Homo sapiens gene HIST1H4D, encoding histone cluster 1, H4d.
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SUMMARY back to top
RefSeq summary
[HIST1H4D] 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 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].

RefSeq annotates one representative transcript.

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at low level, only 3.7% of the average gene in this release. The sequence of this gene is defined by 5 GenBank accessions, some from adipose (seen once).
Function: There are 9 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in pathway (Systemic lupus erythematosus). Proteins are expected to localize in cytoplasm. This gene contains domains Core histone H2A/H2B/H3/H4, TATA box binding protein associated factor (TAF) [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 6, links to other databases and other names
Map: This gene HIST1H4D maps on chromosome 6, at 6p21.3 according to Entrez Gene. In AceView, it covers 0.40 kb, from 26189323 to 26188922 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from KEGG_05322, the SNP view, gene overviews from Entrez Gene 8360, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as HIST1H4D, H4/b, H4FB, HIST4H4, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B or dJ221C16.9, LOC8360. It has been described as histone H4, histone 1, H4d, H4 histone family, member B.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Hist1h4b (e=2 10-40), Hist2h4 (e=2 10-40), Hist4h4 (e=2 10-40), Hist1h4a (e=2 10-40), Hist1h4f (e=2 10-40), Hist1h4d (e=2 10-40), Hist1h4c (e=2 10-40), Hist1h4m (e=2 10-40), LOC100041230 (e=2 10-40), Hist1h4h (e=2 10-40), Hist1h4k (e=2 10-40), Hist1h4j (e=2 10-40), Hist1h4i (e=3 10-40), mimemo (e=3 10-40), mesomo (e=3 10-40).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes his-50 (e=8 10-41), his-28 (e=8 10-41), his-56 (e=8 10-41), his-46 (e=8 10-41), his-60 (e=10-40), his-37 (e=2 10-40), his-26 (e=2 10-40), his-14+his-16 (e=2 10-40), his-14 (e=2 10-40), his-10 (e=2 10-40), his-5 (e=8 10-41), his-1 (e=2 10-40), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes HIS4 (e=4 10-41), AT5G59690 (e=2 10-40), AT3G53730 (e=2 10-40), AT1G07660 (e=10-39), vudu (e=2 10-39), AT1G07820 (e=2 10-39), teydu (e=3 10-39), AT5G59970 (e=10-38), swoybo (e=2 10-38), karbor (e=3 10-38), AT3G46320 (e=3 10-38), AT3G45930 (e=5 10-38), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
HIST1H4D Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.78 23.2 20.2 9.41 9.41 9.41 23.2 8.19 23.2 20.2 40.3 0.34 0.34 0.27 0.14 0.45 0.55 0.32 0.89 524 13.3 49.7 106 1826 8.19 26.6 37.6 0.55 0.89 0.51 524 6.21 24.8 131 6.21 32.8 12.4 161 185 28.5 35.1 30.6 18.8 49.7 57.1 11.6 3.82 213 151 795 24.8 37.6 14.3 524 37.6 10.8 913 6.21 40.3 4.39 37.6 37.6 14.3 0.68 795 122 53.2 75.3 371 32.8 37.6 46.3 0.96 1291 80.7 75.3 199 323 12.4 3.57 14.3 40.3 262 8.19 49.7 9.41 21.6 213 18.8 161 602 20.2 13.3 40.3 4.10 1.91 49.7 11.6 40.3 151 301 12.4 35.1 46.3 92.7 53.2 17.6 1.78 978 70.2 151 26.6 602 17.6 35.1 7.13 61.1 6.65 3.33 65.5 151 852 26.6 28.5 70.2 37.6 32.8 913 21.6 8.78 20.2 10.8 30.6 1.66 30.6 602 18.8 37.6 14.3 24.8 106 92.7 92.7 61.1 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene HIST1H4D 5' 3' encoded on minus strand of chromosome 6 from 26,189,323 to 26,188,922 50bp 0 402 bp exon 402 bp exon 402 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10-unspliced 402 bp 103 aa 19 bp 71 bp 2kb probably including promoter 402 bp 1kb

