Gene detail

Detailed information of gfas1.m1.5347.m1 in Galaxea fascicularis

Genomic Location: Sc0000298:131090...148698
NR annotation: XP_022785601.1, LOW QUALITY PROTEIN: TFIIH basal transcription factor complex helicase XPB subunit-like [Stylophora pistillata]
Species Galaxea fascicularis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

gfas1.m1.5347.m1

ATGAAAAGCCATAAGCGTAAAACAGACGACTCCTCAAAACCGTCAAGAAAGGCAAAGAAAAGCAAGATTGAGGACGATGATGATTTTGCTGACGAGGAATCCATAGATGATGTGGAGATTGCTCCCAAGTCATCCGCTGCTGCTGTGACAGATGAGGCAAATGAAGATGAGTTTGGAGCCAAAGATTATCGCAAAATGACAGAACTCAAAGCTGACCATGCTTCCAGACCTCTTTGGGTGGCGCCTGATGGGCACATTTTCTTGGAGTCATTTTCTCCTGTGTATAAACATGCTCATGACTTTCTTATTGCTATTTCAGAGCCCGTTTGCAGACCTGAACATATCCATGAGTACAGACTAACTGCTTATTCTCTGTATGCTGCTGTGTCAGTCGGTCTTCAGGATGTTCTGCAGCACCTTTTACAAGATCCTGAGATTGAAAATTGTCGCAAGCGCACAGATGGGGACCTTGAACTTGGTTCAGGGGAGGATCAACTTGTGAAGTCAACTGTGGGTGGAAAGTCGTCATTAAAGGTGCTATTGCATTTGAACAAACCACAGGAATCCAATGGCAGTTCTTCTCAAACAACAGAACAGGATCAACCATCAGAAGGAACAGTCATACCAACAGACATTTCTGATTACATTGAAAGGATTGATCAGGATGAGGATGAAGAAGAGAGCCAGACGTATTCCTTTGAGGTGGCTCAGGAGAACATTGAAACTTTACAGCGGAAGTGTATTGAGCTGGACTACCCTTTGTTAGCTGAATATGATTTCAAAAATGACACTGTAAACCCAGACTTGAATATGGACTTAAAACCAACAACAGTTTTACGACCTTATCAGGAGAAAAGTCTTCGTAAGATGTTTGGCAATGGTCGTGCGAGGTCTGGTGTCATTGTACTGCCTTGTGGGGCGGGTAAGACTCTTGTTGGTGTGACGGCAGCCTGTACAGTAAGGAAACGATGTCTTGTGCTTTGTACATCAGGCGTTGCAGTGGAGCAATGGAAAAGTCAGTTCAAGATGTGGTCCACAATTGATGATCGCACCATCTGCCGTTTCACCTCAGATGCCAAAGATAAGCCTGTCAACTGTAATATTGCCATTTCAACGTATTCTATGGTGTCATTCACTGGCAAAAGATCCTGGGAAGCAGGCGAGGTGATGAATTTTATGCAGACACAGGAATGGGGTCTAATGATTTTAGATGAGGTTCATACTATCCCAGCCAAGCAATTCAGAAGGGTATTAACAGTCGTTCAAGCACATTGTAAGCTGGGGCTTACAGCAACGCTGGACTTAAATTTCCTGATTGGACCCAAGCTTTACGAAGCTAATTGGATGGAACTCCAAAACAATGGATTTATTGCACGGGTCCAGTGTGCAGAGGTTTGGTGCCCGATGACGCCTGAATTTTACAGAGAATATCTTAACATCAGAACGCGAAAGAGAAAGTTATTATATGTAATGAATCCAAACAAGTTTCGTTCTTGTGAGTTCTTGATTCGTTATCATGAAAGACGGAATGATAAAGTCATCGTGTTCTCCGATAATGTCTTTGCTCTAAAAAAGTACGCTGAAAAGTTAAAGAAGCCTTTCATCTACGGGCCAACATCACAAGGTGAACGCATGCACATTTTACAGAACTTTCAGCACAACCCACTCGTCAATACGGTGTTCATTTCCAAGGTCGGAGATAATTCCTTTGATCTCCCGGAAGCCAACGTTTTAATTCAGATTTCTTCTCATGGTGGATCAAGAAGGCAGGAAGCTCAGCGACTTGGAAGAATTCTACGTGCGAAAAAAGATATGGCTGCCGAGGAGTACAACGCATTCTTTTACACACTTGTCTCCACGGACACTGAAGAAATGTACTATTCTGCTAAACGACAGCGGTTTTTAGTCAATCAAGGTTACAGCTTTAAGGTTATTACCAGGCTTGCTGGAATGGAGGAGGAGAATTTAGAACTTGGCGACAAAAGAAAACAACAGGAACTTCTGCAACAGGTCCTTGCTGCTAGTGAAGCAGACGCTGATGAGGAAAGAGTAGCTTCTGACGCAATAAGCCGCAGCAGCTCATCGAATTCTCTGGTGTCTCGTCGACAAGGTTCGATGGCATCCATGTCAGGAGCGGATGACATGATGTACCTTGAATACAGGAGCAGCTCCAAGTCTTCTAAAAACAGACATCCGCTCTTCAAACAGTTCAGGAATTGA

