Genomic Location: NC_064034.1:15300239...15328746
NR annotation: XP_032230598.2, nipped-B-like protein isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families
| CDS |
| LOC5506309 |
| Transcript |
| rna-XM_032374707.2 |
| Protein |
| XP_032230598.2 |
| UniProt accession | Description |
|---|---|
| Q6KCD5 | Nipped-B-like protein OS=Mus musculus OX=10090 GN=Nipbl PE=1 SV=1 |
| F1QBY1 | Nipped-B-like protein B OS=Danio rerio OX=7955 GN=nipblb PE=2 SV=1 |
| Q6KC79 | Nipped-B-like protein OS=Homo sapiens OX=9606 GN=NIPBL PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002809 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF12830 all species → | Nipped-B_C | Sister chromatid cohesion C-terminus | Repeat | Interproscan |
| PF12765 all species → | Cohesin_HEAT | HEAT repeat associated with sister chromatid cohesion | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR016024 all species → | Homologous_superfamily | Armadillo-type fold | Interproscan |
| IPR033031 all species → | Family | Scc2/Nipped-B family | Interproscan |
| IPR011989 all species → | Homologous_superfamily | Armadillo-like helical | Interproscan |
| IPR024986 all species → | Domain | Sister chromatid cohesion C-terminal domain | Interproscan |
| IPR026003 all species → | Repeat | HEAT repeat associated with sister chromatid cohesion protein | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR21704 all species → | NIPPED-B-LIKE PROTEIN DELANGIN SCC2-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003682 all species → | Molecular Function | chromatin binding | Interproscan |
| GO:0010468 all species → | Biological Process | regulation of gene expression | Interproscan |
| GO:0034087 all species → | Biological Process | establishment of mitotic sister chromatid cohesion | Interproscan |
| GO:0061780 all species → | Biological Process | obsolete mitotic cohesin loading | Interproscan |
| GO:0071169 all species → | Biological Process | establishment of protein localization to chromatin | Interproscan |
| GO:0090694 all species → | Cellular Component | Scc2-Scc4 cohesin loading complex | Interproscan |
| GO:1990414 all species → | Biological Process | replication-born double-strand break repair via sister chromatid exchange | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K06672 | SCC2, NIPBL; cohesin loading factor subunit SCC2 | - | Chromosome and associated proteins | ko03036 | deepkoala |
Transcript abundance of XP_032230598.2 across 48 RNA-seq samples of Nematostella vectensis. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| whole 6 week old aboral regenerate · regenerate 96hpa | 3 | 3 | 10.62 | 13.21 | |
| whole 6 week old aboral regenerate · regenerate 144hpa | 3 | 3 | 6.70 | 10.12 | |
| whole 6 week old aboral regenerate · regenerate 0hpa | 3 | 3 | 6.10 | 7.54 | |
| whole 6 week old aboral regenerate · regenerate 2hpa | 3 | 3 | 8.71 | 11.07 | |
| whole 6 week old aboral regenerate · regenerate uncut | 3 | 3 | 6.27 | 7.38 | |
| whole 6 week old aboral regenerate · regenerate 4hpa | 3 | 1 | 3.27 | 9.80 | |
| whole 6 week old aboral regenerate · regenerate 120hpa | 3 | 2 | 6.15 | 10.59 | |
| whole 6 week old aboral regenerate · regenerate 36hpa | 3 | 3 | 10.37 | 12.85 | |
| whole 6 week old aboral regenerate · regenerate 24hpa | 3 | 2 | 6.14 | 9.83 | |
| whole 6 week old aboral regenerate · regenerate 20hpa | 3 | 3 | 8.58 | 10.01 | |
| whole 6 week old aboral regenerate · regenerate 16hpa | 3 | 3 | 8.92 | 10.62 | |
| whole 6 week old aboral regenerate · regenerate 72hpa | 3 | 2 | 6.27 | 9.86 | |
| whole 6 week old aboral regenerate · regenerate 60hpa | 3 | 3 | 8.31 | 10.06 | |
| whole 6 week old aboral regenerate · regenerate 48hpa | 3 | 2 | 7.34 | 12.48 | |
| whole 6 week old aboral regenerate · regenerate 8hpa | 3 | 3 | 9.59 | 9.67 | |
| whole 6 week old aboral regenerate · regenerate 12hpa | 3 | 1 | 3.11 | 9.34 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR6320863 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 13.21 |
| SRR6320836 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 9.39 |
| SRR6320837 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 9.27 |
| SRR6320847 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 10.12 |
| SRR6320841 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 6.03 |
| SRR6320838 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 3.96 |
| SRR6320846 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 7.54 |
| SRR6320839 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 5.90 |
| SRR6320840 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 4.86 |
| SRR6320861 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 11.07 |
| SRR6320842 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 8.65 |
| SRR6320848 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 6.43 |
| SRR6320843 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 7.38 |
| SRR6320844 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 6.90 |
| SRR6320845 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 4.53 |
| SRR6320872 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 9.80 |
| SRR6320849 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 0.00 |
| SRR6320873 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 0.00 |
| SRR6320882 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 10.59 |
| SRR6320883 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 7.86 |
| SRR6320850 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 0.00 |
| SRR6320855 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 12.85 |
| SRR6320851 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 9.80 |
| SRR6320852 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 8.46 |
| SRR6320854 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 9.83 |
| SRR6320853 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 8.58 |
| SRR6320856 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 0.00 |
| SRR6320860 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 10.01 |
| SRR6320857 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 9.06 |
| SRR6320859 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 6.67 |
| SRR6320880 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 10.62 |
| SRR6320881 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 8.65 |
| SRR6320858 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 7.50 |
| SRR6320862 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 9.86 |
| SRR6320865 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 8.94 |
| SRR6320864 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 0.00 |
| SRR6320866 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 10.06 |
| SRR6320867 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 7.97 |
| SRR6320869 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 6.90 |
| SRR6320870 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 12.48 |
| SRR6320871 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 9.52 |
| SRR6320868 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 0.00 |
| SRR6320874 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 9.67 |
| SRR6320875 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 9.57 |
| SRR6320876 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 9.54 |
| SRR6320877 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 9.34 |
| SRR6320878 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 0.00 |
| SRR6320879 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (NVECT_TPM,
StringTie quantification over 48 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Peptides from this gene's protein product were identified in 1 re-processed proteomic dataset at a false discovery rate of q ≤ 0.01 (Comet + Percolator).
