Detailed information of XP_074630405.1 in Acropora palmata

Genomic Location: NC_133889.1:8056562...8060362
NR annotation: XP_029201889.2, neutral and basic amino acid transport protein rBAT-like [Acropora millepora]
Species Acropora palmata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q64319Amino acid transporter heavy chain SLC3A1 OS=Rattus norvegicus OX=10116 GN=Slc3a1 PE=1 SV=1
Q91WV7Amino acid transporter heavy chain SLC3A1 OS=Mus musculus OX=10090 GN=Slc3a1 PE=1 SV=1
O16098Maltase 1 OS=Drosophila virilis OX=7244 GN=Mal-B1 PE=3 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003162 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00128
all species →		Alpha-amylaseAlpha amylase, catalytic domainDomainInterproscan
PF16028
all species →		SLC3A2_NSolute carrier family 3 member 2 N-terminusFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR006047
all species →		DomainGlycosyl hydrolase, family 13, catalytic domainInterproscan
IPR045857
all species →		Homologous_superfamilyOligo-1,6-glucosidase, domain 2Interproscan
IPR017853
all species →		Homologous_superfamilyGlycoside hydrolase superfamilyInterproscan
IPR031984
all species →		DomainSolute carrier family 3 member 2, N-terminal domainInterproscan
IPR013780
all species →		Homologous_superfamilyGlycosyl hydrolase, all-betaInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10357
all species →		ALPHA-AMYLASE FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005975
all species →		Biological Processcarbohydrate metabolic processInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K14210SLC3A1, RBAT; solute carrier family 3 (neutral and basic amino acid transporter), member 1-Exosomeko04147deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_074630405.1 across 84 RNA-seq samples of Acropora palmata. 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.

84Samples
83TPM > 0
2Conditions
479.9Max TPM
216.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 46 175.02 461.45
all_coral_tissue · baseline 38 37 267.24 479.88

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800075 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 461.45
SRR8800039 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 424.87
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 370.19
SRR8800042 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 363.82
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 306.85
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 303.79
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 301.49
SRR8800066 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 295.98
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 288.25
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 286.06
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 266.70
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 262.18
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 257.98
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 251.94
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 245.95
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 244.32
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 233.80
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 224.41
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 223.04
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 221.22
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 210.76
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 208.27
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 206.66
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 204.70
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 152.80
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 152.22
SRR8800086 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 103.11
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 100.88
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 88.00
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 86.11
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 73.80
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 71.60
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 69.56
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 59.26
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 51.58
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 51.50
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 46.74
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 43.31
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 42.96
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 37.99
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 35.82
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 30.06
SRR8800029 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 27.40
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 26.69
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 20.68
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 14.09
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 479.88
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 439.30
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 416.13
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 400.36
SRR8800052 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 398.15
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 397.86
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 392.78
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 389.66
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 384.75
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 377.66
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 376.63
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 372.78
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 368.55
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 365.63
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 363.12
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 362.68
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 356.33
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 356.19
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 343.43
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 340.62
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 318.06
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 313.60
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 300.82
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 290.87
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 273.10
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 186.41
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 144.77
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 93.69
SRR8800059 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 87.81
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 76.46
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 65.79
SRR8800055 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 63.05
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 59.53
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 54.97
SRR8800054 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 54.64
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 46.35
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 42.71
SRR8800046 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00

Source: CnidoSite RNA-seq expression matrices (APALM_TPM, StringTie quantification over 84 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 palmata 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated74XP_074606095.10.960806552458708
Negatively correlated20XP_074616221.1-0.823861619837971

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 palmata, 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
Polyp_Underside_Control_2open
Polyp_Underside_Control_3open
Polyp_Underside_Treatment_1open
Polyp_Upperside_Control_1open
Polyp_Upperside_Treatment_3open
Polyp_Upperside_Treatment_4open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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