Aliases for HIST1H1D Gene
Aliases for HIST1H1D Gene
External Ids for HIST1H1D Gene
- HGNC: 4717
- Entrez Gene: 3007
- Ensembl: ENSG00000124575
- OMIM: 142210
- UniProtKB: P16402
Previous HGNC Symbols for HIST1H1D Gene
- H1F3
Previous GeneCards Identifiers for HIST1H1D Gene
- GC06M026291
- GC06M026118
- GC06M026342
- GC06M026177
Summaries for HIST1H1D Gene
-
Histones are basic nuclear proteins responsible for 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 H1 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 HIST1H1D Gene
HIST1H1D (Histone Cluster 1 H1 Family Member D) is a Protein Coding gene. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Apoptosis induced DNA fragmentation. GO annotations related to this gene include poly(A) RNA binding and chromatin DNA binding. An important paralog of this gene is HIST1H1E.
UniProtKB/Swiss-Prot for HIST1H1D Gene
-
Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H1D Gene
Genomics for HIST1H1D Gene
Regulatory Elements for HIST1H1D Gene
Enhancers for HIST1H1D Gene
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around HIST1H1D on UCSC Golden Path with GeneCards custom track
- Transcription factor binding sites by QIAGEN in the HIST1H1D gene promoter:
Regulatory Element Products
Genomic Location for HIST1H1D Gene
- Chromosome:
- 6
- Start:
- 26,234,212 bp from pter
- End:
- 26,234,988 bp from pter
- Size:
- 777 bases
- Orientation:
- Minus strand
Genomic View for HIST1H1D Gene
Genes around HIST1H1D on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 6p22.2 by Ensembl
- 6p22.2 by Entrez Gene
- 6p22.2 by HGNC
HIST1H1D Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for HIST1H1D Gene
Proteins for HIST1H1D Gene
-
Protein details for HIST1H1D Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- P16402-H13_HUMAN
- Recommended name:
- Histone H1.3
- Protein Accession:
- P16402
- B2R751
- Q2M2I2
Protein attributes for HIST1H1D Gene
- Size:
- 221 amino acids
- Molecular mass:
- 22350 Da
- Quaternary structure:
- No Data Available
Protein Expression for HIST1H1D Gene
Post-translational modifications for HIST1H1D Gene
- Citrullination at Arg-55 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance.
- H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter.
- Modification sites at PhosphoSitePlus
- Modification sites at neXtProt
Other Protein References for HIST1H1D Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- EMD Millipore Complete listing of Mono and Polychlonal Antibodies for HIST1H1D
-
Custom Antibody ServicesOriGene Antibodies for HIST1H1D
- Novus Biologicals Antibodies for HIST1H1D
-
Abcam antibodies for HIST1H1D
- Invitrogen Antibodies for HIST1H1D
- GeneTex HIST1H1D antibody for HIST1H1D
Protein Products
-
OriGene Purified Proteins for HIST1H1D
- Search Origene for MassSpec and Protein Over-expression Lysates for HIST1H1D
- Origene Custom Protein Services for HIST1H1D
- Search GeneTex for Proteins for HIST1H1D
Assay Products
No data available for DME Specific Peptides for HIST1H1D Gene
Domains & Families for HIST1H1D Gene
Gene Families for HIST1H1D Gene
- HGNC:
Protein Domains for HIST1H1D Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for HIST1H1D Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P16402UniProtKB/Swiss-Prot:
H13_HUMAN :- The C-terminal domain is required for high-affinity binding to chromatin.
- Belongs to the histone H1/H5 family.
- Domain:
-
- The C-terminal domain is required for high-affinity binding to chromatin.
- Family:
-
- Belongs to the histone H1/H5 family.
