WormMine: Gene WBGene00001939

• WormBase Gene ID: WBGene00001939
• Gene Name: his-65
• Sequence Name: H02I12.7
• Brief Description: his-65 encodes an H2A histone.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA binding activity and protein heterodimerization activity. Predicted to be a structural constituent of chromatin. Predicted to be part of nucleosome. Human ortholog(s) of this gene implicated in oral mucosa leukoplakia and oral squamous cell carcinoma. Is an ortholog of human H2AX (H2A.X variant histone).
• Biotype: SO:0001217
• Genetic Position: IV :4.97543±
• Length (nt): 384

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001939

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:H02I12.7.1	H02I12.7.1	384	IV: 11401092-11401475

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:H02I12.7	H02I12.7	384	IV: 11401092-11401475

35 RNAi Result

• WBRNAi00035860
• WBRNAi00073290
• WBRNAi00085707
• WBRNAi00073157
• WBRNAi00024356
• WBRNAi00025632
• WBRNAi00025686
• WBRNAi00025785
• WBRNAi00090824
• WBRNAi00090833
• WBRNAi00049266
• WBRNAi00048335
• WBRNAi00053923
• WBRNAi00068649
• WBRNAi00068650
• WBRNAi00068651
• WBRNAi00068652
• WBRNAi00068653
• WBRNAi00073159
• WBRNAi00073292
• WBRNAi00033648
• WBRNAi00073158
• WBRNAi00073291
• WBRNAi00025128
• WBRNAi00096916
• WBRNAi00096915
• WBRNAi00096917
• WBRNAi00096919
• WBRNAi00069033
• WBRNAi00080674

10 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963703
• gk963917
• WBVar02121216
• WBVar02124419
• WBVar02124420
• gkDf85

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001939
• Start: 11401092
• End: 11401475
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_11401476..11401944
• Length (nt): 469
• Chromosome Location: IV: 11401476-11401944
• Organism: Caenorhabditis elegans

46 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly increased expression in his-3(RNAi) comparing to in vector control animals.	The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed.	WBPaper00053402:his-3(RNAi)_upregulated
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts that showed significantly decreased expression in mir- 229,64,65,66(nDf63) III comparing to in N2 animals.	DESeq2 v1.30.1, fold change > 2, FDR < 0.05.	WBPaper00064999:miR-229-64-65-66_downregulated
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated_P.aeruginosa-infection
	Transcripts expressed in germline, according to RNA tomography.	RNA tomography	WBPaper00055648:germline_expressed
	Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing.	DESeq2, fold change > 2,, p-value < 0.01	WBPaper00055334:DLC-1_interacting
	Transcripts that showed significantly increased expression in animals exposed to Leptomycin B for 3 hours at 2C.	p < 0.01, logFC > 1 or p < 0.01, logFC < -1.	WBPaper00066610:Leptomycin-B_upregulated_2C_3h
Bacteria infection: N.ausubeli	Transcripts that showed significantly altered expression in C. elegans wild isolate strain N2 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:N2_N.ausubeli_regulated
	mRNAs that showed significantly increased expression in monosomal fractions in N2 comparing to in daf-2(e1370), according to RNAseq study.	Differentially expressed genes were determined using cuffdiff across all pairs.	WBPaper00046337:monosomal_N2_vs_daf-2_upregulated
	mRNAs that showed significantly increased expression in polysomal fractions in daf-2(e1370) comparing to in daf-2(e1370);daf-16(mu86), according to RNAseq study.	Differentially expressed genes were determined using cuffdiff across all pairs.	WBPaper00046337:polysomal_daf-2_vs_daf-2;daf-16_upregulated
	Transcriptions that showed significantly decreased expression in daf-16(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:daf-16(RNAi)_downregulated
	Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals.	edgeR p-value < 0.01 and fold change > 4.	WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated
	Transcripts that showed significantly increased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_upregulated
mitochondrial sulfide delivery molecule (mtH2S) AP39	Transcripts that showed significantly decreased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:mtH2S-AP39-D0-treatment_downregulated_Day11
Temperature shift: 15C vs 20 C.	Proteins that showed significantly decreased expression in CF512 (fer-15(b26)II;fem-1(hc17)IV) treated with empty RNAi vector at 15C comparing to at 20C.	Two-tailed Student's t-test (n=3, P-value <0.05 was considered significant).	WBPaper00057288:Cold_downregulated_protein
spaceflight-induced microgravity on the ISS (International Space Station).	Transcripts that showed significantly increased expression in animals grew under spaceflight-induced microgravity on the ISS (International Space Station).	N.A.	WBPaper00061274:microgravity_upregulated
	Proteins down-regulated in glp-1(e2141) mutants vs. wild type N2	The abundance of proteins with a fold change of >1.2 or <0.83 and corrected p-values < 0.05 was considered to be significantly altered in the glp-1 mutant.	WBPaper00050686:glp-1(e2141)_downregulated
	Transcripts up regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to N2.	DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05.	WBPaper00048988:daf-2(e1370)_daf-16(mu86)_upregulated_neuron

3 Expression Patterns

• Primary Identifier: Expr1153010
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2030713
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr2012474
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

4 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001939
• Start: 11401092
• End: 11401475
• Strand: 1

4 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 384

1 Sequence Ontology Term