H3-7

gene
On this page

Also known as p06H3.7

Summary

H3-7 (H3.7 histone (putative), HGNC:32060) is a protein-coding gene on chromosome 1q21.1, encoding Histone H3-7 (Q5TEC6). Core component of nucleosome.

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 a member of the H3 family, but is found outside of the histone cluster. There is evidence that it is transcribed and has an intact CDS, but residue changes in the protein suggest that it may be on its way to becoming a psuedogene.

Source: NCBI Gene 440686 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 2 total
  • MANE Select transcript: NM_001372105

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:32060
Approved symbolH3-7
NameH3.7 histone (putative)
Location1q21.1
Locus typegene with protein product
StatusApproved
Aliasesp06, H3.7
Ensembl geneENSG00000273213
Ensembl biotypeprotein_coding
Entrez440686

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000392948, ENST00000609879, ENST00000650532

RefSeq mRNA: 2 — MANE Select: NM_001372105 NM_001355409, NM_001372105

CCDS: CCDS30842

Canonical transcript exons

ENST00000392948 — 1 exons

ExonStartEnd
ENSE00001513688143905510143905977

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 86.56.

Top tissues by expression

234 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left ovaryUBERON:000211986.56gold quality
right adrenal glandUBERON:000123385.30gold quality
right ovaryUBERON:000211885.16gold quality
right adrenal gland cortexUBERON:003582784.60gold quality
left adrenal glandUBERON:000123484.58gold quality
left adrenal gland cortexUBERON:003582584.40gold quality
adrenal tissueUBERON:001830383.15gold quality
adrenal cortexUBERON:000123582.70gold quality
body of stomachUBERON:000116182.67gold quality
adrenal glandUBERON:000236982.67gold quality
ovaryUBERON:000099282.04gold quality
cerebellar hemisphereUBERON:000224581.24gold quality
cerebellar cortexUBERON:000212981.17gold quality
right hemisphere of cerebellumUBERON:001489080.74gold quality
lower esophagus mucosaUBERON:003583480.38gold quality
stomachUBERON:000094579.70gold quality
cerebellumUBERON:000203779.52gold quality
buccal mucosa cellCL:000233676.49gold quality
monocyteCL:000057676.14gold quality
spleenUBERON:000210676.12gold quality
ventricular zoneUBERON:000305375.43gold quality
leukocyteCL:000073875.29gold quality
C1 segment of cervical spinal cordUBERON:000646974.68gold quality
stromal cell of endometriumCL:000225574.19gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047374.04silver quality
medial globus pallidusUBERON:000247773.98gold quality
smooth muscle tissueUBERON:000113573.86gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099172.97gold quality
right lobe of thyroid glandUBERON:000111972.86gold quality
spinal cordUBERON:000224072.65gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.87

Regulation

Is transcription factor: no

Cross-species orthologs

23 orthologs

OrganismSymbolGene ID
danio_reriozgc:173552ENSDARG00000051737
danio_reriosi:ch1073-153i20.2ENSDARG00000105345
danio_reriozgc:173552ENSDARG00000110909
danio_reriosi:ch211-113a14.27ENSDARG00000111396
danio_reriosi:ch211-113a14.20ENSDARG00000112131
danio_reriozgc:173552ENSDARG00000112175
danio_reriosi:ch211-113a14.23ENSDARG00000114334
drosophila_melanogasterHis3:CG33812FBGN0053812
caenorhabditis_elegansWBGENE00001876
caenorhabditis_elegansWBGENE00001880
caenorhabditis_elegansWBGENE00001883
caenorhabditis_elegansWBGENE00001887
caenorhabditis_elegansWBGENE00001891
caenorhabditis_elegansWBGENE00001899
caenorhabditis_elegansWBGENE00001901
caenorhabditis_elegansWBGENE00001906
caenorhabditis_elegansWBGENE00001914
caenorhabditis_elegansWBGENE00001916
caenorhabditis_elegansWBGENE00001919
caenorhabditis_elegansWBGENE00001923
caenorhabditis_elegansWBGENE00001929
caenorhabditis_elegansWBGENE00001933
caenorhabditis_elegansWBGENE00001937

