Gene detail

Detailed information of XP_068756940.1 in Montipora capricornis

Genomic Location: chr6:72460137...72485899
NR annotation: CAH3025702.1, unnamed protein product [Porites evermanni]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068900839.1

ACCCGTAATCCTTCTTGAGCTTGTTGGGTGATCCAGCTTCGCTTGTGTACGTGGTGAAAGGTGCGAAATTCGTGGGTGAGTCGTCCCCTTTCCGGTCCTCGCTGGGAGCAATAGAAATATGGAAGGACCTAAGGCTGTATGTGTCTTGTTGCCAAATAATAGCGAAGTACAAGGTGTCATTCATTTTGAGCAGAAAGGGGAATTGTGCAGGATTCATGGGGAAGTTAAAGGTCTCACACCTGGACTACATGGCTTCCATGTCCATCAGTTTGGAGATGGTACAAATGGTTGTACAAGTGCTGGTCCTCATTTCAACCCAGCTGGGAAATTGCATGGAGGCCCAGAGGATGAGCAACGTCATTATGGAGACCTTGGTAACATTATCGCAGATGATACAGGTGTAGCCAAAGTTGACATAACAGACAGACTGGTTACTCTAGTTGGAAATAATTCAGTTGTTGGACGAACCATTGTGGTTCATGCAAAGGAAGATGATTTGGGAAAAGGTGGCAATGAGGAAAGCACAAAGACTGGAAATGCTGGAGGACGTTTTGCTTGTGGTGTTATTGGCATCACTAAGTTCATGGCACGTGCAGTATGTAATCTAACAGGTTCCGTTCGAGGATCAATAACATTTTCGCAAGAGTTCCCAGGAGCAGCTTGTGAAATCACAGGGGTATTAGCAGGACTGACGGAGGGAAAACATGGCTTCCACATCTTGGAGTATGGTGACATTTCAGAAGGGGGTACTTCAGCTGGAGCACATTTCAATCCATTAAATAAAAGCCATGGGGGACCCAATGATGAAGAAAGACATACTGGTGACCTTGGTAACATTGAAGCTGACAGCCAAGGCCAGGCAGAAGTGAATATTGTTGACAGTACTGTGTCATTGATGGGAGAATATTCAGTGATAGGCCGTGCCGTAGAGATTTGTGAAGGTGTTGATGATCTTGGAAGAGGAGGGCATGAACTGAGTCTCACCTCTGGAAATTCTGGAGCTTGTTTGGCCTGTGGAGTGATTGGAGTGGCCACAAATAcaacaaaatattatttaaaaacTCCACTTAACAGTGGATCTCTTATTGATGAGAATGGTTTTTACTAATAGGTGGATTTATTTTCATGTGGAGATATTATTGAGCTGGCTGATTTCTGCTTCAAATTACGAAAGTGTTCTTATTTTACATCCAAAATTGTGAAATTGAGTTAAAGGCAACATTTGGTATTTTGACCAACACTCTTTTAATGCAAATCGGTCCTATTGTAGTCCTATTTTCAATGAACCACAGTTGTTGAACACTCTCACTACACAGTTACTTTAAAGAGCCCTCCAGCTGTACCACTACGGGTGGGTTCGATTGACCGTAGAGTGAtaatttaaaacggtatgtctggcgttttgaagccaACCAAGATAATAAGATATGTTTAAAGTAGCGTTTTAGCAggttttgacaattttaatgtgaatctcttcagaaacgaaggatttctaacttctattccatgtattcctatgccagaatacggtcaatcgaacgcaccctaactAGACTCTGCATTAACTCTAGCCTCCTTCACAGtgcagtaaatatccaccaccagccacctccacttcggtgaatagttgcttgTTATTGTAGATGGTAATTATTAATTATCGCGTTGGTTGGCAATAACTTATGATTCTGGAAATATGCCGATAAGAATTTCTACTGTATAGAAGGTGCACTGCTGCCCAAGCTTTGGAAACATTCTTGATAAGATGTACATATTCAGGAGctcatgataattattattatagtaaaACTAAATGTTGGAGGTTAGTTGATGGGACTGTAGAGAAAAAGAGGACACTACATTTACTAACCATATCATTGGACTTTGATCGTGCTGGTGAAGGTAGCCTTGAGAAGGACTACTGTTTGTAACTGGCTTTTGACAACCTCTCAGATTGTTGAAGGTCAGTTTCAAACAGTCGTTATCAGGACGACTCTCACCTGGACAATCAAATTCTATTAAGGTATGACATCCCTGGTTTCATTGTACAGCAGTTCTATTTTTATTTAAGTGCCTGTAATAGTGAATTATTTTTCAATTGAATTGTTATGTTTGTTGTAACTTACCGTTGTAAAATATATGACATAAAATATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q52RN5	Superoxide dismutase [Cu-Zn] OS=Bos mutus grunniens OX=30521 GN=SOD1 PE=2 SV=3
P00442	Superoxide dismutase [Cu-Zn] OS=Bos taurus OX=9913 GN=SOD1 PE=1 SV=2
Q8HXQ3	Superoxide dismutase [Cu-Zn] OS=Hylobates lar OX=9580 GN=SOD1 PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000995 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00080 all species →	Sod_Cu	Copper/zinc superoxide dismutase (SODC)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001424 all species →	Domain	Superoxide dismutase, copper/zinc binding domain	Interproscan
IPR036423 all species →	Homologous_superfamily	Superoxide dismutase-like, copper/zinc binding domain superfamily	Interproscan
IPR024134 all species →	Family	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Interproscan
IPR018152 all species →	Binding_site	Superoxide dismutase, copper/zinc, binding site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10003 all species →	SUPEROXIDE DISMUTASE CU-ZN -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006801 all species →	Biological Process	superoxide metabolic process	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005507 all species →	Molecular Function	copper ion binding	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
K04565	SOD1; superoxide dismutase, Cu-Zn family	EC:1.15.1.1	Pathways of neurodegeneration - multiple diseases	ko05022	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_068756940.1 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

30TPM > 0

1Conditions

187.8Max TPM

101.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	101.60	187.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	187.82
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	182.74
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	178.86
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	169.73
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	159.16
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	157.48
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	150.67
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	149.48
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	149.21
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	134.08
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	130.58
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	128.45
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	127.58
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	126.12
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	124.37
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	118.91
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	107.04
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	104.10
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	103.27
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	94.54
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	91.96
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	90.80
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	90.80
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	89.47
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	88.90
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	87.98
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	86.77
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	84.12
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	82.53
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	79.93
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
SRR12963484	Polyps	Polyps	E3 day0	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.