Gene detail

Detailed information of agem_s0110.g13.t1 in Acropora gemmifera

Genomic Location: sc0000110_pilon:198396...200918
NR annotation: XP_044174391.1, uncharacterized protein LOC122958021 [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

agem_s0110.g13.t1

ATGGATATCAAAACCTTTCTGGACAATATATACGAACATGTATGCTGTCCTGTGTGTATGAACAGGTTCACTAATCCAAAACTGCTTCCTTGTTTGCACACGTTTTGCCTTCACTGTCTGCAAAGAATTCAAACAACCAGCGGGATTCGAGACACTATTTTATGTCCCGAGTGTCGTCGAAACTTCGCCATTCCTGGAAACGGTGATCTCAACACTTTACCGACAAACTTTCGCTTGAACAGTTTGTTGGATGCTTTGCCCGTCACAGAGTGCAATACTAGTGGCGTCAAGTGTGGAAATTGCGAGAAAACAAGACAACAATCTGCCTACTGCTTTACTTGTTGTTCGTTCTGGTGCGATGACTGCCTTCCTTTCCATAACGGGATAAGAACCAATAAAGAACACCACGTGTTGGCTTTGAAAGATTTTCGAGATGAAGACTTTGAGAACATTCTCAAGCAGCCACCATTTTGTGCAAAACACGAGGAGACATTAAAGTTCTTCTGTCAGCTTTGCGAAACAACAATATGTCATTCGTGTGCGGTAACAGACCACGATGGTCACGCTAAGATTGATTTGGAAGACGCTGCAAAAGAACGCAAGTTGAGAATAGTTAGAGCCCTTGAATTCAAGAAACGAAAAGCCCAAAACAAGGTGACAAGAATTGCCAAACTTGGTGAAAGCGGTATCCAAGTTCAAGAAGAAGCCGCAAGAATAAAGAGCGACATACAGAAATTTACCAACAATCTCATTGCAGCCATTGAAGCAAAAATGAACGAGATCTTTCAAGAGGTAGAAATGAAAGTAAAACAGTGTCTGGAGCATCTaggagaaaaaagaagggagattgaaggagaaatgaaaaaggaCCAAACAGCAATCGAAAAAAGCGACATGATTTTAAAGCGAAGCACAAGCGCTCAAATCATGCAACCAAATGATTTTCTAGATAAACTGTTTCGGGAGGAAGGTGAGCAAGAAGACGCGGTTGACCTTAACGGCGAACATGTCATAGATTTTTATTTTCAAAGAAATGAAGAATTGTTTAGTGACGTTTACGCTAGACAACTGGGATTTTTGAAAAGAAAAACTAGCCCGAAAGAGTCGACGGTTGAGGGAAAAGGAATCAGCGAAGGAACTGTTGGACTTAAAGCCGAGATTGTTGTCAAAACACGAAACATTCAGGGGAAACAAGTCTACCATGAAAATAACCATGTAACGATGGATATCAGAAATCATGAAGGACATGGCCTTTCAACAAAACCGCAAATCCACGACAACAAAGATGGCAGCTATAAGATCAGCTTCTTTGCTAAAGAACGCGGACCATGTCAAGCATCCGTGAAAGTTAATGGACAACATGTGCGTGGCAGTCCCTTTAAAACTGAATTGAAACCCAGACTGTTCAAACCCGTGTTATCCTTTGGAAAACAAGGATCAGCTGATGGAATGTTTATTAGACCTTGGGGGATAGCAGTGAATGACAAAGATGAGATTGCAGTGACTGATTGTCATAACCATCGCATACAAATATTTAAAAGTGATGGTACTCACTTAAGATCGTTTGGTAGACTAGGTAATCAGCAGGGACAGTTCAACGGGCCTTTTGGGATAGCTTTCTATAATAATAACATTATAGTGTCAGATACTGGTAACCACCGAGTTCAAATATTTGATGATCAGGGACACTATCTTGATCAGTTTGGAGAACAGGGAAAACTGAATCACCAGCTTGACTATCCTTTTGGGCTGTCAATTGACAGGGATGGCAACATCATTGTCGCTGATTGTGGTAACAAGTCAATCAAGATCTTTAAGCTTGACGGCCGGTTTTTGCGTAGAGTCGGCGAAGAAGGTTCTTTCAGCGCTTTCTGTCACTGCATACAACACGACAACTATTTTATTGTATCAGACACTGGAGACCATTGTATAAAAGTTTTTGATGAACAGGGCAAGTTTCTTTATCAATTCGGGAGGAGGGGGACAGGGGATGGGGATTTTTACGAGCCTGCCTACCTGTCTGTGAACAGAGTAGGACATCTGTTGGTTTGTGATTCAATGAATCACCTAGTGCAGGTGTTTAAACTCAACGGAGAGTTTGTAACAAAGTTTGGAGCATCTGGTGAAGAAGAAGGAAAGTTCAATATGCCAATCTCCACGACAATACTTAGCGATGGTAGAATAATTGTCACTGACCTTGACAACCATCGAGTTCAGGTTTTTGAGTAG

