnson,B.H. and Reeck,G.R.
TITLE A human placental cDNA clone that encodes nonhistone chromosomal
protein HMG-1
JOURNAL Nucleic Acids Res. 17 (3), 1197-1214 (1989)
PUBMED 2922262
REFERENCE 10 (bases 1 to 3428)
AUTHORS Bernues,J., Espel,E. and Querol,E.
TITLE Identification of the core-histone-binding domains of HMG1 and HMG2
JOURNAL Biochim. Biophys. Acta 866 (4), 242-251 (1986)
PUBMED 3697355
COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
AA430980.1, BC030981.1 and AL353648.27.
On Dec 7, 2006 this sequence version replaced gi:31982879.
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 :: BC030981.1, AK291494.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
ERS025084, ERS025088 [ECO:0000348]
##Evidence-Data-END##
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-68 AA430980.1 22-89
69-837 BC030981.1 1-769
838-3428 AL353648.27 16116-18706 c
FEATURES Location/Qualifiers
source 1..3428
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/chromosome="13"
/map="13q12"
gene 1..3428
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="high mobility group box 1"
/db_xref="GeneID:3146"
/db_xref="HGNC:4983"
/db_xref="HPRD:01228"
/db_xref="MIM:163905"
exon 1..149
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/inference="alignment:Splign:1.39.8"
exon 150..313
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/inference="alignment:Splign:1.39.8"
misc_feature 155..157
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="upstream in-frame stop codon"
CDS 164..811
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="Sulfoglucuronyl carbohydrate binding protein;
Amphoterin; high-mobility group (nonhistone chromosomal)
protein 1; high-mobility group box 1; high mobility group
protein 1; HMG-1"
/codon_start=1
/product="high mobility group protein B1"
/protein_id="NP_002119.1"
/db_xref="GI:4504425"
/db_xref="CCDS:CCDS9335.1"
/db_xref="GeneID:3146"
/db_xref="HGNC:4983"
/db_xref="HPRD:01228"
/db_xref="MIM:163905"
/translation="
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE
"
misc_feature 179..391
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="HMGB-UBF_HMG-box, class II and III members of the
HMG-box superfamily of DNA-binding proteins. These
proteins bind the minor groove of DNA in a non-sequence
specific fashion and contain two or more tandem HMG boxes.
Class II members include non-histone...; Region:
HMGB-UBF_HMG-box; cd01390"
/db_xref="CDD:238686"
misc_feature order(185..187,200..205,209..214,221..226,233..235,
245..247,290..292,299..301,308..310,365..367)
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:238686"
misc_feature 251..253
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/experiment="experimental evidence, no additional details
recorded"
/note="N6-acetyllysine; propagated from
UniProtKB/Swiss-Prot (P09429.3); acetylation site"
misc_feature 266..268
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/experiment="experimental evidence, no additional details
recorded"
/note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
(P09429.3); phosphorylation site"
misc_feature 446..>592
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="High Mobility Group (HMG)-box is found in a variety
of eukaryotic chromosomal proteins and transcription
factors. HMGs bind to the minor groove of DNA and have
been classified by DNA binding preferences. Two
phylogenically distinct groups of Class I...; Region:
HMG-box; cd00084"
/db_xref="CDD:238037"
misc_feature order(452..454,458..463,467..472,479..484,491..493,
503..505,542..544,551..553,560..562)
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:238037"
misc_feature 461..463
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/experiment="experimental evidence, no additional details
recorded"
/note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
(P09429.3); phosphorylation site"
STS 267..1116
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/standard_name="HMGB1_1600"
/db_xref="UniSTS:277311"
exon 314..459
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/inference="alignment:Splign:1.39.8"
variation 358
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="g"
/db_xref="dbSNP:983723"
STS 364..580
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/standard_name="MARC_26602-26603:1033757772:1"
/db_xref="UniSTS:269038"
variation 383
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="g"
/replace="t"
/db_xref="dbSNP:11546137"
exon 460..634
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/inference="alignment:Splign:1.39.8"
variation 472
