Gene detail

Detailed information of XP_068736444.1 in Montipora capricornis

Genomic Location: chr14:48208353...48225602
NR annotation: XP_029195678.2, splicing factor 1-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068880343.1

ACCCACAATGCATTGCACTCCCTTTGATCTATCGTGGTTTTGTGCTACACATTATTTCGTTGAGGATGAATGTTTGTTCCAATTTCTTTGGCGGGCTGTTTTAAGTTGAGAATTACTTGTGAATATTTTGTCATTCCGGTAGAATTGTCTTGTAGATCAAATAGAACGAGGGAATGTCATTAACAGGAGCTAACACCACTCCGCTGGGAAGACTTCATCCCATATTGGCGGCCAAACAACAAGGGCCCACAAGTCCTGGTGCAAAAAGAGAAGCCGGTAATTTTGATTCAGGGtctgaaagaaaaaggaagagaAGAAGCCGATggggaacagaagaaaaaagaacatttattccTGGCATGCCAACAACCATGCCACCAAACCTGTCACCAGAGCAGCAACAAGCTTATATAGCCCAactgaaaattgaagaaatcaGCAGAATGCTGAGAACAGGGGAGTTGGGAATTCCTGATAACCCAGATGAAAGATCTCCTTCTCCAGAGCCAATTTACAACTCTGAAGGTAAACGATTGAACACACGTGAATTCAGAATTAGAAAAAAGCTTGAGGAAGAGAGGCATTCATTGATAGTAGAAGCCCAAAGCTTGAACGAAGATTACAAGCCTCCAGTAGATTACAAGCCACCTATTATTAAAATCCAAGACAAGGTGATGATTCCTCAAGATGATCATCCTGAAGTCAACTTTATTGGGCTGCTCATTGGGCCACGTGGTAATACTttgaagaaaatggaaaaagagAGTACGGCAAAAATAATGATCAGGGGTAAAGGATCCATAAAAGAAGGCAAAATCCATGTGTGGAACAATGGAGGAAAGGGGGGACAGGTAAACAGTGGTGAAGATGAAGAACTTCATGCACTGGTTACTGGACCAACAAATGAGTCAGTTCAGAGGGCTGTAGCTATGATAAGAGATATCTTACGACAAGGCATAGAAGCCCCTGAAGGACAGAATGATCTCAAGAGAATGCAACTTAGAGAACTTGCTGCATTGAATGGCACTCTACGGGATGATGAGATCCTGAGATGCCGGAACTGTGGATCAGTGGAGCATCGTCACTGGGAGTGTCCAGAACAGAAAAATGTTACTAATAATGTACTGTGTACAAGATGTGGTGCTGCAGGACATCTGGCTACAGATTGCATTCAGACAGATCTGCCTCCAATTCCTATTGTTCAAGTTGACAAAGCAAAAATGGACAGTGAGTACATGTCATTAATGGCTGAGCTGGGAGAAGGGCCACCACCAGAACCTAAGATGCCACCAGCACGACTACCACCACCTCCAGTGGAACAAAATAGACCGCCCCCACGATTTCCCCCAGGTCCCACCCCACCTCCTCCAGGACAGAACACCAATCATGACCGGCCACCACCATCTGGTCCAGCGCCGTCATCTGGGCCTCCACCATGGGCAGGAGCAGCAGCAGCcacaccaccaccaccaccaccacctgCTCCCAAGCCACTGATGAGCACACCAGTAGCAATGCCACCAGGAGGAGGTTTGCCACCACCTCCTCCTCCCCCTAACAACTCTAATGCTCCACCATGGGCAAAGCCAGGGCTCTTACATCCTCCTGGGGGACCCTTAATGGGTCCTCCACCCCCACATCAGCATGGTGGTCCCCCACCACCTCCTCCCCCAGGGGGACCTGGACCATATCCTCCCCAGGGTCCTGGTGGACATGGACCACCACCTCCACCCCCACCAACATCGAGTGGTCCACCGCCCCCTTGGCAAAACCCAGGTCCACCACCCCCTTGGCAAAATCAGCAACCTGGATATGCCCCACCTCCACCCCCAGGGTATGCCCCATTTCATGGCCCTCCACCACTGCCACCACCTTCTGACAACCAGTGGGCGCCTCCTCCCCTGATGGGAGCACCACCacctcccccacccccaccaCCACCTGGCCCACCACCACCCCCATCATCCTAAGAAAACTACAGACAGAGAAGTCCATGGAGTtaacagacaaacaaacaatcaTTTTAAATATTCAACTGGCCTCTTTTATCTTGGTTTCTCTGAGGCAGAAGTCGCTTTATTCAGAAACAAAACACATTACATGGTTTCCTAATGGTACATTCGCAATCATAGACTGCTTGTAGGCGATGATTTGCATGTTTTTATAGATGGAGGAAATGTGGTCGCGATATTGAATGGGTTATTGGAAGATCTGTTTGTTTATTGGTTCTACCATCTTCTGCCAACTCATGCTATATAATAACCAGATTTCCAGGAAGACCACTAACACAAGAAGGCAAATAGAATCAAAACCAGAGATGGTTTTCTTTTCTCAAAAAGAAGTGCCGTTAAAATGAACGGTTATTTGAACATCTGTCAATCCCAGCTTCAGCATCTCTAAAATGCTCAGAATGGGGTTGCGAGAGTTATGGTCATATTGGGTTTTCTTATGTGTTTCAGAGCCAAACTAACCTCTCGTTTACTCTTCGAGTAAATTGCCAATCCGCTAGCACAATTTTCCCGAACTGTTTACTCTTTATCATCCCCAGTCTCCCTGCTGCTTTTAACTGGTGGCTCTTCTAACTAAAAGAACTGGTGGCTCTGGAATAGAGAATGTTCGACAGTAGACCACAAGCACTCGTTTTTTCGTGTAAGACAAAAATAGTTAAAGCAGTCAGCATGTCTCGATGTGGTAGAACTCTGCCAACGTCTTAAAAATTTGATGATTGTTTGACATGATCccgtaataaattattatagaTTTAAGCCCAGTTCTTGGTTTGCCCACGCGCCATCACCGGACATGTTCTGAAAccgaaattaaaaaagaaaaaaaaggattccTGAAGAATGCAGCCTCGTTCGTAAAAACATCGCAACCGTTTGTTTGTTTAGAGACACGAATAGGGAGCTAACGCAAtgacaacgacgacggctacgagaatgttttctgaaaatattatttcccgttttTGTCGATTACTCCAGGTCATActgcatggaaagtgtgtatttAACAtttccaggaataaaattggtatgAACAGTGTAGCTGTTTGGAATGAAAATTCAGAATTTATCGTCAGGTGTTTGCGTCCTCGACAtagcctcaaatttggtcatttcacgtcgttgtcaggacgcgAACGGCAAGGAAATGCACCATGCACGCACACGCGCGGTGTGCAGGGTGTGTCATGACGTGCTCGTAGCCGCGGTCGTTGACCTTTCGTAAGCACTCGTAATATTGTCGTGATGGTGTGATGTGCCAGCCACGAATGAGGCACCCTGCCTCGCTTTGGAGAGCTTTGCTCGCGGGCTAATGAAGAACGGGGTAACTTTCAAATAAGTCATTATTTGCAAGCTCGGTTTGCTCAACAGAGGATCAAAGAGACGAACTATACATTATTTTTGTTGGCGAACGAGTCGGCTCTTTTGTGGATGCTAAGTGTTGCTTATTTTTGTGGTTGAGCAAATTTTTCGAAACATTGGTCTAAAACAGACTGAATGATTCTGCTTACATTATGGCGGATTGTTTCATTTCCTCTACTTACCTGTGTAAAAGTAAATTGCTGGTCAGTAGTGTGCCTAGATGTTGTATCGTAACATTAGATGTTTTTGTCCGCGAACTGAAAATACAGTGATGAGTTTTAAGTC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q15637	Splicing factor 1 OS=Homo sapiens OX=9606 GN=SF1 PE=1 SV=4