Paralogs (20): CENPA (ENSG00000115163), H3-3B (ENSG00000132475), H3-3A (ENSG00000163041), H3-4 (ENSG00000168148), H3C13 (ENSG00000183598), H3-5 (ENSG00000188375), H3C12 (ENSG00000197153), H3C4 (ENSG00000197409), H3C14 (ENSG00000203811), H3C15 (ENSG00000203852), H3Y2 (ENSG00000268799), H3Y1 (ENSG00000269466), H3C8 (ENSG00000273983), H3C6 (ENSG00000274750), H3C11 (ENSG00000275379), H3C1 (ENSG00000275714), H3C7 (ENSG00000277775), H3C10 (ENSG00000278828), H3C2 (ENSG00000286522), H3C3 (ENSG00000287080)

Protein

Protein identifiers

Histone H3-7Q5TEC6 (reviewed: Q5TEC6)

All UniProt accessions (2): A0A590UJL8, Q5TEC6

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. 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. During nucleosome assembly the chaperone ASF1A interacts with the histone H3-H4 heterodimer.

Subcellular location. Nucleus. Chromosome.

Post-translational modifications. Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability. Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription. Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3’ of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters. Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at ‘Lys-120’. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication. Phosphorylated at Thr-4 (H3T3ph) by HASPIN during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MAP3K20 isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 or isoform M2 of PKM (PKM2) is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Ubiquitinated. Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression. Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis. Succinylation at Lys-80 (H3K79succ) by KAT2A takes place with a maximum frequency around the transcription start sites of genes. It gives a specific tag for epigenetic transcription activation. Desuccinylation at Lys-123 (H3K122succ) by SIRT7 in response to DNA damage promotes chromatin condensation and double-strand breaks (DSBs) repair. Serine ADP-ribosylation constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage. Serine ADP-ribosylation at Ser-11 (H3S10ADPr) is mutually exclusive with phosphorylation at Ser-11 (H3S10ph) and impairs acetylation at Lys-10 (H3K9ac).

Similarity. Belongs to the histone H3 family.

RefSeq proteins (2): NP_001342338, NP_001359034* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000164Histone_H3/CENP-AFamily
IPR007125H2A/H2B/H3Domain
IPR009072Histone-foldHomologous_superfamily

Pfam: PF00125

UniProt features (116 total): modified residue 110, cross-link 3, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5MR8X-RAY DIFFRACTION1.74
4H75X-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5TEC6-F186.420.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (113): 5, 80, 81, 87, 108, 116, 116, 123, 123, 123, 123, 5, 123, 123, 123, 15, 19, 24, 5, 5 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_CHROMOSOME_LOCALIZATION, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_ORGANELLE_FISSION, GOBP_MITOTIC_NUCLEAR_DIVISION, GOBP_ORGANELLE_ASSEMBLY, GOBP_MITOTIC_CELL_CYCLE, GOBP_CHROMATIN_REMODELING, GOBP_HETEROCHROMATIN_ORGANIZATION, GOBP_ORGANELLE_LOCALIZATION, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOBP_KINETOCHORE_ORGANIZATION, GOBP_NUCLEAR_CHROMOSOME_SEGREGATION, GOBP_METAPHASE_CHROMOSOME_ALIGNMENT, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN

GO Biological Process (0):

GO Molecular Function (3): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), protein heterodimerization activity (GO:0046982)

GO Cellular Component (4): nucleosome (GO:0000786), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
chromatin2
nucleic acid binding1
structural molecule activity1
protein dimerization activity1
protein-DNA complex1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

8476 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
H3-7H2AC20Q16777998
H3-7H2BC21Q16778998
H3-7H2AC19P20670998
H3-7H4C16P02304997
H3-7WDR5P61964997
H3-7H4C7Q99525997
H3-7CBX5P45973995
H3-7DNMT3LQ9UJW3994
H3-7CBX3Q13185991
H3-7BRD4O60885989
H3-7DNMT3AQ9Y6K1987
H3-7RAG2P55895977
H3-7DNMT1P26358973
H3-7CBX1P23197973
H3-7HDAC1Q13547966