Function for HIST1H1D Gene
Molecular function for HIST1H1D Gene
- UniProtKB/Swiss-Prot Function:
- Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003677 | DNA binding | IEA | -- |
| GO:0003723 | RNA binding | IDA | 22681889 |
| GO:0031490 | chromatin DNA binding | IDA | 15911621 |
Phenotypes for HIST1H1D Gene
- MGI mutant phenotypes for HIST1H1D:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for HIST1H1D:
Animal Models for HIST1H1D Gene
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
-
ViGene Biosciences lentiviral particle packaged cDNA for HIST1H1D gene
-
ViGene Biosciences ready-to-package AAV shRNAs for HIST1H1D gene
- Search ViGene Biosciences for HIST1H1D
CRISPR Products
-
OriGene CRISPR knockouts for HIST1H1D
-
Santa Cruz Biotechnology (SCBT) CRISPR for HIST1H1D
- GenScript: Design CRISPR guide RNA sequences for HIST1H1D
miRNA for HIST1H1D Gene
- miRTarBase miRNAs that target HIST1H1D
miRNA Products
- Search ViGene Biosciences for HIST1H1D
Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for HIST1H1D
- Browse OriGene Inhibitory RNA Products For HIST1H1D
-
ViGene Biosciences ready-to-package AAV shRNAs for HIST1H1D gene
Clone Products
-
OriGene ORF clones in human for HIST1H1D
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat
Cell Line Products
-
Horizon Cell Lines for HIST1H1D
-
ViGene Biosciences adenoviral particle packaged cDNA for HIST1H1D gene
-
ViGene Biosciences lentiviral particle packaged cDNA for HIST1H1D gene
-
ViGene Biosciences ready-to-package AAV shRNAs for HIST1H1D gene
Flow Cytometry Products
No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HIST1H1D Gene
Localization for HIST1H1D Gene
Subcellular locations from UniProtKB/Swiss-Prot for HIST1H1D Gene
- Nucleus. Chromosome. Note=According to PubMed:15911621 more commonly found in euchromatin. According to PubMed:10997781 is associated with inactive chromatin.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 2 |
| cytoskeleton | 1 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000786 | nucleosome | IEA | -- |
| GO:0000790 | nuclear chromatin | IDA | 19882353 |
| GO:0005634 | nucleus | IEA | -- |
| GO:0005694 | chromosome | IEA | -- |
| GO:0005719 | nuclear euchromatin | IDA | 15911621 |
Pathways & Interactions for HIST1H1D Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Apoptosis induced DNA fragmentation | ||
| 2 | CDK-mediated phosphorylation and removal of Cdc6 |
.31
|
|
| 3 | Cellular Senescence | ||
| 4 | DNA Damage/Telomere Stress Induced Senescence | ||
| 5 | Activation of cAMP-Dependent PKA |
.56
|
|
Pathways by source for HIST1H1D Gene
9 Reactome pathways for HIST1H1D Gene
2 GeneGo (Thomson Reuters) pathways for HIST1H1D Gene
2 Qiagen pathways for HIST1H1D Gene
Interacting Proteins for HIST1H1D Gene
Selected Interacting proteins:
P16402-H13_HUMAN
ENSP00000244534
for HIST1H1D Gene via
IID
STRING
MINT
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | IEA | -- |
| GO:0006334 | nucleosome assembly | IEA | -- |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | IEA | -- |
| GO:0016584 | nucleosome positioning | IEA | -- |
| GO:0080182 | histone H3-K4 trimethylation | IEA | -- |
No data available for SIGNOR curated interactions for HIST1H1D Gene
Transcripts for HIST1H1D Gene
mRNA/cDNA for HIST1H1D Gene
- (1) REFSEQ mRNAs :
- (3) Additional mRNA sequences :
- (6) Selected AceView cDNA sequences:
- (1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for HIST1H1D Gene
CRISPR Products
-
OriGene CRISPR knockouts for HIST1H1D
-
Santa Cruz Biotechnology (SCBT) CRISPR for HIST1H1D
- GenScript: Design CRISPR guide RNA sequences for HIST1H1D
miRNA Products
- Search ViGene Biosciences for HIST1H1D
Inhibitory RNA Products
- Origene RNAi, siRNA, and shRNA products in human, mouse, rat for HIST1H1D
- Browse OriGene Inhibitory RNA Products For HIST1H1D
-
ViGene Biosciences ready-to-package AAV shRNAs for HIST1H1D gene
Clone Products
-
OriGene ORF clones in human for HIST1H1D
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Flow Cytometry Products
Expression for HIST1H1D Gene
mRNA differential expression in normal tissues according to GTEx for HIST1H1D Gene
This gene is overexpressed in Whole Blood (x12.2) and Vagina (x4.2).
