Gene detail

Detailed information of Aala_g1988.t1 in Alatina alata

Genomic Location: not available for this species
NR annotation: KAI0234680.1, hypothetical protein LSAT2_015021 [Lamellibrachia satsuma]
Species Alatina alata · all data for this species · gene families

Sequence

Sequence data are not available for Alatina alata.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5XK67	DNA-directed RNA polymerases I and III subunit RPAC2 OS=Xenopus laevis OX=8355 GN=polr1d PE=3 SV=1
Q1RMG8	DNA-directed RNA polymerases I and III subunit RPAC2 OS=Bos taurus OX=9913 GN=POLR1D PE=2 SV=1
P0DPB6	DNA-directed RNA polymerases I and III subunit RPAC2 OS=Homo sapiens OX=9606 GN=POLR1D PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000005 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000006 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000684 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001969 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006085 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007780 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0009037 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0009174 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0025653 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0029670 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0059136 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00041 all species →	fn3	Fibronectin type III domain	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF13656 all species →	RNA_pol_L_2	RNA polymerase Rpb3/Rpb11 dimerisation domain	Domain	Interproscan
PF02493 all species →	MORN	MORN repeat	Repeat	Interproscan
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan
PF17917 all species →	RT_RNaseH	RNase H-like domain found in reverse transcriptase	Domain	Interproscan
PF17921 all species →	Integrase_H2C2	Integrase zinc binding domain	Domain	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF07727 all species →	RVT_2	Reverse transcriptase (RNA-dependent DNA polymerase)	Family	Interproscan
PF03437 all species →	BtpA	BtpA family	Family	Interproscan
PF13606 all species →	Ank_3	Ankyrin repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR053336 all species →	Family	Rhoptry Surface-Associated Protein	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR003961 all species →	Domain	Fibronectin type III	Interproscan
IPR036116 all species →	Homologous_superfamily	Fibronectin type III superfamily	Interproscan
IPR050449 all species →	Family	Ephrin receptor tyrosine kinases	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR008193 all species →	Conserved_site	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Interproscan
IPR022905 all species →	Family	DNA-directed RNA polymerase subunit Rpo11-like	Interproscan
IPR036603 all species →	Homologous_superfamily	RNA polymerase, RBP11-like subunit	Interproscan
IPR033898 all species →	Family	DNA-directed RNA polymerases I and III subunit AC19	Interproscan
IPR009025 all species →	Domain	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Interproscan
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR003409 all species →	Repeat	MORN repeat	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR053064 all species →	Family	Ankyrin repeat and MYND domain-containing protein	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR041373 all species →	Domain	Reverse transcriptase, RNase H-like domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR041588 all species →	Domain	Integrase zinc-binding domain	Interproscan
IPR027124 all species →	Family	SWR1-complex protein 5/Craniofacial development protein 1/2	Interproscan
IPR013103 all species →	Domain	Reverse transcriptase, RNA-dependent DNA polymerase	Interproscan
IPR052510 all species →	Family	Oomycete RxLR Effector	Interproscan
IPR005137 all species →	Family	Membrane complex biogenesis protein, BtpA family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37320 all species →	AG-1 BLOOD STAGE MEMBRANE PROTEIN HOMOLOGUE	Interproscan
PTHR46877 all species →	EPH RECEPTOR A5	Interproscan
PTHR19446 all species →	REVERSE TRANSCRIPTASES	Interproscan
PTHR13946 all species →	DNA-DIRECTED RNA POLYMERASE I,II,III	Interproscan
PTHR15897 all species →	ANKYRIN REPEAT AND MYND DOMAIN PROTEIN 1	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR13491 all species →	ZCCHC10 PROTEIN	Interproscan
PTHR23227 all species →	BUCENTAUR RELATED	Interproscan
PTHR45895 all species →	INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR21381 all species →	ZGC:162297	Interproscan
PTHR47027 all species →	REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005005 all species →	Molecular Function	transmembrane-ephrin receptor activity	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	Interproscan
GO:0007411 all species →	Biological Process	axon guidance	Interproscan
GO:0030425 all species →	Cellular Component	dendrite	Interproscan
GO:0048013 all species →	Biological Process	ephrin receptor signaling pathway	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0046983 all species →	Molecular Function	protein dimerization activity	Interproscan
GO:0001054 all species →	Molecular Function	RNA polymerase I activity	Interproscan
GO:0001056 all species →	Molecular Function	RNA polymerase III activity	Interproscan
GO:0005666 all species →	Cellular Component	RNA polymerase III complex	Interproscan
GO:0005736 all species →	Cellular Component	RNA polymerase I complex	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	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
K03020	RPAC2, RPC19, POLR1D; DNA-directed RNA polymerases I and III subunit RPAC2	-	Transcription machinery	ko03021	deepkoala
K24631	ANKMY1, ZMYD13; ankyrin repeat and MYND domain-containing protein 1	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

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

Co-expression network

Genes whose expression across the transcriptome samples of Alatina alata 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Alatina alata, 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.	sequence table not available	–
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.	sequence table not available	–
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.	no expression matrix	–
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 →