Gene detail

Detailed information of HSymV2.0_g13.22985_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_13:14967788...14988972
NR annotation: XP_012566859.1, pre-mRNA-processing factor 19 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

HSymV2.0_g13.22985_t1

ATTAACGAAACGATTTTCTTGTGTATTATGTATTTCGCGCGCTTTTGATACTGAACTGGCGCGTCACAACTTTGACCCATGGAAAAAAGACTGGACGCTAGAGTTGAATTTTACCGAAATATAATCACAACAAAATGGAGGCGAGCGCTGCTGTTTTTACGAGacaaaaagaaaatatgtgcccactattaaagtgaatgtaaaaagacccaataacagcatcgaaaattactagaattaaagtatttaaaaaaatacaatcgattactgcaagataattaacataactggatagaagattggCACAAATTGAGGAATTTCGTGTCCAGGATACTTTGTAGCACCGAAAAATCTGTCTTCCACGGGCGGCCGTTTGATGCAAAATTAGCCGTCTCGAATATTCAATGAAGTTTTCCTGACATTTATATTGCGCATGCATTAGTTATCGAGATATTCAATACATGTGAAAAAAGAAAAATGGCGCTCGTCTGTTCAATTAGTGGTGAAGTTCCTGAACATCCTGTTATTTCACCAGTTTCGAAACATATATTTGAAAAGCGTCTCATTGAGAAGTTTATCTCAGAAAATGGAACAGACCCCATAACTGGTGATAGTTTATCTGAATCCGAGCTCATAGAATTGAAAACCACTCCTTTGACAAAACCTCGTCCTCCATCAGCTACAAGTATTCCTGCCATATTAAAAGCTCTTCAAGATGAATGGGATGCTGTTATGCTCCACAGTTTCACATTACGACAACAGCTTCAAGCTGCTAGACAAGAACTTTCACATGCGTTGTACCAACATGATGCTGCTTGCCGTGTCATTGCTCGATTGACTAAAGAAGCTACAGCTGCAAGAGAAGCTCTTGCAACACTGAAGCCACAAGCTGGTGCTTCTGTCACTTCTGGCCAAGTATCACATGTGTCAGGTGCAACTAAGATTGATGACACAGACATTGTGGAACCTGCTGAAGTTGGCATGTCTGATGAAGTGCTACAGAAATTACAAGACAAAGCTACAGAACTCACCAGTGAGAGAAGAAAGAAAGGAAAGAAGGCCCCAGAAGATTTGACACCTGCTGATGACCTTCGTTCCTTCAAACAGATTGCGACGCATCCAGGACTTCACAGTGCTAGTGTTCCTGGCATCTTGGCTTTGGACTTACAGGATCAGGACACTTCGAAAGCAATAACAGGTGGTATGGACAAGACTGCGGTTGTATTTAACAAAGAAAATGAACAGGTTGTTGCCACTCTTAGAGGACATACAAAGAAAGTCACGTCAGTTATATACCATCCGAGAGAAGAAATTGCAATTACTGCATCTGCTGACAATACTGTTCGTGTGTGGAGCATACCCAATAGCTCTTGTGCTTACGTCATAAAGGCTCACGATGCTGCAGTAACTGGCTTGAGCTTACACGCTACTGGTGATTACGTGTTGACATGTTCCAGTGATCAGTACTGGGCCTTCTCTGATATTCAAACTGGTAAAATCCTCTGCAAGAACATCTCGGATCCAAATGCTAGCCATGGTTTAACTTGTGCTCAGCTACATCCTGACGGTTTGATCTTTGGAACCGGAACAACTGACAGCGTTGTGAAAATTTGGGATTTGAAAGAACGAGAAAACGTGGCAAACTTCCCTGGACATTCTGGACCTATTACGTCAATCGCCTTCTCTGAAAACGGATACTACTTAGCGACAAGTGCTGATGATTCCGTTGTCAAACTTTGGGATTTAAGAAAACTAAAGAACTTCAAAACGATTACCTTGGATGAAAGTGATGAGATCAAGTCTTTATGTTTTGACAAAAGTGGAAACTATCTAGCAGTAGCAGGTTCAAATATTCAATTGTACGTGGTGAAGCAATGGGAACTGCTGAAGAAACTCACAGATCATACTGGACTCGTGACGTCAGTGAAGTTCGGAAAGAGCGCTTCATTTATTGCCAGCGCGAGTTTGGATAGAAACATCAAGTATTTCGCTCGCTGAAGAGATGAGCAGATGCAAAAGCGTATGATACGTGTATCTCACGTGTAAAACGATAACGGGTTGAAGAAAAATTAGCGAAAAGAGACATTTATAGAAACGATAATAAAAAAATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q08E38	Pre-mRNA-processing factor 19 OS=Bos taurus OX=9913 GN=PRPF19 PE=2 SV=1
Q99KP6	Pre-mRNA-processing factor 19 OS=Mus musculus OX=10090 GN=Prpf19 PE=1 SV=1
Q9JMJ4	Pre-mRNA-processing factor 19 OS=Rattus norvegicus OX=10116 GN=Prpf19 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006979 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08606 all species →	Prp19	Prp19/Pso4-like	Domain	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF04564 all species →	U-box	U-box domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR013915 all species →	Domain	Pre-mRNA-splicing factor 19	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR003613 all species →	Domain	U-box domain	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR038959 all species →	Family	Pre-mRNA-processing factor 19	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43995 all species →	PRE-MRNA-PROCESSING FACTOR 19	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000974 all species →	Cellular Component	Prp19 complex	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0071006 all species →	Cellular Component	U2-type catalytic step 1 spliceosome	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
K10599	PRPF19, PRP19; pre-mRNA-processing factor 19	EC:2.3.2.27	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 HSymV2.0_g13.22985_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

361.6Max TPM

219.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	201.34	361.57
Whole embryo · Triptolide 20 uM	4	4	292.93	349.36
Whole embryo · DMSO 0.5%	4	4	304.25	344.07

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	361.57
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	354.41
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	297.65
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	295.06
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	276.20
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	274.01
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	261.18
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	260.68
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	256.57
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	253.40
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	246.22
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	244.70
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	241.96
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	235.82
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	234.89
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	213.08
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	207.32
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	202.97
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	197.80
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	193.97
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	193.32
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	190.37
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	178.10
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	173.30
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	167.54
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	167.43
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	161.87
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	160.28
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	158.27
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	156.11
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	94.25
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	79.14
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	70.24
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	68.08
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	64.44
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	56.11
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	349.36
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	294.25
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	271.80
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	256.30
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	344.07
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	331.91
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	275.04
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	265.98

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	38	HSymV2.0_g01.00213_t1	0.981449554507073
Negatively correlated	11	HSymV2.0_g12.20973_t1	-0.913194172503373

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 →