Gene detail

Detailed information of HSymV2.0_g12.21953_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_12:21759778...21773668
NR annotation: XP_012557822.1, RNA-binding motif, single-stranded-interacting protein 1 isoform X2 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

HSymV2.0_g12.21953_t1

TTTatagatatataaatagaacataaataaagtgaaattatatagataatataCTACACGAAAGAGGTTTAGACAAATCAGAAGAAAGGCTGTATGGAAATATTATGGTCCAGACATCATTAAATGAAACACGGTACCCTGTGGAAACAATAAAAGGACAGGCGGAACCGGATGCTTCTTCCCCGAGTGATAAGAACATGATCAATGGGAGTATCATTGATTTAAAGAAACCTGCCAAAACTCGGGGGGAGACAGAGTATTGGCGCCACAGTCCTGAACTGGACACCAACGAAAATATGAACAAATTAAACAATGATAAAGACGAAATAAACGATGCTAAGAATGATAAAATTGAGCGAAAGTCTCCTGTTCCGCAACAGAAACGGGGTAGCACACCTGTTAGTACAGAGAAAACAAAACAAACTGCTGACAAGAGACAGACTCGATCAAATCAAAACACATCCAGCTATGGGCGATCCTTTCGACCAGGTCTAGTGCCCACTCCAAACGTTGCATACCCGTGGCCAAATCATATCAACTGGCAAAATTATTACTTAGCAAGCCAACAGAGGCATGCGAGTCCGGTGGTTTATGGATATCAACCAGCATACTATCAATACGCATCAACAGTGAACAGCCATCACTCTACAAATAGCTCACCGACTTCCAATCATATGTATGCAAATTCATACACAGATACACAAGATGGCGAGAAACTTAGTAAAACAAACTTATACATCCGAGGCTTGCATAGTTCCACGACAGACGAAGATTTAGTGAACATGTGTAGAATATATGGTAATATTATTTCGACAAAGGCAATACTACACAAAGACACTAACCAATGCAAAGGGTATGGCTTTGTTGATTTTGACAGTCCAGTTGCAGCACAAAGAGCCGTCAGTGCTCTACAAAACAAGGGGATACAGGCACAAATGGCTAAACAACAAGAACAAGATCCCACAAATTTATATTTATCTAATTTACCCAAGCAAATCGACGAGCAGCAATTACAACATTTATTAGCATCGTATGGAAATGTAATATCAACCAGGATTTTAAGAGATACTTCAGGTTCCAGTAAATGTGTCGGATTTGCTAGATTGGAATCGACAGAAATTTGTGAGCAAGTGATCGATAAGTTAAATGGACAATATTTATCAGGCTCCAACGAACAATTATTAGTGAAATTTGCAGATGGTGGACCAAAGAAAACGAAACAAGATAAAACTTGGAGAAATCCGTCTGAGGATTATATGAATTACGGTGTGAGAAGTCCTGTTTCCAGGACAATGAGCAATCCACCAACAGCACGAGTCACACCAGTCATCCAAAGTCCAATGGGTCATGGTGCAGGGACAAACATAGCTGCTTACCACATGCCTGTTACAGGTGTAAGCTGGGGTGTTCAACCTCAATCATATACCGTGCCTGTATCTCCGCATCAGTTACCTACAGATACTATCCAATCAATGCACTCTCCCATGTCTCAAATGAACAATCAGATGGCACAAATGCATATCCATGGTGGAACTAATCAATACATCATGCCAGCACCAGGAGGGTATAGTCAGCAAAATTCATGGCAGATGACTCAAACGCTTCCTCAGGAGTCGCCAGTAATTATGACGGCAACCGAAGTTGAAAGTAACTATCCTCCTCCACATATGCATCACCATGGCAACGAACCAATATATTCTGATGATCAACAAACTAGAGTGGTGTACGCCTATCAACGGAAGTGAGGCACTGAACTTAGATGAGGAACACGTTTTTTAATCATTTTTTGTTATTGTTTTAACCTGTGTACAAAAATGAATTTTCTTTCTTTTGAAGAGATAGAAGGTTTTTATTTCAGTCGTTAATAATTTTTACATTTTTTGTTGTCGTAATTTTGTTTTTGTATTGTGAATGTGATGAAAGATGGAAGTTATTTGTCTGCAATTTTCAGATATTTCATCACCGTAACCGTACCAATTTTTAAGGAGAATTTTACGGGATTAATTACACCCGAGATTTATTTTCTGTAATTTGTAAAATTATTAATACTCGTGAAACACAAAAATTTTACGACTAGCGAAAATTGGTACAtctctttaataatagccgtcgtctgtctgtgtgtccacgaaagct

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3ZBP3	RNA-binding motif, single-stranded-interacting protein 1 OS=Bos taurus OX=9913 GN=RBMS1 PE=2 SV=1
P29558	RNA-binding motif, single-stranded-interacting protein 1 OS=Homo sapiens OX=9606 GN=RBMS1 PE=1 SV=3
Q3ZC34	RNA-binding motif, single-stranded-interacting protein 2 OS=Bos taurus OX=9913 GN=RBMS2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002156 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR050502 all species →	Family	Eukaryotic RNA-binding	Interproscan
IPR002343 all species →	Family	Paraneoplastic encephalomyelitis antigen	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48025 all species →	OS02G0815200 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:1990904 all species →	Cellular Component	ribonucleoprotein 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
K24990	RBMS; RNA-binding motif, single-stranded-interacting protein	-	Domain-containing proteins not elsewhere classified	ko04990	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_g12.21953_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

43TPM > 0

3Conditions

146.0Max TPM

27.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	35	29.28	146.02
Whole embryo · Triptolide 20 uM	4	4	18.88	22.72
Whole embryo · DMSO 0.5%	4	4	23.09	26.41

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	146.02
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	121.88
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	54.55
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	43.57
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	42.17
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	35.76
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	35.61
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	31.20
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	27.56
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	26.53
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	24.54
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	24.04
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	23.23
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	22.24
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	22.01
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	21.95
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	21.27
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	21.14
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	20.92
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	20.25
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	19.99
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	18.86
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	18.72
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	18.56
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	18.48
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	18.22
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	18.14
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	17.91
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	17.87
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	17.60
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	17.59
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	17.59
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	17.17
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	15.44
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	15.44
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	0.00
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	22.72
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	21.76
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	18.44
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	12.60
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	26.41
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	23.88
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	22.31
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	19.76

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.