| Dataset | Species | Tissue / condition | Peptides | PSMs | Coverage | Best q | |
|---|---|---|---|---|---|---|---|
| PXD033068 | Nematostella vectensis | Embryos | 5 | 12 |
28.5%
|
0.0000678288 | peptides |
|
K.MSQSLDTDPTIVSGQKPGTTK.L q=0.0000678288
K.DAADQNFDYMFK.L q=0.0000678288 R.LVDIICDK.M q=0.0000678288 K.QLADQLGLEFYETSAK.D q=0.00110382 K.TSFLFR.Y q=0.00181798 | |||||||
Search parameters for this evidence: Comet 2026.01,
precursor 10 ppm, fragment 0.02 Da,
fixed C+57.021464, variable M+15.9949,
PSM-level q ≤ 0.01 against
.
·
all proteins for Nematostella vectensis
Genes whose expression across the transcriptome samples of Nematostella vectensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 31 | XP_032235298.1 | 0.940765225786417 |
| Negatively correlated | 3 | XP_001629182.1 | -0.626790667246612 |
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Nematostella vectensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.
| Dataset | Tissue / stage | Cells | Cell types | This gene | Marker of |
|---|---|---|---|---|---|
| NVECT_2month | 2 month animal · Adult tissues/organs | 1,614 | 23 | not in this dataset | – |
| NVECT_bodywall | body wall with mesenteries · 6-8 weeks adults | 11,742 | 13 | not in this dataset | – |
| NVECT_embryo | embryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h) | 9,711 | 17 | not in this dataset | – |
| NVECT_gastrula | Blastula-gastrula intermediate · Developmental stages | 49,166 | 27 | not in this dataset | – |
| NVECT_gastruloid | dissociated and reaggregated embryos · 4-48 hpa | 36,550 | 8 | not in this dataset | – |
| NVECT_neoplasm | neoplasm · Adult tissues/organs | 2,532 | 16 | not in this dataset | – |
| NVECT_nervous | Gastrula Cells · nervous system | 16,590 | 27 | unmapped | – |
| NVECT_notch48h | embryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf | 19,044 | 7 | not in this dataset | – |
| NVECT_tentacle | tentacle · Adult tissues/organs | 7,977 | 19 | not in this dataset | – |
A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.
Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.
| Assay | Sample | Peaks | Region |
|---|---|---|---|
| ChIP-seq | H3K27ac_gastrulae_24h | 3 | Promoter (<=1kb) 1 · Intron 1 · Exon 1 |
| H3K27ac_planulae_4days | 1 | Promoter (<=1kb) 1 | |
| H3K4me2_gastrulae_24h | 3 | Promoter (<=1kb) 2 · Intron 1 | |
| H3K4me2_polyps | 4 | Promoter (<=1kb) 2 · Intron 2 | |
| H3K4me3_gastrulae_24h | 1 | Promoter (<=1kb) 1 | |
| H3K4me3_planulae_4days | 1 | Promoter (<=1kb) 1 | |
| H3K4me3_polyps | 2 | Promoter (<=1kb) 1 · Intron 1 | |
| H3K27ac_Ncol3_negative | 1 | Promoter (<=1kb) 1 | |
| H3K27ac_Ncol3_positive | 1 | Promoter (<=1kb) 1 | |
| H3K27ac_Nep3_negative | 1 | Promoter (<=1kb) 1 | |
| H3K27ac_Nep3_positive | 1 | Promoter (<=1kb) 1 | |
| H3K36me3_gastrulae_24h | 9 | Exon 5 · Intron 2 · Promoter (<=1kb) 1 · Promoter (1-2kb) 1 | |
| H3K36me3_planulae_4days | 11 | Exon 5 · Intron 3 · Promoter (<=1kb) 2 · Promoter (1-2kb) 1 | |
| H3K36me3_polyps | 15 | Exon 7 · Intron 7 · Promoter (1-2kb) 1 | |
| H3K4me1_gastrulae_24h | 3 | Distal Intergenic 1 · Promoter (<=1kb) 1 · Intron 1 |
5 further sample(s) also have peaks at this gene; open the assay page below to see them all.
Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.
| Sample | Methylation profile |
|---|---|
| Whole_adults | open |
The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.
Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.
| Analysis | What it does | Status | |
|---|---|---|---|
| Primer design | Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed. | template found | open → |
| BLAST | Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start. | template found | open → |
| Expression heatmap | Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it. | ready | open → |
| Gene family / orthogroup | Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue. | open → | |
| Gene set analysis | Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it. | open → |
