Gene detail

Detailed information of HSymV2.0_g06.10874_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_6:21359807...21382959
NR annotation: XP_047144520.1, succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

HSymV2.0_g06.10874_t1

GGAAttctcgctggtcatttaaatatcaaaaaagagaaaaaaagccctgcgatcgaggttgCCTAGGTGTCGTTTTACACGTAAAAAAGATGCCACCCTTGTTCGCAGTGATTTTTTTCTATCAATCAAAAAAGCAAAACAAGGGGATACCTTGTGGTCCGGCGTCTGTGTAGTATCATTCCCCCGAGCAAAAACAAACGTGCCTTCCCTCATTCGATTGAGGTGTGTATTTTAAGGAACTGTTTATATTCAAATAAAGTTACGTCACTTATGGTATTGTGCTGCAGCGTGCAGGCTTGACAGAGCACAAGAAGAAGCAAGGTCACATCGGTTATGTTGTCTTTGCGGAGGCTAGTATCCCTAAAAAAGTTTTCAAGGTGCACTCCTTCTGCAAGCCGTGCATTTCATTTCACAGTAGATGGATCAAGAAGCTCGGACAAAACAACTAGGGGAGAGCTGAGTCGTCAGTATCCAGTTATTGATCATACATATGACTGTGTTGTTGTTGGAGCAGGTGGCGCTGGTTTGAGAGCAGCATTTGGTTTGGCAAATGCTGGCTTTAAAACAGCATGTGTGACCAAGTTATTTCCAACAAGATCCCACACTGTTGCTGCACAGGGTGGTGTAAATGCAGCTTTAGGCAATATGGAAACTGATAATTGGATATGGCACATGTATGATACAGTTAAAGGATCTGATTGGTTGGGAGACCAGGATGCAATACACTACATGACACGTGAAGCACCACAGGCTGTATACGAATTAGAAAATTATGGCATGCCTTTCAGTCGAACAGAAGAGGGACGTATTTATCAAAGAGCTTTTGGAGGACAAAGTTTAAATTTTGGTAAAGGCGGGCAAGCACATCGTTGTTGCGCTGTTGCTGACAGAACTGGGCACTCCCTGCTACATACATTATATGGACAGTCACTTCGATACGACTGTCAATATTTCATTGAATATTTCGCTATGGACCTGCTAATGGATAAAGGTAGATGCTTGGGTGTGATGGCACTTAATTTAGAGGATGGCTCATTGCATCGAATTAAAGCCAAAAATACAATCATCGCTACTGGTGGCTATGGACGTGCTTACTTTTCATGCACGTCTGCTCACACTTGCACTGGTGATGGCACTGCAATGGTAACACGAGCAGGACTACCCAATGAAGATCTTGAATTTGTACAGTTTCACCCAACTGGTATATATGGTGCTGGTTGTCTCATCACAGAAGGAAGCAGAGGGGAAGGTGGATATCTATTGAACAGCGAGGGTGAACGATTTATGGAACGCTATGCACCGACTGCTAAAGATTTGGCATCACGTGATGTGGTGTCACGTTCAATGACAATTGAAATGAGAGAAGGAAGAGGTTGTGGACCTGAGAAAGATCACATTCACTTGCAATTGTCTCACTTACCTGCTGACGTATTAAAGACTCGCTTACCTGGTATTTCGGAGACTGCTATGATTTTTGCTGGTGTTGATGTTACACGAGATCCTATTCCAGTCCTGCCAACTGTACATTACAACATGGGAGGTGTGCCTACCAATTACTTGGGACAGGTATTGGATCACAAAGATGGTAAAGATGTTTTGATTGATGGTCTTTATGCTGCTGGTGAAGCTGCTTGTGCGTCAGTGCACGGTGCAAACAGGCTTGGTGCAAACTCCCTATTGGATCTTGTCATCTTTGGTCGTGCATGCGCACTTGATATTATTGATAAACACAAGCCAGGCGATAAGATCCCAGATATTCCATCGAATGCCGGTGAGGAATCAGTTGCAAATTTGGATAAAGTGAGATTTGCGAATGGACGAACACCTGTTGCTGCTTTGAGATTGAAAATGCAAAAGACTATGCAAGATTACGCCTCTGTGTTTCGAACTGGCGATGTTCTGAAGGAAGGCTGTGTGAAAATGGCGGAAATTTACAATGAACTCGAAGATATCAAGTTGTATGATCGCGGCATGGTGTGGAATACGGACCTCGTGGAAGCACTCGAACTTCAGAACTTAATGATAAATGCTGTGCAGACTATTGAAAGCGCAGAAGCAAGAAAAGAAAGTAGAGGAGCGCATGCGCGAGAAGATTTTAAGGATCGGCTTGATGAATACGATTATAGTAAACCTTTGGAAGGACAAGTAAAAAAACCAATGGAACAACATTGGAGAAAACACACGTTAAGCTACCAAGACCCTGAAACTGGAAAGGTTACGCTAGCATATCGAGCTGTTATTGATGAAACCCTGGATGAGAAAGAATGCGCTACTGTTCCACCGGCTGTACGATCGTACTAAAATAAAGTATTAATTTTTTTGTAAATATGCATATCTTGCAAATAATGTTATCTTCTTACTGAAATCGTGTGTTTTTATCAGCCAACTCTGTGTTTTAAAATTGGTTTCACATATTGTATCTAAAGGAACCTTTTAAATAATTCTGTTCACAAGTTTTTTTGCTTGTAGTTTTCCGTCAGCTCAGtgttgtgttgttgttgtcattgttgttgtttgtttatttattgtgtttgtgtatttgtttttAACTTTAATATGGTTGTTAGCCAAGAGATAAAaagaaaagaaaaatggataatgtaaatccttgcattttgccacaaagccagctgttttcttcagtgcaaacatcatggggtttATTGCCTCACCG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R616	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial OS=Pongo abelii OX=9601 GN=SDHA PE=2 SV=1
P31040	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial OS=Homo sapiens OX=9606 GN=SDHA PE=1 SV=2
Q7ZVF3	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial OS=Danio rerio OX=7955 GN=sdha PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003918 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02910 all species →	Succ_DH_flav_C	Fumarate reductase flavoprotein C-term	Domain	Interproscan
PF00890 all species →	FAD_binding_2	FAD binding domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR030664 all species →	Family	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Interproscan
IPR027477 all species →	Homologous_superfamily	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Interproscan
IPR011281 all species →	Family	Succinate dehydrogenase, flavoprotein subunit	Interproscan
IPR014006 all species →	Family	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Interproscan
IPR037099 all species →	Homologous_superfamily	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Interproscan
IPR003952 all species →	Binding_site	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Interproscan
IPR015939 all species →	Domain	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Interproscan