Gene neighbors and Navigator on chromosome 6p21.3 back to top
C I R P SLC17A4 C R P TRIM38 D C I R P R R HIST1H3A D C I P HIST1H4A C I P HIST1H3C C I P HFE D C I R P HIST1H4C D C P HIST1H2AC C I R P C C HIST1H1E C I P HIST1H2BD C I R P HIST1H2BE C P C HIST1H2BF C P HIST1H4E C P HIST1H2AE C I P HIST1H3E D C I R P HIST1H4F C I P HIST1H2BH C R P HIST1H2BI C P BTN3A2 D C R P BTN2A2andBTN3A1 D C R P BTN2A3 C R P BTN3A3andBTN2A1 D C R P BTN1A1 D I P HMGN4 R P ABT1 C I R P RPS10P1 HCG11 D C I R P D C R P HIST1H2APS2andSLC17A3 C R P SLC17A2 R C I P HIST1H1A C C P HIST1H4B C I P HIST1H3B C P HIST1H2AB C I P HIST1H2BB C I R P HIST1H1C D C P HIST1H1T D C I R P HIST1H2BC C C P HIST1H4D C R P HIST1H2ADandHIST1H3D I P HIST1H2BG D C P HIST1H1D P HIST1H4G D C I P HIST1H3F C I R P HIST1H3G C R P HIST1H4H G R C R P ZNF322A 100kb 0 SCGN, 113 accessions, 5 variants HIST1H2BA, 52 accessions 5 variants SLC17A4, 41 accessions 10 variants TRIM38, 377 accessions 13 variants roysmaby, 3 accessions vysnerby, 17 accessions 3 variants HIST1H3A, 28 accessions HIST1H4A, 28 accessions HIST1H3C, 5 accessions HFE, 145 accessions, 15 variants HIST1H4C, 261 accessions HIST1H2AC, 421 accessions 12 variants blawsnerby, 4 accessions norome, 21 accessions HIST1H1E, 26 accessions HIST1H2BD, 107 accessions 5 variants HIST1H2BE, 5 accessions sohe, 5 accessions HIST1H2BF, 17 accessions HIST1H4E, 38 accessions HIST1H2AE, 1 accession HIST1H3E, 43 accessions 3 variants HIST1H4F, 10 accessions HIST1H2BH, 56 accessions 4 variants HIST1H2BI, 9 accessions BTN3A2, 377 accessions 23 variants BTN2A2andBTN3A1, 443 accessions 36 variants BTN2A3, 33 accessions 7 variants BTN3A3andBTN2A1, 484 accessions 31 variants BTN1A1, 14 accessions 2 variants HMGN4, 575 accessions 12 variants ABT1, 324 accessions, 3 variants nukiya, 1 accession plofloyby, 1 accession sleysnorbu, 1 accession slorsnorbu, 1 accession ployfloyby, 1 accession skofloyby, 1 accession swosoby, 1 accession peyklybu, 2 accessions smawsnorbu, 1 accession bersarby, 1 accession slafloyby, 3 accessions slyfloyby, 1 accession smarjar, 8 accessions sleefloyby, 1 accession smoysnorbu, 2 accessions wosnerby, 5 accessions woysnerby, 4 accessions 2 variants slerfloyby, 5 accessions dusarby, 1 accession royklybu, 1 accession sarklybu, 2 accessions serklybu, 2 accessions smyfloyby, 1 accession smawfloyby, 1 accession bleesnerby, 1 accession soyklybu, 2 accessions snorsnorbu, 2 accessions teyklybu, 2 accessions sorvabo, 6 accessions verklybu, 1 accession sneyfloyby, 2 accessions snorfloyby, 1 accession wuklybu, 1 accession worklybu, 1 accession stubloyby, 41 accessions 2 variants spasnorbu, 4 accessions spusnorbu, 1 accession sparfloyby, 6 accessions spawfloyby, 2 accessions RPS10P1, 4 accessions sporfloyby, 1 accession spoyfloyby, 1 accession garsarby, 3 accessions tarome, 1 accession zorklybu, 1 accession ployblor, 10 accessions stofloyby, 1 accession zoyklybu, 1 accession sarjaw, 2 accessions skublor, 2 accessions steyfloyby, 3 accessions shuklybu, 1 accession storfloyby, 5 accessions