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="c"
/replace="t"
/db_xref="dbSNP:1060348"
variation 628
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="c"
/replace="t"
/db_xref="dbSNP:1929606"
exon 635..3428
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/inference="alignment:Splign:1.39.8"
variation 724..732
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace=""
/replace="ggaggaaga"
/db_xref="dbSNP:56128500"
variation 775..783
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace=""
/replace="agatgaaga"
/db_xref="dbSNP:55678359"
variation 796
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace=""
/replace="gat"
/db_xref="dbSNP:56178645"
variation 837..838
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace=""
/replace="t"
/db_xref="dbSNP:41376448"
STS 857..1009
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/standard_name="GDB:554977"
/db_xref="UniSTS:157665"
variation 1978
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="g"
/db_xref="dbSNP:4097504"
variation 2081
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="c"
/replace="g"
/db_xref="dbSNP:4097505"
variation 2164
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="g"
/db_xref="dbSNP:4097506"
variation 2212
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="t"
/db_xref="dbSNP:1854919"
variation 3073
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="g"
/db_xref="dbSNP:1045411"
STS 3123..3311
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/standard_name="RH91371"
/db_xref="UniSTS:85878"
STS 3236..3330
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/standard_name="STS-N92507"
/db_xref="UniSTS:933"
variation 3263
/gene="HMGB1"
/gene_synonym="HMG1; HMG3; SBP-1"
/replace="a"
/replace="g"
/db_xref="dbSNP:12589"
ORIGIN
tggagagtaatgttacagagcggagagagtgaggaggctgcgtctggctcccgctctcacagccattgcagtacattgagctccatagagacagcgccggggcaagtgagagccggacgggcactgggcgactctgtgcctcgctgaggaaaaataactaaacatgggcaaaggagatcctaagaagccgagaggcaaaatgtcatcatatgcattttttgtgcaaacttgtcgggaggagcataagaagaagcacccagatgcttcagtcaacttctcagagttttctaagaagtgctcagagaggtggaagaccatgtctgctaaagagaaaggaaaatttgaagatatggcaaaagcggacaaggcccgttatgaaagagaaatgaaaacctatatccctcccaaaggggagacaaaaaagaagttcaaggatcccaatgcacccaagaggcctccttcggccttcttcctcttctgctctgagtatcgcccaaaaatcaaaggagaacatcctggcctgtccattggtgatgttgcgaagaaactgggagagatgtggaataacactgctgcagatgacaagcagccttatgaaaagaaggctgcgaagctgaaggaaaaatacgaaaaggatattgctgcatatcgagctaaaggaaagcctgatgcagcaaaaaagggagttgtcaaggctgaaaaaagcaagaaaaagaaggaagaggaggaagatgaggaagatgaagaggatgaggaggaggaggaagatgaagaagatgaagatgaagaagaagatgatgatgatgaataagttggttctagcgcagttttttttttcttgtctataaagcatttaacccccctgtacacaactcactccttttaaagaaaaaaattgaaatgtaaggctgtgtaagatttgtttttaaactgtacagtgtctttttttgtatagttaacacactaccgaatgtgtctttagatagccctgtcctggtggtattttcaatagccactaaccttgcctggtacagtatgggggttgtaaattggcatggaaatttaaagcaggttcttgttggtgcacagcacaaattagttatatatggggatggtagttttttcatcttcagttgtctctgatgcagcttatacgaaataattgttgttctgttaactgaataccactctgtaattgcaaaaaaaaaaaaaaagttgcagctgttttgttgacattctgaatgcttctaagtaaatacaattttttttattagtattgttgtccttttcataggtctgaaatttttcttcttgaggggaagctagtcttttgcttttgcccattttgaatcacatgaattattacagtgtttatcctttcatatagttagctaataaaaagcttttgtctacacaccctgcatatcataatgggggtaaagttaagttgagatagttttcatccataactgaacatccaaaatcttgatcagttaagaaatttcacatagcccacttacatttacaaactgaagagtaatcaatctactcaaagcatgggattattagaatcaaacattttgaaagtctgtccttgaaggactaatagaaaagtatgttctaacctttacatgaggactctattctttaactcccattaccatgtaatggcagttatattttgcagttcccacattaaagaagacctgagaatgtatccccaaaagcgtgagcttaaaatacaagactgccatattaaattttttgttgacattagtctcagtgaagactatgaaaatgctggctatagatgtcttttcccatttatctaaatatggactgctcaggaaacgagactttccattacaagtatttttaattaattgggccagcttttcaaacaaagatgccacattcaaaatagggtatattttcctatattacggtttgcccctttataaatccaagtagataggaagaaagaagacaaactttgcatctcagtatgaattattcaatttatttgaatgatttttctttacaaaacaaactcattcattagtcatgtttatctgcttaggagtttagggaacaatttggcaattttgtggttttcgagattatcgttttcttaaagtgccagtattttaaaatagcgttcttgtaattttacacgcttttgtgatggagtgctgttttgttatataatttagacttggattctttccatttgcatttgtttatgtaatttcaggaggaatactgaacatctgagtcctggatgatactaataaactaataattgcagaggttttaaatactagttaaatggctttcacttaagaacttaagattttgttacatatttttaaatcttgtttctaataatacctcttagcagtaccttttaaataagtataagggatggcaaagtttttccctttaaaaatactcactttatgcttataaataggttaatgggctgataaaaggttttgtcaaacattgcaagtattcggtgctatatataaaggaggaaaaactagttttactttcagaatgatttaaacaagatttttaaaaacaagatacatgcaagcgaacagcagggttagtgataggctgcaattgtgtcgaacatcagattttttgttaagaggagcaaatgactcaatctgatttagatggaagtttctactgtatagaaatcaccattaatcaccaacattaataattctgatccatttaaaatgaattctggctcaaggagaatttgtaactttagtaggtacgtcatgacaactaccatttttttaagatgttgagaatgggaacagtttttttagggtttattcttgaccacagatcttaagaaaatggacaaaacccctcttcaatctgaagattagtatggtttggtgttctaacagtatcccctagaagttggatgtctaaaactcaagtaaatggaagtgggaggcaatttagataagtgtaaagccttgtaactgaagatgattttttttagaaagtgtatagaaactattttaatgccaagatagttacagtgctgtggggtttaaagactttgttgacatcaagaaaagactaaatctataattaattgggccaacttttaaaatgaagatgctttttaaaactaatgaactaagatgtataaatcttagtttttttgtattttaaagataggcatatggcatattgattaacgagtcaaatttcctaactttgctgtgcaaaggttgagagctattgctgattagttaccacagttctgatgatcgtcccatcacagtgttgttaatgtttgctgtatttattaattttcttaaagtgaaatctgaaaaatgaaatttgtgtgtcctgtgtacccgaggggtaatgattaaatgataaagataagaaaa
