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Aliases for HIST1H4D Gene

Aliases for HIST1H4D Gene

  • Histone Cluster 1 H4 Family Member D 2 3 5
  • H4 Histone Family, Member B 2 3
  • Histone Cluster 1, H4d 2 3
  • Histone 1, H4d 2 3
  • H4/B 3 4
  • H4FB 3 4
  • HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 4
  • Histone H4 3
  • DJ221C16.9 3
  • HIST2H4 4
  • H4FA 4
  • H4/A 4
  • H4/C 4
  • H4/D 4
  • H4/E 4
  • H4/G 4
  • H4/H 4
  • H4/I 4
  • H4/J 4
  • H4/K 4
  • H4/M 4
  • H4/N 4
  • H4/O 4
  • H4F2 4
  • H4FC 4
  • H4FD 4
  • H4FE 4
  • H4FG 4
  • H4FH 4
  • H4FI 4
  • H4FJ 4
  • H4FK 4
  • H4FM 4
  • H4FN 4
  • H4FO 4

External Ids for HIST1H4D Gene

Previous HGNC Symbols for HIST1H4D Gene

  • H4FB

Previous GeneCards Identifiers for HIST1H4D Gene

  • GC06M026246
  • GC06M026296
  • GC06M026131

Summaries for HIST1H4D Gene

Entrez Gene Summary for HIST1H4D Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H4 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST1H4D Gene

HIST1H4D (Histone Cluster 1 H4 Family Member D) is a Protein Coding gene. Among its related pathways are DNA Double-Strand Break Repair and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include poly(A) RNA binding and histone binding. An important paralog of this gene is HIST1H4H.

UniProtKB/Swiss-Prot for HIST1H4D Gene

  • Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Gene Wiki entry for HIST1H4D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H4D Gene

Genomics for HIST1H4D Gene

Regulatory Elements for HIST1H4D Gene

Enhancers for HIST1H4D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G026162 0.7 Ensembl 12.4 +27.6 27576 0.2 BCOR RNF2 DPF2 MNT FOSL1 ARID1B JUND PRDM6 POLR2A IKZF1 HIST1H4D HIST1H1PS1 HIST1H2AD HIST1H3E HIST1H2APS3 HIST1H2BF RPS10P1 HIST1H4C HIST1H4F HIST1H4H
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST1H4D on UCSC Golden Path with GeneCards custom track

Promoters for HIST1H4D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000194997 176 1001 CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC

Genomic Location for HIST1H4D Gene

Chromosome:
6
Start:
26,188,710 bp from pter
End:
26,189,076 bp from pter
Size:
367 bases
Orientation:
Minus strand

Genomic View for HIST1H4D Gene

Genes around HIST1H4D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H4D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H4D Gene

Proteins for HIST1H4D Gene

  • Protein details for HIST1H4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62805-H4_HUMAN
    Recommended name:
    Histone H4
    Protein Accession:
    P62805
    Secondary Accessions:
    • A2VCL0
    • P02304
    • P02305
    • Q6DRA9
    • Q6FGB8
    • Q6NWP7

    Protein attributes for HIST1H4D Gene

    Size:
    103 amino acids
    Molecular mass:
    11367 Da
    Quaternary structure:
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.
    SequenceCaution:
    • Sequence=AAI28106.1; Type=Frameshift; Positions=3; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HIST1H4D Gene

neXtProt entry for HIST1H4D Gene

Post-translational modifications for HIST1H4D Gene

  • Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.
  • Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.
  • Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
  • Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by KMT5B and KMT5C and induces gene silencing.
  • Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • Phosphorylated by PAK2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4.
  • Sumoylated, which is associated with transcriptional repression.
  • Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me).
  • Ubiquitination at isoforms=32, isoforms=60, posLast=7878, and posLast=8080
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H4D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H4D Gene

Domains & Families for HIST1H4D Gene

Gene Families for HIST1H4D Gene

Protein Domains for HIST1H4D Gene

Graphical View of Domain Structure for InterPro Entry

P62805

UniProtKB/Swiss-Prot:

H4_HUMAN :
  • Belongs to the histone H4 family.
Family:
  • Belongs to the histone H4 family.
genes like me logo Genes that share domains with HIST1H4D: view

No data available for Suggested Antigen Peptide Sequences for HIST1H4D Gene

Function for HIST1H4D Gene

Molecular function for HIST1H4D Gene

UniProtKB/Swiss-Prot Function:
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Gene Ontology (GO) - Molecular Function for HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,TAS 3035717
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 9540062
GO:0019904 protein domain specific binding IPI 22368283
GO:0042393 histone binding IPI 20498094
genes like me logo Genes that share ontologies with HIST1H4D: view

Phenotypes for HIST1H4D Gene

GenomeRNAi human phenotypes for HIST1H4D:
genes like me logo Genes that share phenotypes with HIST1H4D: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H4D Gene

Localization for HIST1H4D Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HIST1H4D gene
Compartment Confidence
extracellular 5
nucleus 5
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000784 nuclear chromosome, telomeric region IDA 19135898
GO:0000786 nucleosome TAS 3035717
GO:0000788 nuclear nucleosome IBA --
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with HIST1H4D: view