Transcript

gfas1.m1.5347.m1

TGCGATGATTAGAAGGGGCTTTTTCGCGGATGTGGCATTTTCATTGCAAAATATTTGCGGTTATTAAAGGAAAATAGTGCACCTCATCTCAACGAGCTGAACGGTCGCCATGAAAAGCCATAAGCGTAAAACAGACGACTCCTCAAAACCGTCAAGAAAGGCAAAGAAAAGCAAGATTGAGGACGATGATGATTTTGCTGACGAGGAATCCATAGATGATGTGGAGATTGCTCCCAAGTCATCCGCTGCTGCTGTGACAGATGAGGCAAATGAAGATGAGTTTGGAGCCAAAGATTATCGCAAAATGACAGAACTCAAAGCTGACCATGCTTCCAGACCTCTTTGGGTGGCGCCTGATGGGCACATTTTCTTGGAGTCATTTTCTCCTGTGTATAAACATGCTCATGACTTTCTTATTGCTATTTCAGAGCCCGTTTGCAGACCTGAACATATCCATGAGTACAGACTAACTGCTTATTCTCTGTATGCTGCTGTGTCAGTCGGTCTTCAGGATGTTCTGCAGCACCTTTTACAAGATCCTGAGATTGAAAATTGTCGCAAGCGCACAGATGGGGACCTTGAACTTGGTTCAGGGGAGGATCAACTTGTGAAGTCAACTGTGGGTGGAAAGTCGTCATTAAAGGTGCTATTGCATTTGAACAAACCACAGGAATCCAATGGCAGTTCTTCTCAAACAACAGAACAGGATCAACCATCAGAAGGAACAGTCATACCAACAGACATTTCTGATTACATTGAAAGGATTGATCAGGATGAGGATGAAGAAGAGAGCCAGACGTATTCCTTTGAGGTGGCTCAGGAGAACATTGAAACTTTACAGCGGAAGTGTATTGAGCTGGACTACCCTTTGTTAGCTGAATATGATTTCAAAAATGACACTGTAAACCCAGACTTGAATATGGACTTAAAACCAACAACAGTTTTACGACCTTATCAGGAGAAAAGTCTTCGTAAGATGTTTGGCAATGGTCGTGCGAGGTCTGGTGTCATTGTACTGCCTTGTGGGGCGGGTAAGACTCTTGTTGGTGTGACGGCAGCCTGTACAGTAAGGAAACGATGTCTTGTGCTTTGTACATCAGGCGTTGCAGTGGAGCAATGGAAAAGTCAGTTCAAGATGTGGTCCACAATTGATGATCGCACCATCTGCCGTTTCACCTCAGATGCCAAAGATAAGCCTGTCAACTGTAATATTGCCATTTCAACGTATTCTATGGTGTCATTCACTGGCAAAAGATCCTGGGAAGCAGGCGAGGTGATGAATTTTATGCAGACACAGGAATGGGGTCTAATGATTTTAGATGAGGTTCATACTATCCCAGCCAAGCAATTCAGAAGGGTATTAACAGTCGTTCAAGCACATTGTAAGCTGGGGCTTACAGCAACGCTGGACTTAAATTTCCTGATTGGACCCAAGCTTTACGAAGCTAATTGGATGGAACTCCAAAACAATGGATTTATTGCACGGGTCCAGTGTGCAGAGGTTTGGTGCCCGATGACGCCTGAATTTTACAGAGAATATCTTAACATCAGAACGCGAAAGAGAAAGTTATTATATGTAATGAATCCAAACAAGTTTCGTTCTTGTGAGTTCTTGATTCGTTATCATGAAAGACGGAATGATAAAGTCATCGTGTTCTCCGATAATGTCTTTGCTCTAAAAAAGTACGCTGAAAAGTTAAAGAAGCCTTTCATCTACGGGCCAACATCACAAGGTGAACGCATGCACATTTTACAGAACTTTCAGCACAACCCACTCGTCAATACGGTGTTCATTTCCAAGGTCGGAGATAATTCCTTTGATCTCCCGGAAGCCAACGTTTTAATTCAGATTTCTTCTCATGGTGGATCAAGAAGGCAGGAAGCTCAGCGACTTGGAAGAATTCTACGTGCGAAAAAAGATATGGCTGCCGAGGAGTACAACGCATTCTTTTACACACTTGTCTCCACGGACACTGAAGAAATGTACTATTCTGCTAAACGACAGCGGTTTTTAGTCAATCAAGGTTACAGCTTTAAGGTTATTACCAGGCTTGCTGGAATGGAGGAGGAGAATTTAGAACTTGGCGACAAAAGAAAACAACAGGAACTTCTGCAACAGGTCCTTGCTGCTAGTGAAGCAGACGCTGATGAGGAAAGAGTAGCTTCTGACGCAATAAGCCGCAGCAGCTCATCGAATTCTCTGGTGTCTCGTCGACAAGGTTCGATGGCATCCATGTCAGGAGCGGATGACATGATGTACCTTGAATACAGGAGCAGCTCCAAGTCTTCTAAAAACAGACATCCGCTCTTCAAACAGTTCAGGAATTGATGAATGAGACCTTATTCTGTTGGTGACGAGGAAGGTGTTTCTGAATACAGAAGAGAGAAATGACAGAAAAAATTAGGGGAGATTCCTGGCAATATACCTGAGAACTGAACGCCTCTGCGCTTCCTGTTTATTCTTAACCTTACCTAAATTGTACCGAATGTAAACTGTAAAAAAGGGATAGCATTAAAAAGAATTTGTTAGTGACTTCTCCTCTTCATTCAGATTGTAGATACATCGGTATTAAGACCGCACGAATTTTCTTCTATACATTGGATAATACCTGTTCCTTTACGCGGAATTATTGTTGTGAAACAAGAGTCAATAACTGAGCAATGCACCAAACCTCATTCTTAGATCGTCATTTATACTACGCTTCTTAGTTGAGCGCGACACCACGCAACTTTCCACAAAAAGTTTTGACGTCAAAACAGTGCGTTTCCGATGGCAACGAGAATGTATCCAATAGAAACAAAGCGCGCCAAAAGCTTTCTGCGCAGACTCCACTCGGCATTTGGGCGGCGCGCTTTGTTTACAGTACGGTTAGCTGATGAGAGTGTATCC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q1RMT1	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Bos taurus OX=9913 GN=ERCC3 PE=2 SV=1
P19447	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Homo sapiens OX=9606 GN=ERCC3 PE=1 SV=1
Q60HG1	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Macaca fascicularis OX=9541 GN=ERCC3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003957 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
PF13625 all species →	Helicase_C_3	Helicase conserved C-terminal domain	Domain	Interproscan
PF16203 all species →	ERCC3_RAD25_C	ERCC3/RAD25/XPB C-terminal helicase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001161 all species →	Family	Helicase XPB/Ssl2	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR032830 all species →	Domain	Helicase XPB/Ssl2, N-terminal domain	Interproscan
IPR032438 all species →	Domain	ERCC3/RAD25/XPB helicase, C-terminal domain	Interproscan
IPR050615 all species →	Family	ATP-dependent DNA Helicase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11274 all species →	RAD25/XP-B DNA REPAIR HELICASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0000112 all species →	Cellular Component	nucleotide-excision repair factor 3 complex	Interproscan
GO:0005675 all species →	Cellular Component	transcription factor TFIIH holo complex	Interproscan
GO:0043138 all species →	Molecular Function	3'-5' DNA helicase activity	Interproscan
GO:0097550 all species →	Cellular Component	transcription preinitiation complex	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
K10843	ERCC3, XPB; DNA excision repair protein ERCC-3	EC:5.6.2.4	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of gfas1.m1.5347.m1 across 22 RNA-seq samples of Galaxea fascicularis. 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.

