Gene detail

Detailed information of g4833.t1 in Montipora capitata

Genomic Location: Sc0000091:405145...424527
NR annotation: XP_020620163.1, cullin-5-like [Orbicella faveolata]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g4833.t1

atggctatcgactctggtgcgagtgcaaacattatcgatgaagaaagatttcagaaaattcaagaaaggtccaaggaaagactccggttagagaagtccaaagttaagctttatgcgtatgccagtgaggcttcgatacccgttgccggaaaattcaatgcaatagttgaaactaataagaaagtggttccggctacctttattgttgtgaaaggcaaaacgaaaggtgaaatgttgcttggatgtgacacggctatggagcttggagtcttaaagattgtaaacggtattgacaaagaggacaaggaattaaggcctgttgttgctgacattgtctcagaatatgactgcttatttcacggcattgggaaggacaacccagcagactacatgtcaagacacccgatacgtaacccagagaatacgactgactacaaggagcagaagcagacggaggaagttgtgaattccattgttagaagaaacgtaccagaatcgatctcggtcgaagaagtcagaatggctaccgtgaatgatcctgtgctgttggaagttatagacattgtgcaaaacggtaatggagaatcaagatataagtcggaagatctaggaccgtatagctgtctgccttgccaagctgcaactcaacagaagcctaaggagcctcttcagatgaccgaattgccagagaggccatggcagaagatttctcttgatttcagtggtccttacccctctggggaatattgtctgatagtggtggatgattattcacgataccccgtggtagaactagtaagcaccacttcagctgcagctgtgattccaagacttgacaagattttttctatgtttggaataccagaagaatgcaagtcagacaatggtccaccctttcaaagcagagagtttgcagactatgcaaagacgcaaggatttagacatcgaaagattacaccgttacatccagaagcaaacggtgaggcagaaagatttgtgaagactctgcagaagtttatcaccactacaacagtcgaaggtagcagttggaggatgtcgttgcctgattttctacgagtgtaccggtcaacgccacacaccgtgactggcagaagtccatattctcaactctttggtggaagagaaatgcgtggcaaaattcctcagttcagctttagcagtgaagaagaccttgaggactcagaaaaatatgtagaggagttacttacgctcttcaacagatttagcaaacttgtgaaagaagcttttaatgacgatccacgctttcttacagcaagagataaggcattcaagacggttgtgaatgatagttcaattttcaagttggaacttccaaacaagaataaatctggtggcggtggtggtctgaatatgaagtcgcagccagagtcccgttgtccagagctattggccaatttctgcgacatgctgcttcggaaaaccccatacagtaaaaaactaacatcggatgaaattcaagcaaagctgaaagacgttgatgtcggaatgcccgcggattacatcaacaaacttgctcgtatgttccaagacatcaaagttagcaacgatttgaatcagggtttcaaggcagaatacatgaacaagggagacattgcagactcggtaaacataaagatactaaacgcaggagcgtggtctagagcttcagagagaattccagtctcgctgcccaccgagattacctttggcaacaagattggaaagtttgacctggaagtaacaacctttcaaatggctgtgttgtttgcctggaatgaacgaccacatgagaagattgccttcgaaaatttgaggcttgcctcagagcttccagattcagaactgcgaagaactctttggtctctagtggccttcgccaagctcaagcgacagattctccaatgtgaacctgaagcaaaatctccaaaggattttagtgatagttctttattctgggtcaatcaagaattcgccgttgtcaaaaatggtaaattacagaaacgcggcaaagtgaatcttatcggtcggttacagctttcgacagaaaaagcaaaacaagaagagaacgatggcatcgttgcattgaggattttaagaatacaggaagcgattgtcaaaattatgaagatgagaaagaggattacgaacgcagctcttcaaacagaactcgtcgagattctaaaaaacatgttcattcctcagaagaagatgataaaggaacaaatcgagtggcttatagatcataagtacatcaaaagggacgaggaggacataaatacatttttatacatggtttag