Q64213	Splicing factor 1 OS=Mus musculus OX=10090 GN=Sf1 PE=1 SV=6
P0CO45	Branchpoint-bridging protein OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) OX=283643 GN=BBP PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005959 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan
PF16275 all species →	SF1-HH	Splicing factor 1 helix-hairpin domain	Domain	Interproscan
PF00013 all species →	KH_1	KH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR047086 all species →	Homologous_superfamily	Splicing factor 1, helix-hairpin domain superfamily	Interproscan
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR004087 all species →	Domain	K Homology domain	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR032570 all species →	Domain	Splicing factor 1, helix-hairpin domain	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR045071 all species →	Family	KH domain-containing BBP-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11208 all species →	RNA-BINDING PROTEIN RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0048024 all species →	Biological Process	regulation of mRNA splicing, via spliceosome	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
K13095	SF1; splicing factor 1	-	Spliceosome	ko03041	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_068736444.1 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

41.0Max TPM

17.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	17.14	40.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	40.96
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	40.69
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	38.94
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	34.84
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	32.32
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	32.17
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	30.57
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	24.08
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	23.69
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	23.12
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	23.00
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	20.82
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	20.02
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	19.15
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	18.82
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	18.28
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	17.88
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	17.66
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	17.05
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	16.47
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	14.94
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	11.63
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	11.09
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	11.05
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	10.73
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	10.69
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	10.45
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	9.00
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	8.71
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	8.30
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.