Gene detail

Detailed information of XP_020624335.1 in Orbicella faveolata

Genomic Location: Sc7jCM8_1227:1020574...1035344
NR annotation: XP_020624335.1, probable D-lactate dehydrogenase, mitochondrial isoform X2 [Orbicella faveolata]
Species Orbicella faveolata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_020768676.1

GTCGTAACtcggagaaacaaaaaaaactaaatatgGAGGTCGTCTCGTTGTGCTTTTTGCACTTATAAACGTTTGTCCTTCTTCACAACTCTGTAGTTGAATTCAACATGACTTCCATTGCTCGAAGTGCTCTTCGCCCGGTTTGTCGGTTTCTTGATCGAAGATTCTTTGTTCCTGCGTGTTGTCATGTTCGATGGAGTTCTGCTTCGTCACAAGTATCGCAGGTTGCCTATTCACCAGTTAATGACGACATAAAAAGAGCTTTTGAAGACATAGTTGGAGAAAACAATGTGTCATCTGCAATGGTTGTGAGGGAACAACACGGAAAAGATGAATCTCACCACAAGTGCCATCCTGCTGATCTCGTAGTATGGCCCACCAGCAGAGAGCAAGTCTGTCAGGTGGCAAAACTTTGCAATGATAATTGTCTCCCGCTGATTCCATTTGGATCTGGGACAGGACTGGAAGGGGGTGTGGTGGCCAAAAAGggtGGTGTTAGTGTGGATGTGACAAAAATGAACGAGATACTAGAGGTTAATGCCGAGGACTTTGATGTGACAGTGCAAGCAGGTGTTACAAGAAACCAGCTTAATAACTATGTGAGAGACACAGGACTGTGGTTCCCTGTTGATCCAGGAGCAGATGCTAGTTTGGGTGGTATGGCTTCTACAAGTGCATCAGGGACAAATGCAGTCAGGTACGGAACAATGCGAGAGAATGTTATGAATTTGGAAGTGGTTCTGGCAGATGGAAGGGTCATCAATACAGCTGGGGAAGGACGTCGGACAAGaaagacGTCGGCAGGATACAACTTGACAAACCTGTTTGTTGGTTCAgagggtactttgggaattatTACGAAGGTGACCCTGAGGCTGTATGGGATACCAGAATCGACAGCATCTGGAGTGTCTTCATTTTCTGACGTGAAGTCTGCTGTTGATGCTGTGGTAGAAATTCTACAGAGCGGCATTCCGATGGCTCGTATTGAGTTTCTAGATGATGTGCAGATTGATGCTTGTAACAAGTTTTCAGGGTTGAACTACCCCGTAACTCCTACCCTGTTCTTGGAGTTTCAAGGATCTGAAAATGGAGTCAAGGAACAAGCCTCTATTGCAGGGGAGATCATCGAAAGCAATGGTGGTTCTAAATTTCAGTGGGCCACTGAACTGGAGGAACGAAACAAATTGTGGAAAGCGAGACATAACGCTTGGTATGCTGACATGGCTCTTAGACCTGGTTGTAAGGGAGTATCAACAGACGTCTGTGTTCCAATCTCGAGGCTGCCTGAAATAATTGTGGAAACAAAGGAAGACATCATAACTTCCAACTTAATTGCCCCAATTGTGGGGCATGTAGGAGATGGAAATTTCCACTGCGTGCTTCCTCTTGATTTGGAATGCGAAGAGGAATTAAAGAGAGCAAAAGAATTTGTAGACAGACTATCCAGACGTGCCTTGGCCATGGGAGGTACCTGTACTGGAGAGCATGGGATAGGGTGTGGCAAGCAAGCCCTGTTACCAGAGGAGATCGGCCCAACTGGAGTTCAAGtgatgaaagaaataaaaaacttgTTGGACCCTAACGGGATCCTGAACCCTGGAAAAGTATTTTTGTAGAGAAAAAACAACTTTGTTGTAAAAATCAAggtctggggcccgtttctggaAAGCCAGAGAAACTTCTTGATTTGTCCTTCGGttgtattctgtttttttttttattgggaCTAAGGTCAGAACGCTTCTACGTTAAAATTAGCAGTAAAAATCgtatagaaataaagaaattagGCTTTTGCTAATTTTTAATCCTACTTCAGCCTATTCTAGTTGTCCTATCTGCTTCCAGAGAACGAAGCCTGTTCTCTGGTTCTCGCTTTAGATTGGAAAGTAAGttgaatgctgtttttatcACATTTTGGTCGCAtaacgcgcgctgtgattggttgtgCCTTCTTTTTGCATGACGTTATGTGACACGGGTATGACGTATCATTGCATTTGACtggctttttattttataaatggAGAATGTCGCTTTTTGTTAGTTCACAAATCCCGGTTGGTGGCAAATACCCTACAAAGatttggaaatttgaaagtgCTTTATATTGATACCGTATGTAAACCGTCGCTGGGGTCATTTCATGAAGAGTTTTAACTCTTTAGCTTACATGTCTGAATAACTCATATAAGATGTATACTTACAAATCTCCTTGATTTGAATTGAAATGTCTTGTAAAGACTTTGCTGTCGTGAAACGCCTGTAGCGCTGGTCAGTGGTTAAAATTAACTGTATATGATAATATAATTCAAATCTAAAGATTTTTTATACCAAGAATATAGCATGCACTACTTCCGCAAATAAGCCGTCATGCCTTAGAGACAGATCTTATGATTTTAGGTAGAAAGTAAATTATCTAGATTCTGTAAAGTAGATTGAGAACTTCAGGCGTGTACTAGACGTGTATGAATCATCAACATTAATGATCCTAATAGCAAATAGGTGaagataattaaatttctaattCGATCCTGTATGCTTTACAAAGATATATTTTCCCAGTGCATAATCATACACTTTCAGTAGAATTGGGAAACAAACAGGAAAATCTTGTAGAAagtcaaaattaataaatatgaaTGAGTTTTGGGAAACCCGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
F1QXM5	Probable D-lactate dehydrogenase, mitochondrial OS=Danio rerio OX=7955 GN=ldhd PE=2 SV=1
Q7TNG8	Probable D-lactate dehydrogenase, mitochondrial OS=Mus musculus OX=10090 GN=Ldhd PE=1 SV=1
Q86WU2	Probable D-lactate dehydrogenase, mitochondrial OS=Homo sapiens OX=9606 GN=LDHD PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004544 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02913 all species →	FAD-oxidase_C	FAD linked oxidases, C-terminal domain	Domain	Interproscan
PF01565 all species →	FAD_binding_4	FAD binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016171 all species →	Homologous_superfamily	Vanillyl-alcohol oxidase, C-terminal subdomain 2	Interproscan
IPR004113 all species →	Domain	FAD-binding oxidoreductase/transferase, type 4, C-terminal	Interproscan
IPR016166 all species →	Domain	FAD-binding domain, PCMH-type	Interproscan
IPR016164 all species →	Homologous_superfamily	FAD-linked oxidase-like, C-terminal	Interproscan
IPR036318 all species →	Homologous_superfamily	FAD-binding, type PCMH-like superfamily	Interproscan
IPR016169 all species →	Homologous_superfamily	FAD-binding, type PCMH, subdomain 2	Interproscan
IPR006094 all species →	Domain	FAD linked oxidase, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11748 all species →	D-LACTATE DEHYDROGENASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0071949 all species →	Molecular Function	FAD binding	Interproscan
GO:0004458 all species →	Molecular Function	D-lactate dehydrogenase (cytochrome) activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0008720 all species →	Molecular Function	D-lactate dehydrogenase activity	Interproscan
GO:1903457 all species →	Biological Process	lactate catabolic process	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
K00102	LDHD, dld; D-lactate dehydrogenase (cytochrome)	EC:1.1.2.4	Pyruvate metabolism	ko00620	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_020624335.1 across 70 RNA-seq samples of Orbicella faveolata. 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.

