Gene detail

Detailed information of g15967.t1 in Montipora capitata

Genomic Location: Sc0000650:18326...57943
NR annotation: CAH3024771.1, unnamed protein product [Porites evermanni]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g15967.t1

atggcttctaggacacaaaacccacatgggttgcgccagattaacttggatgagatttgggatgaccttaaggaaggaattcaacatgtttacaagcaacaaagtatgtcgaggcctcggcacatggaactttacacccatgtgtacaattactgtacaagtgtccatcaacaatcacaatccagagttccaaaacagaaaaaagctccaaatcaaggtggagctcagtttgttggtcatgaattgtacaaaagacttaaagacttccttaagaactacctcactggaatgcaaaaggatggttctgatctcatggatgagtcagtgttgaagttctacactcagcgttgggaggattatagattttcaagcaaagtattgaatggagtatgtgcatatttgaatcgacattgggttcgacgagagtgtgatgaaggaaggaaaggcatttatgaaatttattcgctagccttagttacctggagagagaatcttttccgaccactaaacagacaggttacaaatgcagtgcttcggttaattgaaagagaaagaaatggcgaaacaattaacaccagacttgtgagtggtgttatccagtgttatgttgaactgggtctgaatgaagaggatccctcaacaaaaggccccacccttaatgtctataaatcatcttttgagtcggtgtttttagatgatacagaaagattttataccacagagagtacagaatttcttagagaaaaccctgttacagagtatatgaaaaaggctgaagctcgtctgttagaagagcaaagaagagtccaggtctacttacatgaaagtacacaagatgagcttgccagaaagtgtgaacaagttttgattgaaaaacacctggacatcttctatgcagaatttcagaacctcctcgatgatgataagaatgaagatcttggtcgcatgtacaatttggttgccaggatacctgatggacttgggcaacttcgaaccctgctggaaaaccacattaccaatcagggactgaatgcgttagaaaaatgcggggatcaggctttcaatgaccccaaggtatatgtggaaatgatacttgaagttcatcacaagtacaatgcactagtactgacagcatttagcaatgatgcaggtttcgtggcagctcttgacaaggcctgcggcaagtttataaataacaattttgtcactaaacaagctcagagttcttccaagtcacctgaactgctggcaagatactgtgattccttgctaaagaaaagttcaaagaatccagaagaggctgaactagaagacattcttaattcagtgatggttgtgtttaagtacatcgaagacaaagatgtgtttcagaagttttattccaagatgttggcgaagcggctagtacaacacaactcggcgtcagatgatgctgaagccagcatgatttcaaaacttaagcaagcgtgtgggtttgagtacacctccaaactgcaaagaatgttccaagacatcggtgttagcaaagatctcaatgacaaattcaagactcatctagcaaatacagatgccttagatttggacttttcaatccaggttcttagttctggatcgtggccattccaacagtcggcaccattctctctaccagcagagatggaaagaagtcatcagcgttttacaacattctatagcagtcagcacagtggtcggaaactccactggctttatcacatgtcaaagggtgaactcgtaacgaattgtttcaagaatcgctacactcttcaggcttccacttatcaaatggcagtacttctgatgttcaataactcggaccatctgactttggagcaaattcaagaacatactcaacttaaaccggatattctttctcaagtcctaggaatattgttaaagtcgaaacttcttgtttgcgaaacatctgaagatggctctaacttagatcgccactcatccgttagtctttttcttggatataaaaataaaaagctaagagttaatatcaacgtaccgatgaaaacagagcagaggcaggaacaagaacaaactcacaaatatattgaagaggacagaaaactgcttattcaggcagccattgttcggatcatgaaaatgaggaaaatgctaaaacaccagcctctgctggcggaggtgttgtcacagctgtccagcagattcaaacccagagttcctgtcataaagaagtgtattgatatcttaattgaaaaagaataccttgagcgagtggagggagagaaagacacttacgcttacttggcgtga