IntAct

110 interactions, top by confidence:

ABTypeScore
HSPA8GAKpsi-mi:“MI:0914”(association)0.760
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
ANXA9PPLpsi-mi:“MI:0914”(association)0.660
AIPL1PDE5Apsi-mi:“MI:0914”(association)0.640
H2BC1PPM1Gpsi-mi:“MI:0914”(association)0.640
MACROD1PARP1psi-mi:“MI:0914”(association)0.620
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
HSD3B2NARS1psi-mi:“MI:0914”(association)0.530
LACC1DUSP14psi-mi:“MI:0914”(association)0.530
HERC3H3-7psi-mi:“MI:0914”(association)0.530
H2AC20PPM1Gpsi-mi:“MI:0914”(association)0.530
C1orf174AHCYL1psi-mi:“MI:0914”(association)0.530
RRP7AATP4Apsi-mi:“MI:0914”(association)0.530
ZNF428PIP4K2Apsi-mi:“MI:0914”(association)0.530
NASPH4C16psi-mi:“MI:0914”(association)0.530
TOMM20TPP1psi-mi:“MI:0914”(association)0.480
CENPQCENPXpsi-mi:“MI:0914”(association)0.350
CCNYL1A2ML1psi-mi:“MI:0914”(association)0.350
CDK15A2ML1psi-mi:“MI:0914”(association)0.350
CDX1ZNF724psi-mi:“MI:0914”(association)0.350
RRP7AMAPTpsi-mi:“MI:0914”(association)0.350
CENPAOIP5psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A2XHJ3, C6Y4D0, G2TRL2, O60076, O97484, P06353, P06902, P15512, P16890, P22843, P41353, P59169, P68431, P68432, P68433, P69071, P69074, P69076, P69078, P69149, P69150, P69244, P69245, P80553, Q0JCT1, Q16695, Q22RG7, Q27489, Q27490, Q2Z2F4, Q3C2E5, Q3E835, Q55BN9, Q55BP0, Q5MYA4, Q5TEC6, Q64400, Q6LBF0, Q6LED0, Q6NXT2

Diamond homologs: A2XHJ3, A2Y533, A5DWE2, A5PK61, C0HL66, C0HL67, P02299, P02301, P02302, P06352, P08437, P08898, P08903, P09988, P22843, P50564, P59169, P59226, P68427, P68428, P68429, P68430, P68431, P68432, P68433, P69071, P69072, P69073, P69074, P69075, P69076, P69077, P69078, P69079, P69244, P69245, P69246, P69248, P80553, P84227

SIGNOR signaling

12 interactions.

AEffectBMechanism
SLBP“up-regulates quantity by expression”H3-2“translation regulation”
BAZ2B“down-regulates activity”H3-2binding
KAT2A“down-regulates activity”H3-2acetylation
KAT2B“down-regulates activity”H3-2acetylation
“SAGA complex”“down-regulates activity”H3-2acetylation
KDM3A“up-regulates activity”H3-2demethylation
SIRT7“up-regulates activity”H3-2deacetylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Nucleosome assembly527.7×4e-05
Deposition of new CENPA-containing nucleosomes at the centromere1018.4×7e-08
SIRT1 negatively regulates rRNA expression917.8×4e-07
FXIIa activates plasma kallikrein-kinin system816.1×5e-06
Packaging Of Telomere Ends615.3×6e-05
RNA Polymerase I Promoter Opening715.0×4e-05
Chromosome Maintenance614.8×7e-05
DNA methylation714.5×4e-05

GO biological processes:

GO termPartnersFoldFDR
heterochromatin formation918.2×1e-06
nucleosome assembly910.0×1e-04
double-strand break repair69.7×6e-03
chromatin organization97.1×2e-03
DNA damage response114.7×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

2 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

89 predictions. Top by Δscore:

