Gene detail

Detailed information of XP_068733034.1 in Montipora capricornis

Genomic Location: chr13:40854978...40857239
NR annotation: XP_015749486.1, PREDICTED: transcription factor Sox-2-like [Acropora digitifera]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068876933.1

TGACGTTCAGTGGGTCGAGTTTGAAATCACAACACCTGCTAAATACGAGCTAATTTCCATGTTCGGACAGATGACAGCTCATTTCCTTAGGCTCGGGTGATTAAGGCTTAATTGGACCAGCTGACGAGTGGATCACACGAGCTGATTTGTCGACGAATCGGTCGGATCTCGGAATCAAAACGTCGAATCCCGCCCCTTTTGACAAGCGCGCCAACAACTTGTCACATTGGCTGTCGGCCTGTCAAACGAACTGACGTGAGTAACGCAACCAAAACTTCATTTATCAAGTGTGTCATCGAGtgaacgctgattggctaattcgTGCGAGCTCGCTTTCTGCCAATCAATATCACATGGAGTCGAGGAGGTGAGAGTCAAAAATAACGTGTGGTCTTCATCAGCGTGTAACGAGATTTTGAGAGCGTACCTCGACAGAACGACAAACCAACTCTCGACAAACCGACAGAAATTTGTCGTGGAAAAATTTCACCGCCAACGACAAAAGggtaattttatttaaatttgtatCGTTGGATCAAGCGATGTCGACAACCACGATTTTGACACCGTCGCCAAATGCGGGCTCGAACACGAACGGCGAGAGCAATGGAAAGTGTAGCCCAGACCGAGTTAAGCGACCCATGAATGCATTTATGGTTTGGAGTAGAGAGCGGCGACGCCGCATGGCTCAGGAAAATCCGAAGATGCACAACTCTGAAATTTCGAAACGTTTGGGAGCCGAATGGAAACAGTTATCTGACCCGGAAAAGCGACCCTATGTAGATGAAGCGAAGAGATTGCGAGCGGTTCACATGAAAGATCACCCAGACTACAAGTACAGACCGAGACGAAAGAGTAAAACTTTGCTCAAGAAAGATAACAAGTACACTTTGTCCATGCTTGGAGCTCAAGGTGGACCGCCTGTGCAGAGATCGGTGGTTCAAAATCCGAGCGATCACTTTGCCCAATTGAACGGTTACACTTACGGTCCTATTACGGGCTACAGCCAAATGAATGTCAGTGATCCTTATAGTAATATCTACGCTGCTCATCCTCTATCACCGCATACCCCTACTCAAATCCAGCCATCAAACGGCTTACATCACTCTGGATATTCGCATATGGCAAGCAATCCGATTTACCCTGCTGTTTCTACCCAAGGCCAAGTGTATAGCATGAATGGGACTCAGTCGATGAACTCGATGACTCCGCTGTCGTACTCACAACCTAACAGTCAAGTCCTTCTTCCAAACATTAAACAAGAAATGCCAAGTCCTGGTTCTCAGGCTAGCCGCGGTCGAAGCTGTACAGATCAACTTGGCGACATGATTAACACTTATCTTCCTGGTGAAAGCGGTGCTCCCAACACAAATCACCACCCAGTCACTGCAAGCCACATCCCTGCAAATCGCTACGCTCAGTGGCAAGAACCCAGTTCTGTGGCAAGCAATTTGCCTGTTCATAGTGGCGTACCCTCGGCAAGCATTTCTAGTGTTACTGGAGTAAGTGGGACGATTCCGTTAACTCATTTGCCGTGAGGGAATTGCCTGAATTTTTCTGCTCATTTCTACCGCGAGCGCGGTAAATTTATTCTGTATTTTGCTTCCCGATCTGTCTCGTCGTTTGTTTAGGGATGACACAGAGAAAGGGAAATTAAGTATGTCTTGACTCGACTTTCACCTTGAGAGTCAAAATGCGAGGGCTGACGACAcagaaaaagagagagaaatgaCCCGACAGCTATTCTGACGCGGAACTGAATTGACAAGTTAAGTTCAGTAAAATTTATAAACCGTACCGATGAGTTATTTAAGAAACTCGTTAACAGTCTCTATGGATATGAGAAGTTAAGAGTTCAGTTGAGAACTAAAGCGAAGTTAATTTTAATAACGCGTGTGATGTCAATATTCGCTAGATTGTATCTGAGCGAAAAAAAATCTTGCTTAGCAAAACTGGTTTTGTGAAGGTGCTCTAGTTGAACGAAGAATGTTCACAAGTGCATTCATTGCCGGCGAGATCGTAATTTTTGAACTTTTGGTGTTGGTTGCGTTTCTTGTTTGAATTGCTTTGTAGAAATAATGCACGTTTGTATGAATTTCTAACTCTTCTGTGTACCGAGCTAATATCAGTTAGTATTGCGGAGTTAAGTGAATCATACCTCCATGAAAAGCATCAACTTGTATATAACTTCAGATAAAAGAGAAAAGATaatatttcctttattttccttttgaagaaataaaaaaagcaCATTAAAATAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6NVN0	Transcription factor Sox-2 OS=Xenopus tropicalis OX=8364 GN=sox2 PE=2 SV=1
Q6EJB7	Transcription factor Sox-3 OS=Danio rerio OX=7955 GN=sox3 PE=1 SV=1
O42569	Transcription factor Sox-2 OS=Xenopus laevis OX=8355 GN=sox2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000488 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF12336 all species →	SOXp	SOX transcription factor	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR050140 all species →	Family	SRY-related HMG-box transcription factors	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR022097 all species →	Family	Transcription factor SOX	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10270 all species →	SOX TRANSCRIPTION FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	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
K16796	SOX2; transcription factor SOX2 (SOX group B)	-	Transcription factors	ko03000	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_068733034.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

28TPM > 0

1Conditions

23.6Max TPM

9.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	28	9.54	23.60

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	23.60
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	23.36
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	20.65
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	20.51
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	20.10
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	19.77
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	18.33
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	17.77
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	17.47
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	15.95
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	13.86
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	13.51
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	13.06
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	13.04
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	12.44
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	11.79
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.96
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.36
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.34
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.53
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.39
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.27
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	4.93
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.58
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.52
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	4.49
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.02
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	3.76
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.