Transcript

g15967.t1

ATGGCTTCTAGGACACAAAACCCACATGGGTTGCGCCAGATTAACTTGGATGAGATTTGGGATGACCTTAAGGAAGGAATTCAACATGTTTACAAGCAACAAAGTATGTCGAGGCCTCGGCACATGGAACTTTACACCCATGTGTACAATTACTGTACAAGTGTCCATCAACAATCACAATCCAGAGttccaaaacagaaaaaagctCCAAATCAAGGTGGAGCTCAGTTTGTTGGTCATGAATTGTACAAAAGACTTAAAGACTTCCTTAAGAACTACCTCACTGGAATGCAAAAGgaTGGTTCTGATCTCATGGATGAGTCAGTGTTGAAGTTCTACACTCAGCGTTGGGAGGATTATAGATTTTCAAGCAAAGTATTGAATGGAGTATGTGCATATTTGAATCGACATTGGGTTCGACGAGAGTGTGATGAAGGAAGGAAAGGCATTTATGAAATTTATTCGCTAGCCTTAGTTACCTGGAGAGAGAATCTTTTCCGACCACTAAACAGACAGGTTACAAATGCAGTGCTTCGGTTAATTGAAAGAGAAAGAAATGGCGAAACAATTAACACCAGACTTGTGAGTGGTGTTATCCAGTGTTATGTTGAACTGGGTCTGAATGAAGAGGATCCCTCAACAAAAGGCCCCACCCTTAATGTCTATAAATCATCTTTTGAGTCGGTGTTTTTAGATGATACAGAAAGATTTTATACCACAGAGAGTACAGAATTTCTTAGAGAAAACCCTGTTACAGAGTATATGAAAAAGGCTGAAGCTCGTCTGTTAGAAGAGCAAAGAAGAGTCCAGGTCTACTTACATGAAAGTACACAAGATGAGCTTGCCAGAAAGTGTGAACAAGTTTTGATTGAAAAACACCTGGACATCTTCTATGCAGAATTTCAGAACCTCCTCGATGATGATAAGAATGAAGATCTTGGTCGCATGTACAATTTGGTTGCCAGGATACCTGATGGACTTGGGCAACTTCGAACCCTGCTGGAAAACCACATTACCAATCAGGGACTGAATGCGTTAGAAAAATGCGGGGATCAGGCTTTCAATGACCCCAAGGTATATGTGGAAATGATACTTGAAGTTCATCACAAGTACAATGCACTAGTACTGACAGCATTTAGCAATGATGCAGGTTTCGTGGCAGCTCTTGACAAGGCCTGCGGCAAGTTTATAAATAACAATTTTGTCACTAAACAAGCTCAGAGTTCTTCCAAGTCACCTGAACTGCTGGCAAGATACTGTGATTCCTTGCTAAAGAAAAGTTCAAAGAATCCAGAAGAGGCTGAACTAGAAGACATTCTTAATTCAGTGATGGTTGTGTTTAAGTACATCGAAGACAAAGATGTGTTTCAGAAGTTTTATTCCAAGATGTTGGCGAAGCGGCTAGTACAACACAACTCGGCGTCAGATGATGCTGAAGCCAGCATGATTTCAAAACTTAAGCAAGCGTGTGGGTTTGAGTACACCTCCAAACTGCAAAGAATGTTCCAAGACATCGGTGTTAGCAAAGATCTCAATGACAAATTCAAGACTCATCTAGCAAATACAGATGCCTTAGATTtGGACTTTTCAATCCAGGTTCTTAGTTCTGGATCGTGGCCATTCCAACAGTCGGCACCATTCTCTCTACCAGCAGAGaTGGAAAGAAGTCATCAGCGTTTTACAACATTCTATAGCAGTCAGCACAGTGGTCGGAAACTCCACTGGCTTTATCACATGTCAAAGGGTGAACTCGTAACGAATTGTTTCAAGAATCGCTACACTCTTCAGGCTTCCACTTATCAAATGGCAGTACTTCTGATGTTCAATAACTCGGACCATCTGACTTTGGAGCAAATTCAAGAACATACTCAACTTAAACCGGATATTCTTTCTCAAGTCCTAGGAATATTGTTAAAGTCGAAACTTCTTgttTGCGAAACATCTGAAGATGGCTCTAACTTAGATCGCCACTCATCCGTTAGTCTTTTTCTTGGATATAAAAATAAAAAGCTAAGAGTTAATATCAACGTACCGATGAAAACAGAGCAGAGGCAGGAACAAGAACAAACTCACAAATATATTGAAGAGGACAGAAAACTGCTTATTCAGGCAGCCATTGTTCGGATCATGAAAATGAGGAAAATGCTAAAACACCAGCCTCTGCTGGCGGAGGTGTTGTCACAGCTGTCCAGCAGATTCAAACCCAGAGTTCCTGTCATAAAGAAGTGTATTGATATCTTAATTGAAAAAGAATACCTTGAGCGAGTGGAGGGAGAGAAAGACACTTACGCTTACTTGGCGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q13616	Cullin-1 OS=Homo sapiens OX=9606 GN=CUL1 PE=1 SV=2
Q9WTX6	Cullin-1 OS=Mus musculus OX=10090 GN=Cul1 PE=1 SV=1
Q5R4G6	Cullin-1 OS=Pongo abelii OX=9601 GN=CUL1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000554 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|Cullin · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10557 all species →	Cullin_Nedd8	Cullin protein neddylation domain	Domain	Interproscan
PF00888 all species →	Cullin	Cullin family	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016158 all species →	Domain	Cullin homology domain	Interproscan
IPR036317 all species →	Homologous_superfamily	Cullin homology domain superfamily	Interproscan
IPR045093 all species →	Family	Cullin	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR019559 all species →	Domain	Cullin protein, neddylation domain	Interproscan
IPR016157 all species →	Conserved_site	Cullin, conserved site	Interproscan
IPR001373 all species →	Domain	Cullin, N-terminal	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR016159 all species →	Homologous_superfamily	Cullin repeat-like-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11932 all species →	CULLIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0031146 all species →	Biological Process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0031461 all species →	Cellular Component	cullin-RING ubiquitin ligase complex	Interproscan
GO:0031625 all species →	Molecular Function	ubiquitin protein ligase binding	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein 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
K03347	CUL1, CDC53; cullin 1	-	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g15967.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

335.7Max TPM

207.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	205.31	319.44
whole organisms · low pH treatment	15	15	209.24	325.53
whole organisms · extra low pH treatment pH treatment	12	12	210.42	335.73

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	319.44
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	317.15
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	315.59
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	299.33
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	286.75
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	281.91
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	275.34
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	272.08
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	264.78
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	244.57
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	219.13
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	188.09
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	168.87
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	168.82
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	157.11
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	123.97
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	107.76
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	82.35
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	80.83
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	74.33
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	63.39
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	325.53
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	318.40
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	309.60
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	292.20
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	279.81
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	245.97
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	236.01
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	229.71
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	199.53
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	172.68
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	168.39
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	151.57
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	72.27
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	69.19
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	67.72
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	335.73
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	311.89
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	290.60
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	286.98
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	265.26
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	240.43
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	219.46
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	183.87
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	181.57
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	82.60
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	64.54
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	62.11

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.