Human Gene BATF3 (uc001hjl.2) Description and Page Index
  Description: Homo sapiens basic leucine zipper transcription factor, ATF-like 3 (BATF3), mRNA.
RefSeq Summary (NM_018664): This gene encodes a member of the basic leucine zipper protein family. The encoded protein functions as a transcriptional repressor when heterodimerizing with JUN. The protein may play a role in repression of interleukin-2 and matrix metalloproteinase-1 transcription.[provided by RefSeq, Feb 2009]. 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 :: SRR1163655.579318.1, AF255346.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2149004, SAMN03465406 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000243440.2/ ENSP00000243440.1 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:212,859,759-212,873,327 Size: 13,569 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:212,860,133-212,873,104 Size: 12,972 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:212,859,759-212,873,327)mRNA (may differ from genome)Protein (127 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Basic leucine zipper transcriptional factor ATF-like 3; Short=B-ATF-3; AltName: Full=21 kDa small nuclear factor isolated from T-cells; AltName: Full=Jun dimerization protein p21SNFT;
FUNCTION: AP-1 family transcription factor that controls the differentiation of CD8(+) thymic conventional dendritic cells in the immune system. Required for development of CD8-alpha(+) classical dendritic cells (cDCs) and related CD103(+) dendritic cells that cross-present antigens to CD8 T-cells and produce interleukin-12 (IL12) in response to pathogens (By similarity). Acts via the formation of a heterodimer with JUN family proteins that recognizes and binds DNA sequence 5'-TGA[CG]TCA-3' and regulates expression of target genes.
SUBUNIT: Heterodimer; heterodimerizes with JUN family proteins. Interacts with JUN.
SIMILARITY: Belongs to the bZIP family.
SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.52 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 61.11 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -107.00223-0.480 Picture PostScript Text
3' UTR -135.72374-0.363 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004827 - bZIP
IPR000837 - Leuzip_Fos

Pfam Domains:
PF00170 - bZIP transcription factor
PF03131 - bZIP Maf transcription factor
PF07716 - Basic region leucine zipper

ModBase Predicted Comparative 3D Structure on Q9NR55
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0009615 response to virus
GO:0043011 myeloid dendritic cell differentiation
GO:0097028 dendritic cell differentiation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AK093671 - Homo sapiens cDNA FLJ36352 fis, clone THYMU2007258.
AX748255 - Sequence 1780 from Patent EP1308459.
AF255346 - Homo sapiens Jun dimerization protein p21SNFT (SNFT) mRNA, complete cds.
AK094854 - Homo sapiens cDNA FLJ37535 fis, clone BRCAN2021669.
BC117489 - Homo sapiens basic leucine zipper transcription factor, ATF-like 3, mRNA (cDNA clone MGC:151098 IMAGE:40126040), complete cds.
BC117491 - Homo sapiens basic leucine zipper transcription factor, ATF-like 3, mRNA (cDNA clone MGC:151100 IMAGE:40126042), complete cds.
HQ258061 - Synthetic construct Homo sapiens clone IMAGE:100072370 basic leucine zipper transcription factor, ATF-like 3 (BATF3) gene, encodes complete protein.
KJ894205 - Synthetic construct Homo sapiens clone ccsbBroadEn_03599 BATF3 gene, encodes complete protein.
AB463432 - Synthetic construct DNA, clone: pF1KB7515, Homo sapiens BATF3 gene for basic leucine zipper transcription factor, ATF-like 3, without stop codon, in Flexi system.
JD348379 - Sequence 329403 from Patent EP1572962.
JD164594 - Sequence 145618 from Patent EP1572962.
JD147525 - Sequence 128549 from Patent EP1572962.
JD281822 - Sequence 262846 from Patent EP1572962.
JD394334 - Sequence 375358 from Patent EP1572962.
JD452156 - Sequence 433180 from Patent EP1572962.
JD295547 - Sequence 276571 from Patent EP1572962.
JD240171 - Sequence 221195 from Patent EP1572962.
JD083804 - Sequence 64828 from Patent EP1572962.
JD532413 - Sequence 513437 from Patent EP1572962.
JD387569 - Sequence 368593 from Patent EP1572962.
JD541125 - Sequence 522149 from Patent EP1572962.
JD459034 - Sequence 440058 from Patent EP1572962.
JD057790 - Sequence 38814 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BATF3_HUMAN, NM_018664, NP_061134, Q9NR55, SNFT
UCSC ID: uc001hjl.2
RefSeq Accession: NM_018664
Protein: Q9NR55 (aka BATF3_HUMAN)
CCDS: CCDS1508.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_018664.2
exon count: 3CDS single in 3' UTR: no RNA size: 992
ORF size: 384CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 941.00frame shift in genome: no % Coverage: 98.89
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
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