WormMine: Gene WBGene00003847

• WormBase Gene ID: WBGene00003847
• Gene Name: blmp-1
• Sequence Name: F25D7.3
• Brief Description: blmp-1 encodes a zinc finger and SET domain-containing protein that is the C. elegans BLIMP1 (B lymphocyte-induced maturation protein 1) ortholog; loss of blmp-1 activity via deletion mutation has been reported to result in small, dumpy animals with abnormal fat content, while loss of blmp-1 activity via RNAi reportedly results in animals that are small, dumpy, have an amorphous pharynx, and are uncoordinated with patchy coloration and protruding vulvae; a blmp-1::gfp transcriptional fusion is expressed from late embryogenesis through adulthood and found in a variety of tissues including hypodermis, seam cells, gonad distal tip cells and vulva, ventral nerve cord, amphids and phasmids, and rectal muscles.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of distal tip cell migration; regulation of developmental process; and regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Expressed in several structures, including distal tip cell; dorsal nerve cord; enteric muscle; neurons; and tail hypodermis. Human ortholog(s) of this gene implicated in gastrointestinal system cancer (multiple); lung adenocarcinoma; and non-Hodgkin lymphoma (multiple). Is an ortholog of human PRDM1 (PR/SET domain 1).
• Biotype: SO:0001217
• Genetic Position: I :4.9856 ±0.009659
• Length (nt): 5472

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003847

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F25D7.3b.1	F25D7.3b.1	3389	I: 10409302-10414772
Transcript:F25D7.3a.1	F25D7.3a.1	3438	I: 10409302-10414773

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F25D7.3a	F25D7.3a	2454	I: 10409359-10409536
CDS:F25D7.3b	F25D7.3b	2406	I: 10409359-10409536

23 RNAi Result

• WBRNAi00115427
• WBRNAi00070595
• WBRNAi00022334
• WBRNAi00073051
• WBRNAi00073053
• WBRNAi00073052
• WBRNAi00025216
• WBRNAi00045492
• WBRNAi00025217
• WBRNAi00113461
• WBRNAi00076335
• WBRNAi00031366
• WBRNAi00115665
• WBRNAi00070594
• WBRNAi00070593
• WBRNAi00070175
• WBRNAi00092008
• WBRNAi00091527
• WBRNAi00091529
• WBRNAi00114534
• WBRNAi00116854
• WBRNAi00116180
• WBRNAi00087689

68 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• h12867
• h15089
• s71
• tm548
• WBVar01822920
• ns823
• ns830
• tp5
• tk41
• WBVar02001728
• WBVar00156486
• gk446009
• gk511515
• gk597123
• gk823615
• WBVar01910312
• WBVar01910313
• WBVar01910314
• WBVar01910315
• WBVar01910311
• gk563817
• gk120616
• gk555050
• gk120617
• gk953933
• gk656070

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003847
• Start: 10409302
• End: 10414773
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_10414774..10418233
• Length (nt): 3460
• Chromosome Location: I: 10414774-10418233
• Organism: Caenorhabditis elegans

188 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	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 decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
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 increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated

15 Expression Patterns

• Primary Identifier: Expr1031815
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2009633
• 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: Expr7519
• Remark: Clone: pUL#JRH6E7
• Pattern: Expression is observed from late embryogenesis to adult in hypodermis, seam cells, gonad distal tip cells and vulva, ventral nerve cord, amphids and phasmids, and rectal muscles.

• Primary Identifier: Expr11673
• Remark: Temporal description
• Pattern: BLMP-1::GFP showed overlapping expression with DRE-1::GFP in seam and hypodermal cells as well as the dtcs. In the dtcs, BLMP-1::GFP was expressed from mid-L2, when gonadal outgrowth initiates toward head and tail. By mid-L3 (28-30 hr developmental age [DA]), just prior to the dorsal gonadal turn, BLMP-1::GFP levels in the dtcs dropped dramatically. Correlatively, DRE-1::GFP levels in the dtcs increased steadily from L2 to L4. In seam and hypodermal cells BLMP-1::GFP levels were largely constant throughout larval development, except for a transient peak early in L4, which coincides with the time of seam cell fusion, suggesting this BLMP-1 pulse could trigger the fusion event.

• Primary Identifier: Expr11550
• Pattern: Expressed in head and tail neurons, VCNs, DCNs, hypodermis.

• Primary Identifier: Expr14381

• Primary Identifier: Expr1200008
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr11053
• Pattern: A transgenic line expressing a BLMP-1::GFP fusion protein shows both nuclear and cytoplasmic expression in hyp8-11 throughout development, although cytoplasmic expression is most intense during tail tip retraction.