70Samples

40TPM > 0

4Conditions

168.6Max TPM

29.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · control.pH_high.temp	21	12	26.72	102.29
holobiont · low.pH_high.temp	19	10	28.34	168.58
holobiont · low.pH Control.temp	16	10	33.97	86.64
holobiont · control.pH Control.temp	14	8	29.03	122.68

Per sample · hover a bar for the full sample record

Show the sample table (70 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214539	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	102.29
SRR22214541	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	81.69
SRR22214542	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	71.23
SRR22214497	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	62.48
SRR22214533	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	42.85
SRR22214543	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	36.65
SRR22214502	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	34.39
SRR22214532	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	32.86
SRR22214498	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	30.77
SRR22214534	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	26.35
SRR22214501	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	20.29
SRR22214536	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	19.30
SRR22214496	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214499	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214500	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214531	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214537	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214538	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214540	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214544	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214545	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214478	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	168.58
SRR22214476	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	67.18
SRR22214479	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	65.34
SRR22214488	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	41.38
SRR22214474	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	39.50
SRR22214473	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	38.43
SRR22214485	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	37.59
SRR22214489	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	31.50
SRR22214490	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	29.46
SRR22214482	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	19.57
SRR22214472	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214475	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214477	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214480	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214483	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214484	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214486	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214487	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214491	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214517	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	86.64
SRR22214522	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	70.28
SRR22214520	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	69.08
SRR22214525	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	57.46
SRR22214529	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	53.63
SRR22214521	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	49.17
SRR22214494	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	48.51
SRR22214530	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	43.17
SRR22214518	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	33.31
SRR22214526	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	32.33
SRR22214493	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214495	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214519	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214523	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214527	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214528	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214507	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	122.68
SRR22214504	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	49.49
SRR22214513	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	45.06
SRR22214510	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	42.65
SRR22214514	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	42.11
SRR22214515	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	37.40
SRR22214509	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	36.88
SRR22214505	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	30.16
SRR22214401	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214503	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214508	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214511	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214512	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214516	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00

Source: CnidoSite RNA-seq expression matrices (OFAVE_TPM, StringTie quantification over 70 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 Orbicella faveolata 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	4	XP_020609741.1	0.800285424136328
Negatively correlated	4	XP_020612021.1	-0.358169203623149

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 Orbicella faveolata, 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 →