Gene detail

Detailed information of HSymV2.0_g09.17477_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_9:27934503...27939164
NR annotation: XP_002163175.1, microtubule-associated proteins 1A/1B light chain 3C [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9BXW4	Microtubule-associated protein 1 light chain 3 gamma OS=Homo sapiens OX=9606 GN=MAP1LC3C PE=1 SV=1
Q2HJ23	Microtubule-associated protein 1 light chain 3 alpha OS=Bos taurus OX=9913 GN=MAP1LC3A PE=2 SV=1
Q9H492	Microtubule-associated protein 1 light chain 3 alpha OS=Homo sapiens OX=9606 GN=MAP1LC3A PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001129 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02991 all species →	ATG8	Autophagy protein Atg8 ubiquitin like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004241 all species →	Family	Autophagy protein Atg8 ubiquitin-like	Interproscan
IPR027731 all species →	Family	Microtubule-associated protein 1A/1B light chain 3C	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10969 all species →	MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006914 all species →	Biological Process	autophagy	Interproscan
GO:0000045 all species →	Biological Process	autophagosome assembly	Interproscan
GO:0000421 all species →	Cellular Component	autophagosome membrane	Interproscan
GO:0000422 all species →	Biological Process	autophagy of mitochondrion	Interproscan
GO:0005776 all species →	Cellular Component	autophagosome	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006995 all species →	Biological Process	cellular response to nitrogen starvation	Interproscan
GO:0016236 all species →	Biological Process	macroautophagy	Interproscan
GO:0031625 all species →	Molecular Function	ubiquitin protein ligase binding	Interproscan
GO:0097352 all species →	Biological Process	autophagosome maturation	Interproscan

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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10435	MAP1LC; microtubule-associated protein 1 light chain	-	Cytoskeleton proteins	ko04812	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of HSymV2.0_g09.17477_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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.

44Samples

44TPM > 0

3Conditions

582.7Max TPM

333.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	312.13	582.67
Whole embryo · Triptolide 20 uM	4	4	402.37	495.38
Whole embryo · DMSO 0.5%	4	4	453.48	559.06

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	582.67
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	555.76
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	530.47
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	459.84
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	434.93
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	418.36
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	412.43
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	407.50
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	383.20
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	365.67
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	350.95
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	350.60
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	344.53
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	340.83
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	339.48
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	320.95
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	316.06
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	313.75
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	285.11
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	282.08
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	272.94
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	271.94
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	268.19
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	258.21
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	255.50
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	252.42
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	244.76
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	244.36
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	228.28
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	184.92
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	171.62
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	168.52
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	161.28
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	159.96
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	158.73
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	140.03
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	495.38
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	429.12
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	367.19
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	317.81
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	559.06
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	519.88
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	377.26
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	357.74

Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM, StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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	40	HSymV2.0_g09.17478_t1	0.953763673917656
Negatively correlated	40	HSymV2.0_g14.24438_t1	-0.914737213797768

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 Hydractinia symbiolongicarpus, 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.

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 →