This gene is overexpressed in Tlymphocyte (34.1) and Cervix (6.7).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HIST1H1D Gene
NURSA nuclear receptor signaling pathways regulating expression of HIST1H1D Gene:
HIST1H1DSOURCE GeneReport for Unigene cluster for HIST1H1D Gene:
Hs.136857Evidence on tissue expression from TISSUES for HIST1H1D Gene
- Spleen(4.5)
- Nervous system(4.3)
- Lung(2.1)
- Intestine(2)
Primer Products
-
OriGene qPCR primer pairs for HIST1H1D
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H1D Gene
Orthologs for HIST1H1D Gene
This gene was present in the common ancestor of chordates.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | HIST1H1D 35 |
|
OneToOne | |
| LOC472227 34 |
|
||||
| cow (Bos Taurus) |
Mammalia | HIST1H1E 35 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | LOC611113 34 |
|
||
| -- 35 |
|
OneToMany | |||
| -- 35 |
|
OneToMany | |||
| mouse (Mus musculus) |
Mammalia | Hist1h1d 34 16 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | -- 35 |
|
ManyToMany | |
| -- 35 |
|
ManyToMany | |||
| platypus (Ornithorhynchus anatinus) |
Mammalia | -- 35 |
|
OneToMany | |
| chicken (Gallus gallus) |
Aves | HIST1H111L 35 |
|
ManyToMany | |
| HIST1H111R 35 |
|
ManyToMany | |||
| -- 35 |
|
ManyToMany | |||
| zebrafish (Danio rerio) |
Actinopterygii | CABZ01086354.1 35 |
|
ManyToMany | |
| CU457819.3 35 |
|
ManyToMany | |||
| FP325123.1 35 |
|
ManyToMany | |||
| si:ch211-113a14.12 35 |
|
ManyToMany | |||
| zgc:110425 35 |
|
ManyToMany | |||
| zgc:153405 35 |
|
ManyToMany | |||
| histh1l 35 |
|
ManyToMany | |||
| si:ch211-113a14.18 35 |
|
ManyToMany | |||
| si:ch211-113a14.24 35 |
|
ManyToMany | |||
| si:dkey-261m9.12 35 |
|
ManyToMany | |||
| zgc:163061 35 35 |
|
ManyToMany | |||
| si:dkey-108k21.10 35 |
|
ManyToMany | |||
| si:dkey-108k21.14 35 |
|
ManyToMany | |||
| si:dkey-108k21.21 35 |
|
ManyToMany |
- Species where no ortholog for HIST1H1D was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Ashbya gossypii)
- 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)
- baker's yeast (Saccharomyces cerevisiae)
- barley (Hordeum vulgare)
- beta proteobacteria (Neisseria meningitidis)
- bread mold (Neurospora crassa)
- Chromalveolata (Phytophthora infestans)
- common water flea (Daphnia pulex)
- corn (Zea mays)
- E. coli (Escherichia coli)
- filamentous fungi (Aspergillus nidulans)
- Firmicute bacteria (Streptococcus pneumoniae)
- fission yeast (Schizosaccharomyces pombe)
- fruit fly (Drosophila melanogaster)
- green algae (Chlamydomonas reinhardtii)
- honey bee (Apis mellifera)
- K. lactis yeast (Kluyveromyces lactis)
- lizard (Anolis carolinensis)
- loblloly pine (Pinus taeda)
- malaria parasite (Plasmodium falciparum)
- medicago trunc (Medicago Truncatula)
- moss (Physcomitrella patens)
- orangutan (Pongo pygmaeus)
- pig (Sus scrofa)
- rainbow trout (Oncorhynchus mykiss)
- rat (Rattus norvegicus)
- 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)
- tropical clawed frog (Silurana tropicalis)
- wheat (Triticum aestivum)
- worm (Caenorhabditis elegans)
Paralogs for HIST1H1D Gene
Variants for HIST1H1D Gene