IPR003953 all species →	Domain	FAD-dependent oxidoreductase 2, FAD binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11632 all species →	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000104 all species →	Molecular Function	succinate dehydrogenase activity	Interproscan
GO:0005749 all species →	Cellular Component	obsolete mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)	Interproscan
GO:0006121 all species →	Biological Process	mitochondrial electron transport, succinate to ubiquinone	Interproscan
GO:0008177 all species →	Molecular Function	succinate dehydrogenase (quinone) activity	Interproscan
GO:0009055 all species →	Molecular Function	electron transfer activity	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0006099 all species →	Biological Process	tricarboxylic acid cycle	Interproscan
GO:0016627 all species →	Molecular Function	oxidoreductase activity, acting on the CH-CH group of donors	Interproscan
GO:0022900 all species →	Biological Process	electron transport chain	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	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
K00234	SDHA, SDH1; succinate dehydrogenase (ubiquinone) flavoprotein subunit	EC:1.3.5.1	Non-alcoholic fatty liver disease	ko04932	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_g06.10874_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

337.5Max TPM

234.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	225.12	337.50
Whole embryo · Triptolide 20 uM	4	4	281.71	331.24
Whole embryo · DMSO 0.5%	4	4	269.02	315.54

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
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	337.50
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	325.65
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	325.38
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	321.19
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	311.00
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	309.80
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	306.22
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	281.62
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	277.21
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	275.19
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	264.37
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	261.22
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	256.72
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	249.46
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	249.18
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	248.25
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	245.57
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	240.30
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	239.93
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	239.30
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	237.39
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	223.33
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	221.82
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	197.11
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	195.45
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	189.16
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	184.04
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	174.51
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	168.74
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	159.50
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	123.74
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	114.66
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	113.26
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	84.88
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	84.75
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	67.05
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	331.24
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	300.80
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	252.48
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	242.31
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	315.54
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	302.94
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	234.59
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	223.00

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	35	HSymV2.0_g12.21759_t1	0.984044000842864
Negatively correlated	11	HSymV2.0_g01.00348_t1	-0.91754406266066

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 →