22Samples

16TPM > 0

4Conditions

75.7Max TPM

23.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
coral holosome · Control	7	4	14.84	36.40
coral holosome · 30ic treatment	6	4	18.05	28.54
coral holosome · Prometryn (herbicidess) treatment	5	4	31.08	75.73
coral holosome · Prometryn (herbicidess) and 30ic treatment	4	4	36.12	55.83

Per sample · hover a bar for the full sample record

Show the sample table (22 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR27118480	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	36.40
SRR27118486	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	24.44
SRR27118487	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	23.26
SRR27118492	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	19.79
SRR27118485	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	0.00
SRR27118488	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	0.00
SRR27118491	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	0.00
SRR27118478	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	28.54
SRR27118479	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	28.50
SRR27118476	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	26.40
SRR27118466	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	24.87
SRR27118468	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	0.00
SRR27118477	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	0.00
SRR27118483	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	75.73
SRR27118469	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	29.52
SRR27118484	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	25.35
SRR27118481	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	24.82
SRR27118482	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	0.00
SRR27118489	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	55.83
SRR27118472	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	33.15
SRR27118475	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	32.10
SRR27118490	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	23.41

Source: CnidoSite RNA-seq expression matrices (GFASC_TPM, StringTie quantification over 22 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 Galaxea fascicularis 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	36	gfas1.m1.10754.m1	0.9275421696585
Negatively correlated	12	gfas1.m1.3080.m1	-0.789622827435886

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 Galaxea fascicularis, 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 →