Transcript

agem_s0110.g13.t1

GGTGCAATAGAGTACAGCAAAATTAACAACTGTCCATTGTAAACTTAGCTCATTTTGAGGAGTGTTCAATGTAAATGTTGACCTATTTCCGCATTTATAATGGATATCAAAACCTTTCTGGACAATATATACGAACATGTATGCTGTCCTGTGTGTATGAACAGGTTCACTAATCCAAAACTGCTTCCTTGTTTGCACACGTTTTGCCTTCACTGTCTGCAAAGAATTCAAACAACCAGCGGGATTCGAGACACTATTTTATGTCCCGAGTGTCGTCGAAACTTCGCCATTCCTGGAAACGGTGATCTCAACACTTTACCGACAAACTTTCGCTTGAACAGTTTGTTGGATGCTTTGCCCGTCACAGAGTGCAATACTAGTGGCGTCAAGTGTGGAAATTGCGAGAAAACAAGACAACAATCTGCCTACTGCTTTACTTGTTGTTCGTTCTGGTGCGATGACTGCCTTCCTTTCCATAACGGGATAAGAACCAATAAAGAACACCACGTGTTGGCTTTGAAAGATTTTCGAGATGAAGACTTTGAGAACATTCTCAAGCAGCCACCATTTTGTGCAAAACACGAGGAGACATTAAAGTTCTTCTGTCAGCTTTGCGAAACAACAATATGTCATTCGTGTGCGGTAACAGACCACGATGGTCACGCTAAGATTGATTTGGAAGACGCTGCAAAAGAACGCAAGTTGAGAATAGTTAGAGCCCTTGAATTCAAGAAACGAAAAGCCCAAAACAAGGTGACAAGAATTGCCAAACTTGGTGAAAGCGGTATCCAAGTTCAAGAAGAAGCCGCAAGAATAAAGAGCGACATACAGAAATTTACCAACAATCTCATTGCAGCCATTGAAGCAAAAATGAACGAGATCTTTCAAGAGGTAGAAATGAAAGTAAAACAGTGTCTGGAGCATCTaggagaaaaaagaagggagattgaaggagaaatgaaaaaggaCCAAACAGCAATCGAAAAAAGCGACATGATTTTAAAGCGAAGCACAAGCGCTCAAATCATGCAACCAAATGATTTTCTAGATAAACTGTTTCGGGAGGAAGGTGAGCAAGAAGACGCGGTTGACCTTAACGGCGAACATGTCATAGATTTTTATTTTCAAAGAAATGAAGAATTGTTTAGTGACGTTTACGCTAGACAACTGGGATTTTTGAAAAGAAAAACTAGCCCGAAAGAGTCGACGGTTGAGGGAAAAGGAATCAGCGAAGGAACTGTTGGACTTAAAGCCGAGATTGTTGTCAAAACACGAAACATTCAGGGGAAACAAGTCTACCATGAAAATAACCATGTAACGATGGATATCAGAAATCATGAAGGACATGGCCTTTCAACAAAACCGCAAATCCACGACAACAAAGATGGCAGCTATAAGATCAGCTTCTTTGCTAAAGAACGCGGACCATGTCAAGCATCCGTGAAAGTTAATGGACAACATGTGCGTGGCAGTCCCTTTAAAACTGAATTGAAACCCAGACTGTTCAAACCCGTGTTATCCTTTGGAAAACAAGGATCAGCTGATGGAATGTTTATTAGACCTTGGGGGATAGCAGTGAATGACAAAGATGAGATTGCAGTGACTGATTGTCATAACCATCGCATACAAATATTTAAAAGTGATGGTACTCACTTAAGATCGTTTGGTAGACTAGGTAATCAGCAGGGACAGTTCAACGGGCCTTTTGGGATAGCTTTCTATAATAATAACATTATAGTGTCAGATACTGGTAACCACCGAGTTCAAATATTTGATGATCAGGGACACTATCTTGATCAGTTTGGAGAACAGGGAAAACTGAATCACCAGCTTGACTATCCTTTTGGGCTGTCAATTGACAGGGATGGCAACATCATTGTCGCTGATTGTGGTAACAAGTCAATCAAGATCTTTAAGCTTGACGGCCGGTTTTTGCGTAGAGTCGGCGAAGAAGGTTCTTTCAGCGCTTTCTGTCACTGCATACAACACGACAACTATTTTATTGTATCAGACACTGGAGACCATTGTATAAAAGTTTTTGATGAACAGGGCAAGTTTCTTTATCAATTCGGGAGGAGGGGGACAGGGGATGGGGATTTTTACGAGCCTGCCTACCTGTCTGTGAACAGAGTAGGACATCTGTTGGTTTGTGATTCAATGAATCACCTAGTGCAGGTGTTTAAACTCAACGGAGAGTTTGTAACAAAGTTTGGAGCATCTGGTGAAGAAGAAGGAAAGTTCAATATGCCAATCTCCACGACAATACTTAGCGATGGTAGAATAATTGTCACTGACCTTGACAACCATCGAGTTCAGGTTTTTGAGTAGACGAATAGTTTTCTAGTAATTATATTCACTCTGAATAATTCTTTCAGTGACAAAAAAAGCTTTTTTGTATTGTAAATATCTTTATTCGCATATACATTTTTTACATTTCAATACGGTGTGGGAAAAGACTTCATTTAATTGTAACAAATAACGCGAGGTGAGATTTTTCCCTGGTAAGAAAATTTACTTAGTGAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5BIM1	E3 ubiquitin-protein ligase TRIM45 OS=Bos taurus OX=9913 GN=TRIM45 PE=2 SV=1
Q9ESN6	Tripartite motif-containing protein 2 OS=Mus musculus OX=10090 GN=Trim2 PE=1 SV=1
D3ZQG6	Tripartite motif-containing protein 2 OS=Rattus norvegicus OX=10116 GN=Trim2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000211 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01436 all species →	NHL	NHL repeat	Repeat	Interproscan
PF00630 all species →	Filamin	Filamin/ABP280 repeat	Domain	Interproscan
PF13445 all species →	zf-RING_UBOX	RING-type zinc-finger	Domain	Interproscan
PF00643 all species →	zf-B_box	B-box zinc finger	Domain	Interproscan
PF17170 all species →	DUF5128	6-bladed beta-propeller	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001258 all species →	Repeat	NHL repeat	Interproscan
IPR017868 all species →	Repeat	Filamin/ABP280 repeat-like	Interproscan
IPR000315 all species →	Domain	B-box-type zinc finger	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR027370 all species →	Domain	Zinc finger, RING-type, eukaryotic	Interproscan
IPR050952 all species →	Family	Tripartite Motif and NHL Repeat Containing E3 Ligases	Interproscan
IPR011042 all species →	Homologous_superfamily	Six-bladed beta-propeller, TolB-like	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR014756 all species →	Homologous_superfamily	Immunoglobulin E-set	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR001298 all species →	Repeat	Filamin/ABP280 repeat	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24104 all species →	E3 UBIQUITIN-PROTEIN LIGASE NHLRC1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase 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
K12035	TRIM71; tripartite motif-containing protein 71	EC:2.3.2.27	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of agem_s0110.g13.t1 across 48 RNA-seq samples of Acropora gemmifera. 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.