| SNP ID | Clin | Chr 06 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000001786 | -- | 26,234,203(+) | TTGAC(C/T)GAGAC | downstream-variant-500B | |
| rs1000688486 | -- | 26,234,106(+) | CCCAA(A/C)CAGCA | downstream-variant-500B | |
| rs1000795773 | -- | 26,234,709(+) | TTTTT(G/T)TCTAC | reference, missense | |
| rs1001326976 | -- | 26,234,124(+) | GATAG(A/G)CCGTG | downstream-variant-500B | |
| rs1001559225 | -- | 26,234,994(+) | TCCTC(C/T)ACGAG | upstream-variant-2KB |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv5926n100 | CNV | gain | 25217958 |
| nsv1021294 | CNV | loss | 25217958 |
| nsv1023453 | CNV | gain | 25217958 |
| nsv428137 | CNV | loss | 18775914 |
Residual Variation Intolerance Score:
51.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
5.50;
71.80% of all genes are more intolerant (likely to be disease-causing)
Relevant External Links for HIST1H1D Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- HIST1H1D
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H1D Gene
Disorders for HIST1H1D Gene
Relevant External Links for HIST1H1D
No disorders were found for HIST1H1D Gene.
No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H1D Gene
Publications for HIST1H1D Gene
- The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
- Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 2 3 4 64
- Identification of 15 loci influencing height in a Korean population. (PMID: 19893584) Kim J.J. … Lee J.K. (J. Hum. Genet. 2010) 3 46 64
- Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study. (PMID: 20846217) Lee J.J. … Hirschhorn J. (Ann. Hum. Genet. 2010) 3 46 64
- Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (PMID: 19343178) Soranzo N. … Deloukas P. (PLoS Genet. 2009) 3 46 64
Products for HIST1H1D Gene
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- Mammalian expression: PiggyBac
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- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for HIST1H1D Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
- (84) DISEASES
- (85) SIMAP
- (86) GenomeRNAi
- (87) LifeMap
- (88) miRTarBase
- (89) MalaCards
- (90) Invitrogen
- (91) BitterDB
- (92) Vector BioLabs
- (93) ESI-BIO
- (94) RefSeq
- (95) BioSystems
- (96) MaxQB
- (97) IUPHAR
- (98) BioGPS
- (99) Illumina
- (100) COMPARTMENTS
- (101) HOMER
- (102) PaxDb
- (103) ApexBio
- (104) Addgene
- (105) antibodies-online
- (106) CYP
- (107) NONCODE
- (108) SwitchGear Genomics
- (109) TreeFam
- (110) PathCards
- (111) GeneReviews
- (112) GeneTex
- (113) Taconic Biosciences
- (114) GTEx
- (115) ProteomicsDB
- (116) SCBT
- (117) DGIdb
- (118) ClinicalTrials
- (119) FDA Approved Drugs
- (120) RVIS
- (121) SIGNOR
- (122) diseasecard
- (123) NIH Rare Diseases
- (124) Orphanet
- (125) UMLS
- (126) GTR
- (127) Disease Ontology
- (128) Genetics Home Reference
- (129) MeSH
- (130) MedlinePlus
- (131) CDC
- (132) NINDS
- (133) NCBI Bookshelf
- (134) ClinVar
- (135) Gene Damage Index
- (136) ViGene Biosciences
- (137) HPO
- (138) UDN
- (139) VISTA
- (140) FANTOM5
- (141) ENCODE
- (142) ProSci
- (143) Horizon
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- (154) TISSUES
- (155) Gene ORGANizer