//
ANNOTATIONS from NCBI Entrez Gene (20130726):
GeneID:3146 -> Molecular function: GO:0003684 [damaged DNA binding] evidence: ISS
GeneID:3146 -> Molecular function: GO:0003690 [double-stranded DNA binding] evidence: ISS
GeneID:3146 -> Molecular function: GO:0003697 [single-stranded DNA binding] evidence: ISS
GeneID:3146 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IDA
GeneID:3146 -> Molecular function: GO:0005125 [cytokine activity] evidence: ISS
GeneID:3146 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
GeneID:3146 -> Molecular function: GO:0008134 [transcription factor binding] evidence: IPI
GeneID:3146 -> Molecular function: GO:0008301 [DNA binding, bending] evidence: IMP
GeneID:3146 -> Molecular function: GO:0008301 [DNA binding, bending] evidence: ISS
GeneID:3146 -> Molecular function: GO:0042056 [chemoattractant activity] evidence: ISS
GeneID:3146 -> Molecular function: GO:0050786 [RAGE receptor binding] evidence: ISS
GeneID:3146 -> Molecular function: GO:0070491 [repressing transcription factor binding] evidence: IPI
GeneID:3146 -> Biological process: GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] evidence: IMP
GeneID:3146 -> Biological process: GO:0001773 [myeloid dendritic cell activation] evidence: ISS
GeneID:3146 -> Biological process: GO:0002407 [dendritic cell chemotaxis] evidence: ISS
GeneID:3146 -> Biological process: GO:0002437 [inflammatory response to antigenic stimulus] evidence: IEP
GeneID:3146 -> Biological process: GO:0006265 [DNA topological change] evidence: ISS
GeneID:3146 -> Biological process: GO:0006288 [base-excision repair, DNA ligation] evidence: IDA
GeneID:3146 -> Biological process: GO:0006309 [apoptotic DNA fragmentation] evidence: TAS
GeneID:3146 -> Biological process: GO:0006310 [DNA recombination] evidence: ISS
GeneID:3146 -> Biological process: GO:0006357 [regulation of transcription from RNA polymerase II promoter] evidence: IDA
GeneID:3146 -> Biological process: GO:0006915 [apoptotic process] evidence: TAS
GeneID:3146 -> Biological process: GO:0006921 [cellular component disassembly involved in execution phase of apoptosis] evidence: TAS
GeneID:3146 -> Biological process: GO:0017055 [negative regulation of RNA polymerase II transcriptional preinitiation complex assembly] evidence: IDA
GeneID:3146 -> Biological process: GO:0031175 [neuron projection development] evidence: ISS
GeneID:3146 -> Biological process: GO:0033151 [V(D)J recombination] evidence: IDA
GeneID:3146 -> Biological process: GO:0043065 [positive regulation of apoptotic process] evidence: IDA
GeneID:3146 -> Biological process: GO:0043280 [positive regulation of cysteine-type endopeptidase activity involved in apoptotic process] evidence: IDA
GeneID:3146 -> Biological process: GO:0043388 [positive regulation of DNA binding] evidence: IDA
GeneID:3146 -> Biological process: GO:0045087 [innate immune response] evidence: TAS
GeneID:3146 -> Biological process: GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] evidence: IDA
GeneID:3146 -> Biological process: GO:0050918 [positive chemotaxis] evidence: ISS
GeneID:3146 -> Biological process: GO:0051103 [DNA ligation involved in DNA repair] evidence: ISS
GeneID:3146 -> Biological process: GO:2000426 [negative regulation of apoptotic cell clearance] evidence: IEA
GeneID:3146 -> Cellular component: GO:0000793 [condensed chromosome] evidence: IDA
GeneID:3146 -> Cellular component: GO:0005576 [extracellular region] evidence: TAS
GeneID:3146 -> Cellular component: GO:0005615 [extracellular space] evidence: IDA
GeneID:3146 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
GeneID:3146 -> Cellular component: GO:0005654 [nucleoplasm] evidence: TAS
GeneID:3146 -> Cellular component: GO:0009986 [cell surface] evidence: IDA
GeneID:3146 -> Cellular component: GO:0017053 [transcriptional repressor complex] evidence: IDA
by
@meso_cacase at
DBCLS
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