stasnorbu, 1 accession jasarby, 1 accession stoyfloyby, 1 accession stysnorbu, 1 accession shoyklybu, 1 accession snerjar, 9 accessions bluklybu, 1 accession swofloyby, 4 accessions stusnorbu, 4 accessions stosnorbu, 1 accession swawfloyby, 1 accession jarsarby, 1 accession charsnobu, 1 accession skoblor, 5 accessions steesnorbu, 1 accession sweyfloyby, 2 accessions joysarby, 1 accession steysnorbu, 1 accession storsnorbu, 1 accession HCG11, 75 accessions kosarby, 1 accession swasnorbu, 1 accession swysnorbu, 1 accession blerklybu, 1 accession snoyjar, 4 accessions 2 variants byglaby, 2 accessions losarby, 1 accession spyjar, 26 accessions 2 variants blorklybu, 1 accession boglaby, 1 accession plarfloyby, 1 accession plerfloyby, 3 accessions klerblor, 2 accessions kleyblor, 4 accessions plorfloyby, 1 accession klorblor, 3 accessions kloyblor, 8 accessions skafloyby, 1 accession paklybu, 1 accession skyfloyby, 1 accession sloysnorbu, 1 accession smajar, 9 accessions skufloyby, 1 accession skarfloyby, 1 accession steesoby, 1 accession smasnorbu, 1 accession smysnorbu, 1 accession skawfloyby, 1 accession skeefloyby, 1 accession skerfloyby, 1 accession smeysnorbu, 1 accession slofloyby, 2 accessions slawfloyby, 1 accession ruklybu, 2 accessions cheesnerby, 11 accessions rorklybu, 1 accession snusnorbu, 1 accession nekiya, 7 accessions snosnorbu, 1 accession pleeblor, 3 accessions sujaw, 5 accessions smufloyby, 1 accession plerblor, 4 accessions nokiya, 2 accessions pleyblor, 2 accessions snafloyby, 1 accession terklybu, 1 accession snyfloyby, 1 accession vuklybu, 1 accession snawfloyby, 3 accessions vorklybu, 1 accession glawsnerby, 5 accessions snoyfloyby, 1 accession dosarby, 1 accession spafloyby, 2 accessions spysnorbu, 1 accession zaklybu, 2 accessions spufloyby, 2 accessions sparsnorbu, 4 accessions spawsnorbu, 1 accession skoysnerby, 2 accessions gersarby, 1 accession tavabo, 1 accession geysarby, 1 accession speysnorbu, 3 accessions styfloyby, 9 accessions tyvabo, 2 accessions stawfloyby, 1 accession smarsnerby, 1 accession steefloyby, 6 accessions snarjar, 7 accessions goysarby, 1 accession swafloyby, 1 accession swufloyby, 1 accession tuvabo, 2 accessions bleeklybu, 1 accession swusnorbu, 2 accessions bleyklybu, 1 accession swosnorbu, 4 accessions SLC17A1andHIST1H2AA, 85 accessions 11 variants HIST1H2APS2andSLC17A3 78 accessions, 10 variants SLC17A2, 53 accessions 6 variants smujar, 14 accessions 6 variants HIST1H1A, 23 accessions shysnerby, 11 accessions HIST1H4B, 15 accessions HIST1H3B, 29 accessions HIST1H2AB, 31 accessions HIST1H2BB, 4 accessions HIST1H1C, 266 accessions HIST1H1T, 19 accessions HIST1H2BC, 88 accessions 4 variants gasarby, 2 accessions HIST1H4D, 5 accessions HIST1H2ADandHIST1H3D, 82 accessions 3 variants HIST1H2BG, 127 accessions HIST1H1D, 23 accessions HIST1H4G, 8 accessions HIST1H3F, 1 accession HIST1H3G, 34 accessions HIST1H4H, 81 accessions 5 variants LOC100289545, 2 accessions snorjar, 10 accessions 3 variants ZNF322A, 161 accessions 5 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               9 articles in PubMed back to top
? Gene Summary Gene on genome mRNA Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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