• Primary Identifier: Expr1020166
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2027872
• 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: Expr11855
• Pattern: BLMP-1 was present in DTCs only before the dorsal turn. In animals carrying the integrated Pblmp-1::dgfp transgene, the DTCs of 75.6% of worms expressed GFP in the early and mid L3 stages, while only 4.3% expressed GFP in the late L3 and L4 stages, suggesting that blmp-1 transcription is strongly repressed during, and after, late L3 stage.

• Primary Identifier: Expr15860
• Pattern: We found that blmp-1 transcription is detected in the tail-spike cell as early as the mKatePH reporter (1.5-fold stage). blmp-1 transcription continues until the tail-spike cell dies with a characteristic rounded refractile morphology at the 3.7-fold stage.

• Primary Identifier: Expr15861
• Pattern: We found that, like the transcriptional reporter, endogenous BLMP-1::GFP is detected in the tail-spike cell from the 1.5-fold stage until the cell dies.

• Primary Identifier: Expr13415
• Pattern: Upon examining the expression pattern of BLMP-1 during development by qPCR and Western blot analysis we noted that the messenger RNA (mRNA) and protein levels of BLMP-1 highly increased at the L2 (second larval) stage compared with other developmental stages.

• Primary Identifier: Expr1149411
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

24 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003847
• Start: 10409302
• End: 10414773
• Strand: 1

24 Ontology Annotations

10 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in blmp-1(tm548) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00062347:blmp-1(tm548)_upregulated
	Significantly up-regulated genes (>= 1.5-fold change, q value < 0.05) in blmp-1(tm548) mutant versus N2 L3 larvae as obtained from RNA sequencing analysis (n = 3).	Differential gene expression was performed with cuffdiff - which is part of the cufflinks package (v2.0.2) Genes with a FPKM value >0.5 in at least one of the N2 and blmp1 samples were considered expressed. Those with a q-value < 0.05 and fold change > +/- 1.5 were classified as differentially expressed.	WBPaper00045017:blmp-1(tm548)_upregulated
	Transcripts that showed significantly increased expression in blmp-1(tm548) comparing to in N2.	t-test, fold change > 2.	WBPaper00049732:blmp-1(tm548)_vs_N2_upregulated
	Transcripts that showed significantly decreased expression in blmp-1(tm548) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00062347:blmp-1(tm548)_downregulated
	Significantly down-regulated genes (>= 1.5-fold change, q value < 0.05) in blmp-1(tm548) mutant versus N2 L3 larvae as obtained from RNA sequencing analysis (n = 3).	Differential gene expression was performed with cuffdiff - which is part of the cufflinks package (v2.0.2) Genes with a FPKM value >0.5 in at least one of the N2 and blmp1 samples were considered expressed. Those with a q-value < 0.05 and fold change > +/- 1.5 were classified as differentially expressed.	WBPaper00045017:blmp-1(tm548)_downregulated
	Transcripts that showed significantly decreased expression in blmp-1(tm548) comparing to in N2.	t-test, fold change > 2.	WBPaper00049732:blmp-1(tm548)_vs_N2_downregulated
	Transcripts that showed significantly decreased expression in blmp-1(s71) young adult animals comparing to in N2.	DESeq2(v1.22.0; padj < 0.01 and fold change > 2)	WBPaper00062715:blmp-1(s71)_downregulated
	Transcripts that showed significantly decreased expression in blmp-1(tm548);daf-7(e1372ts) comparing to in daf-7(e1372ts).	t-test, fold change > 2.	WBPaper00049732:blmp-1(tm548);daf-7(e1372ts)_vs_daf-7(e1372ts)_downregulated
	Transcripts that showed significantly increased expression in blmp-1(s71) young adult animals comparing to in N2.	DESeq2(v1.22.0; padj < 0.01 and fold change > 2)	WBPaper00062715:blmp-1(s71)_upregulated
	Transcripts that showed significantly increased expression in blmp-1(tm548);daf-7(e1372ts) comparing to in daf-7(e1372ts).	t-test, fold change > 2.	WBPaper00049732:blmp-1(tm548);daf-7(e1372ts)_vs_daf-7(e1372ts)_upregulated

1 Sequence

• Length: 5472

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00022557
• WBStrain00034109
• WBStrain00034369
• WBStrain00000464

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_10407586..10409301
• Length (nt): 1716
• Chromosome Location: I: 10407586-10409301
• Organism: Caenorhabditis elegans