Detailed information of XP_066930621.1 in Clytia hemisphaerica

Genomic Location: NW_027104356.1:1454696...1456688
NR annotation: XP_002163714.1, clathrin light chain B [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
P04975Clathrin light chain B OS=Bos taurus OX=9913 GN=CLTB PE=1 SV=1
P08081Clathrin light chain A OS=Rattus norvegicus OX=10116 GN=Clta PE=1 SV=1
P09496Clathrin light chain A OS=Homo sapiens OX=9606 GN=CLTA PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007272 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01086
all species →		Clathrin_lg_chClathrin light chainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000996
all species →		FamilyClathrin light chainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10639
all species →		CLATHRIN LIGHT CHAINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005198
all species →		Molecular Functionstructural molecule activityInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0006886
all species →		Biological Processintracellular protein transportInterproscan
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan
GO:0030125
all species →		Cellular Componentclathrin vesicle coatInterproscan
GO:0030130
all species →		Cellular Componentclathrin coat of trans-Golgi network vesicleInterproscan
GO:0030132
all species →		Cellular Componentclathrin coat of coated pitInterproscan
GO:0032050
all species →		Molecular Functionclathrin heavy chain bindingInterproscan
GO:0072583
all species →		Biological Processclathrin-dependent endocytosisInterproscan

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
No KEGG orthology assignment for XP_066930621.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066930621.1 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
479.6Max TPM
260.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 201.46 251.43
medusa · Experiment Condition A1 4 4 245.89 257.41
medusa · Experiment Condition A2 4 4 305.72 308.81
medusa · Experiment Condition A3 4 4 126.51 129.09
Early gastrula 2 2 376.73 396.97
Planula 24hpf 2 2 478.51 479.56
Planula 48hpf 2 2 427.49 436.57
Planula 72hpf 2 2 307.50 322.30
Primary polyp 2 2 203.08 203.85
Gastrozooid 2 2 185.00 187.64
Gonozooid 2 2 274.84 290.10
Stolon 2 2 255.11 263.20
Baby medusa 2 2 247.45 249.89
medusa · Experiment Condition B1 2 2 167.04 174.86
medusa · Experiment Condition B2 2 2 308.18 310.57
Mixed 1 1 230.26 230.26

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 251.43
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 237.67
ERR2816251 Mature medusa not recorded Mature medusa not recorded ERP110164 178.14
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 176.21
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 163.85
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 257.41
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 245.91
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 245.09
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 235.16
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 308.81
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 306.40
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 304.67
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 303.01
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 129.09
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 127.00
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 126.61
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 123.32
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 396.97
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 356.50
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 479.56
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 477.45
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 436.57
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 418.41
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 322.30
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 292.71
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 203.85
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 202.31
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 187.64
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 182.36
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 290.10
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 259.58
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 263.20
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 247.02
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 249.89
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 245.00
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 174.86
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 159.22
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 310.57
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 305.78
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 230.26

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 correlated25XP_066913009.10.93328314191082
Negatively correlated38XP_066914344.1-0.822173920709839

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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