48Samples

11TPM > 0

1Conditions

32.1Max TPM

2.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
branch tip	48	11	2.84	32.14

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR3182784	branch tip	branch tip	not recorded	not recorded	SRP062488	32.14
SRR3182781	branch tip	branch tip	not recorded	not recorded	SRP062488	21.64
SRR2169558	branch tip	branch tip	not recorded	not recorded	SRP062488	17.47
SRR3169425	branch tip	branch tip	not recorded	not recorded	SRP062488	16.01
SRR3223317	branch tip	branch tip	not recorded	not recorded	SRP062488	11.88
SRR3169527	branch tip	branch tip	not recorded	not recorded	SRP062488	10.24
SRR3169532	branch tip	branch tip	not recorded	not recorded	SRP062488	9.95
SRR3223319	branch tip	branch tip	not recorded	not recorded	SRP062488	8.57
SRR3169528	branch tip	branch tip	not recorded	not recorded	SRP062488	4.08
SRR3169422	branch tip	branch tip	not recorded	not recorded	SRP062488	2.99
SRR3182789	branch tip	branch tip	not recorded	not recorded	SRP062488	1.47
SRR3169421	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169423	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169426	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169518	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169529	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169530	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169531	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169533	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169534	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169535	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169536	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169537	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169538	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169539	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169540	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169541	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182410	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182448	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182557	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182684	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182685	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182686	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182775	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182776	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182777	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182778	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182779	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182780	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182785	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182786	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182787	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182788	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182790	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182791	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182792	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182793	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182794	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00

Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM, StringTie quantification over 48 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 Acropora gemmifera 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	0	not in this network	-
Negatively correlated	16	agem_s0094.g46.t1	-0.367738662738736

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 Acropora gemmifera, 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 →