VariantEffectΔscore
1:143905798:T:TAdonor_gain0.7600
1:143905730:AAACT:Adonor_gain0.7500
1:143905912:T:TAdonor_gain0.7400
1:143905858:TC:Tdonor_gain0.6200
1:143905855:TCTTC:Tdonor_gain0.5900
1:143905753:CCAG:Cdonor_gain0.5800
1:143905567:C:CAdonor_gain0.5200
1:143905558:AGG:Adonor_gain0.4600
1:143905752:A:ACdonor_gain0.4600
1:143905753:C:CCdonor_gain0.4600
1:143905583:G:Tdonor_gain0.4500
1:143905683:T:TAdonor_gain0.4500
1:143905925:G:Adonor_gain0.4500
1:143905752:ACCAG:Adonor_gain0.4400
1:143905753:CCAGC:Cdonor_gain0.4400
1:143905748:GCGT:Gdonor_loss0.4300
1:143905749:CGTA:Cdonor_loss0.4300
1:143905750:GT:Gdonor_loss0.4300
1:143905751:T:TGdonor_loss0.4300
1:143905752:A:AAdonor_loss0.4300
1:143905753:C:CGdonor_loss0.4300
1:143905775:G:Adonor_gain0.4300
1:143905558:AGGC:Adonor_gain0.4100
1:143905568:C:Adonor_gain0.4000
1:143905596:T:TAdonor_gain0.4000
1:143905717:G:GAacceptor_gain0.4000
1:143905754:C:Gdonor_loss0.3900
1:143905772:C:Aacceptor_gain0.3900
1:143905816:C:CAdonor_gain0.3900
1:143905940:G:Adonor_gain0.3900

AlphaMissense

862 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:143905712:G:CF85L0.910
1:143905712:G:TF85L0.910
1:143905714:A:GF85L0.910
1:143905763:G:CF68L0.909
1:143905763:G:TF68L0.909
1:143905765:A:GF68L0.909
1:143905952:C:AK5N0.861
1:143905952:C:GK5N0.861
1:143905799:C:AQ56H0.830
1:143905799:C:GQ56H0.830
1:143905812:A:GI52T0.828
1:143905910:C:AK19N0.801
1:143905910:C:GK19N0.801
1:143905856:C:AK37N0.768
1:143905856:C:GK37N0.768
1:143905730:A:CF79L0.758
1:143905730:A:TF79L0.758
1:143905732:A:GF79L0.758
1:143905809:C:GR53P0.758
1:143905758:C:GR70P0.754
1:143905749:C:GR73P0.738
1:143905652:G:CF105L0.733
1:143905652:G:TF105L0.733
1:143905654:A:GF105L0.733
1:143905806:C:GR54P0.733
1:143905818:C:GR50P0.729
1:143905937:C:AK10N0.728
1:143905937:C:GK10N0.728
1:143905824:G:TA48D0.727
1:143905895:T:AK24N0.718

dbSNP variants (sampled 300 via entrez): RS1156929433 (1:143903097 C>T), RS1157042980 (1:143903836 C>T), RS1157280492 (1:143902329 GA>G,GAA), RS1157324457 (1:143903149 G>A,T), RS1157807124 (1:143903415 C>T), RS1157997993 (1:143904687 C>A,T), RS1158140485 (1:143906799 C>T), RS1158163975 (1:143901953 T>G), RS1158265921 (1:143907715 G>A,C), RS1158281554 (1:143902843 C>CCA), RS1158473865 (1:143905365 G>A,C,T), RS1158570697 (1:143903325 C>A,G,T), RS1159402450 (1:143904659 AC>A), RS1159408857 (1:143907600 C>T), RS1159698047 (1:143906688 A>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Idecreases expression1
deoxynivalenolincreases expression1
ferrous chlorideincreases expression1
Atrazineincreases expression1
Doxorubicinaffects response to substance1
Fluorouracildecreases expression1
Furaldehydeaffects cotreatment, affects localization, increases expression1
Ivermectinincreases expression1
Oxygendecreases expression1
Sodium Chlorideincreases expression, affects cotreatment, affects localization1
Thiramdecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.