Pathways & Interactions for HIST1H4D Gene

SuperPathways for HIST1H4D Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 DNA Double-Strand Break Repair
3 Cellular Senescence
4 Chromosome Maintenance
5 Cell Cycle, Mitotic
.60
genes like me logo Genes that share pathways with HIST1H4D: view

Interacting Proteins for HIST1H4D Gene

Selected Interacting proteins: P62805-H4_HUMAN for HIST1H4D Gene via MINT UniProtKB IID

Symbol External ID(s) Details
TP53BP1
KDM4A
BRD2
COPRS
PHF20

SIGNOR curated interactions for HIST1H4D Gene

Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
GO:0006334 nucleosome assembly IDA 20498094
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
genes like me logo Genes that share ontologies with HIST1H4D: view

Transcripts for HIST1H4D Gene

mRNA/cDNA for HIST1H4D Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HIST1H4D Gene

Histone cluster 1, H4d:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H4D Gene

No ASD Table

Relevant External Links for HIST1H4D Gene

GeneLoc Exon Structure for
HIST1H4D
ECgene alternative splicing isoforms for
HIST1H4D

Expression for HIST1H4D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST1H4D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H4D Gene

This gene is overexpressed in Whole Blood (x18.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HIST1H4D Gene



Protein tissue co-expression partners for HIST1H4D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HIST1H4D Gene:

HIST1H4D

SOURCE GeneReport for Unigene cluster for HIST1H4D Gene:

Hs.248179

Evidence on tissue expression from TISSUES for HIST1H4D Gene

  • Liver(4.5)
  • Nervous system(4.5)
  • Eye(4.2)
  • Blood(2.3)
  • Intestine(2.3)
  • Lung(2.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with HIST1H4D: view

Primer Products

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H4D Gene

Orthologs for HIST1H4D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HIST1H4D Gene

Organism Taxonomy Gene Similarity Type Details
rat
(Rattus norvegicus)
Mammalia Hist2h4a 34
  • 85.11 (n)
dog
(Canis familiaris)
Mammalia LOC100856225 34
  • 84.79 (n)
mouse
(Mus musculus)
Mammalia Hist1h4m 34 16
  • 82.85 (n)
chimpanzee
(Pan troglodytes)
Mammalia LOC748513 34
  • 80.26 (n)
cow
(Bos Taurus)
Mammalia LOC100337407 34
  • 77.67 (n)
chicken
(Gallus gallus)
Aves HIST1H46L2 34
  • 84.47 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495739 34
  • 82.52 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100002181 34
  • 77.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta His4:CG33891 34
  • 79.94 (n)
worm
(Caenorhabditis elegans)
Secernentea his-60 34
  • 76.7 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER012C 34
  • 80.26 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E08647g 34
  • 69.9 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHF1 34
  • 69.58 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01634 34
  • 77.78 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hhf3 34
  • 76.05 (n)
Species where no ortholog for HIST1H4D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HIST1H4D Gene

ENSEMBL:
Gene Tree for HIST1H4D (if available)
TreeFam:
Gene Tree for HIST1H4D (if available)

Paralogs for HIST1H4D Gene

(3) SIMAP similar genes for HIST1H4D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H4D: view

Variants for HIST1H4D Gene

Sequence variations from dbSNP and Humsavar for HIST1H4D Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1001626140 -- 26,188,351(+) ATCTC(C/T)TTTGA downstream-variant-500B
rs1002492738 -- 26,188,545(+) CCAGC(A/G)TGGGC downstream-variant-500B
rs1002632495 -- 26,188,966(+) GCCAG(A/G)CGGCG reference, synonymous-codon
rs1003039564 -- 26,189,948(+) GGGCC(C/G)ATTGA upstream-variant-2KB
rs1003639399 -- 26,189,746(+) CACCG(C/T)GCCGG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST1H4D Gene

Variant ID Type Subtype PubMed ID
dgv375n21 CNV loss 19592680
dgv5926n100 CNV gain 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for HIST1H4D Gene

Residual Variation Intolerance Score: 29.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.79; 16.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST1H4D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H4D Gene

Disorders for HIST1H4D Gene

UniProtKB/Swiss-Prot

H4_HUMAN
  • Note=Chromosomal aberrations involving HISTONE H4 is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;6)(q27;p21), with BCL6.

Relevant External Links for HIST1H4D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H4D

No disorders were found for HIST1H4D Gene.

No data available for MalaCards and Genatlas for HIST1H4D Gene

Publications for HIST1H4D Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 3 4 64
  3. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W. … Doenecke D. (Hum. Genet. 1997) 3 4 64
  4. Protein-DNA interactions in vivo upstream of a cell cycle-regulated human H4 histone gene. (PMID: 3035717) Pauli U. … Nick H. (Science 1987) 3 4 64
  5. New host factors important for respiratory syncytial virus (RSV) replication revealed by a novel microfluidics screen for interactors of matrix (M) protein. (PMID: 25556234) Kipper S. … Bajorek M. (Mol. Cell Proteomics 2015) 3 64

Products for HIST1H4D Gene

Sources for HIST1H4D Gene

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