Detailed information of XP_066918805.1 in Clytia hemisphaerica

Genomic Location: NW_027103774.1:652990...666605
NR annotation: AWU22326.1, nuclear lamin protein [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P11048Lamin-A OS=Xenopus laevis OX=8355 GN=lmna PE=2 SV=1
P20700Lamin-B1 OS=Homo sapiens OX=9606 GN=LMNB1 PE=1 SV=2
P70615Lamin-B1 OS=Rattus norvegicus OX=10116 GN=Lmnb1 PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003420 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00038
all species →		FilamentIntermediate filament proteinCoiled-coilInterproscan
PF00932
all species →		LTDLamin Tail DomainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR039008
all species →		DomainIntermediate filament, rod domainInterproscan
IPR001322
all species →		DomainLamin tail domainInterproscan
IPR036415
all species →		Homologous_superfamilyLamin tail domain superfamilyInterproscan
IPR018039
all species →		Conserved_siteIntermediate filament protein, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45721
all species →		LAMIN DM0-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005200
all species →		Molecular Functionstructural constituent of cytoskeletonInterproscan
GO:0005635
all species →		Cellular Componentnuclear envelopeInterproscan
GO:0005652
all species →		Cellular Componentnuclear laminaInterproscan
GO:0006998
all species →		Biological Processnuclear envelope organizationInterproscan
GO:0007097
all species →		Biological Processnuclear migrationInterproscan
GO:0031507
all species →		Biological Processheterochromatin formationInterproscan
GO:0051664
all species →		Biological Processnuclear pore localizationInterproscan
GO:0090435
all species →		Biological Processprotein localization to nuclear envelopeInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
KOEnzymeEnzyme IDPathwayMap IDSource
K07611LMNB; lamin B-Cytoskeleton proteinsko04812deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_066918805.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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.

40Samples
40TPM > 0
16Conditions
1,015.8Max TPM
148.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 77.54 95.43
medusa · Experiment Condition A1 4 4 48.06 52.54
medusa · Experiment Condition A2 4 4 58.52 60.53
medusa · Experiment Condition A3 4 4 13.51 16.54
Early gastrula 2 2 969.31 1,015.82
Planula 24hpf 2 2 409.04 421.02
Planula 48hpf 2 2 230.59 275.74
Planula 72hpf 2 2 145.79 154.30
Primary polyp 2 2 171.08 175.76
Gastrozooid 2 2 105.74 138.59
Gonozooid 2 2 116.44 124.94
Stolon 2 2 150.61 165.27
Baby medusa 2 2 63.56 68.43
medusa · Experiment Condition B1 2 2 29.67 32.83
medusa · Experiment Condition B2 2 2 77.30 78.98
Mixed 1 1 136.70 136.70

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR2816251 Mature medusa not recorded Mature medusa not recorded ERP110164 95.43
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 81.48
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 75.19
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 73.75
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 61.83
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 52.54
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 50.88
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 44.80
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 44.00
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 60.53
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 59.09
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 59.04
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 55.44
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 16.54
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 15.52
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 11.58
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 10.41
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 1,015.82
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 922.81
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 421.02
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 397.06
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 275.74
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 185.44
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 154.30
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 137.29
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 175.76
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 166.40
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 138.59
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 72.90
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 124.94
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 107.94
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 165.27
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 135.95
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 68.43
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 58.68
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 32.83
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 26.50
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 78.98
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 75.62
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 136.70

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 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.

Co-expression network

Genes whose expression across the transcriptome samples of Clytia hemisphaerica 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated27XP_066911590.10.988625935142451
Negatively correlated4XP_066912411.1-0.810536808890408

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.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Clytia hemisphaerica, 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.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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