Transcript

g4833.t1

ATGGCTATCGACTCTGGTGCGAGTGCAAACATTATCGATGAAGAAAGATTTCAGAAAATTCAAGAAAGGTCCAAGGAAAGACTCCGGTTAGAGAAGTCCAAAGTTAAGCTTTATGCGTATGCCAGTGAGGCTTCGATACCCGTTGCCGGAAAATTCAATGCAATAGTTGAAACTAATAAGAAAGTGGTTCCGGCTACCTTTATTGTTGTGAAAGGCAAAACGAAAGGTGAAATGTTGCTTGGATGTGACACGGCTATGGAGCTTGGAGTCTTAAAGATTGTAAACGGTATTGACAAAGAGGACAAGGAATTAAGGCCTGTTGTTGCTGACATTGTCTCAGAATATGACTGCTTATTTCACGGCATTGGGAAGGACAACCCAGCAGACTACATGTCAAGACACCCGATACGTAACCCAGAGAATACGACTGACTACAAGGAGCAGAAGCAGACGGAGGAAGTTGTGAATTCCATTGTTAGAAGAAACGTACCAGAATCGATCTCGGTCGAAGAAGTCAGAATGGCTACCGTGAATGATCCTGTGCTGTTGGAAGTTATAGACATTGTGCAAAACGGTAATGGAGAATCAAGATATAAGTCGGAAGATCTAGGACCGTATAGCTGTCTGCCTTGCCAAGCTGCAACTCAACAGAAGCCTAAGGAGCCTCTTCAGATGACCGAATTGCCAGAGAGGCCATGGCAGAAGATTTCTCTTGATTTCAGTGGTCCTTACCCCTCTGGGGAATATTGTCTGATAGTGGTGGATGATTATTCACGATACCCCGTGGTAGAACTAGTAAGCACCACTTCAGCTGCAGCTGTGATTCCAAGACTTGACAAGATTTTTTCTATGTTTGGAATACCAGAAGAATGCAAGTCAGACAATGGTCCACCCTTTCAAAGCAGAGAGTTTGCAGACTATGCAAAGACGCAAGGATTTAGACATCGAAAGATTACACCGTTACATCCAGAAGCAAACGGTGAGGCAGAAAGATTTGTGAAGACTCTGCAGAAGTTTATCACCACTACAACAGTCGAAGGTAGCAGTTGGAGGATGTCGTTGCCTGATTTTCTACGAGTGTACCGGTCAACGCCACACACCGTGACTGGCAGAAGTCCATATTCTCAACTCTTTGGTGGAAGAGAAATGCGTGGCAAAATTCCTCAGTTCAGCTTTAGCAGTGAAGAAGACCTTGAGGACTCAGAAAAATATGTAGAGGAGTTACTTACGCTCTTCAACAGATTTAGCAAACTTGTGAAAGAAGCTTTTAATGACGATCCACGCTTTCTTACAGCAAGAGATAAGGCATTCAAGACGGTTGTGAATGATAGTTCAATTTTCAAGTTGGAACTTCCAAACAAGAATAAATCTGGTGGCGGTGGTGGTCTGAATATGAAGTCGCAGCCAGAGTCCCGTTGTCCAGAGCTATTGGCCAATTTCTGCGACATGCTGCTTCGGAAAACCCCATACAGTAAAAAACTAACATCGGATGAAATTCAAGCAAAGCTGAAAGACGTTGATGTCGGAATGCCCGCGGATTACATCAACAAACTTGCTCGTATGTTCCAAGACATCAAAGTTAGCAACGATTTGAATCAGGGTTTCAAGGCAGAATACATGAACAAGGGAGACATTGCAGACTCGGTAAACATAAAGATACTAAACGCAGGAGCGTGGTCTAGAGCTTCAGAGAGAATTCCAGTCTCGCTGCCCACCGAGattACCTTTGGCAACAAGATTGGAAAGTTTGACCTGGAAGTAACAACCTTTCAAATGGCTGTGTTGTTTGCCTGGAATGAACGACCACATGAGAAGATTGCCTTCGAAAATTTGAGGCTTGCCTCAGAGCTTCCAGATTCAGAACTGCGAAGAACTCTTTGGTCTCTAGTGGCCTTCGCCAAGCTCAAGCGACAGATTCTCCAATGTGAACCTGAAGCAAAATCTCCAAAGGATTTTAGTGATAGTTCTTTATTCTGGGTCAATCAAGAATTCGCCGTTGTcAAAAATGGTAAATTACAGAAACGCGGCAAAGTGAATCTTATCGGTCGGTTACAGCTTTCGacagaaaaagcaaaacaagaagAGAACGATGGCATCGTTGCATTGAGGATTTTAAGAATACAGGAAGCGATTGTCAAAATTATGAAGATGAGAAAGAGGATTACGAACGCAGCTCTTCAAACAGAACTCGTCGAGATTCTAAAAAACATGTTCATTCCTCAGAAGAAGATGATAAAGGAACAAATCGAGTGGCTTATAGATCATAAGTACATCAAAAGGGACGAGGAGGACATAAATACATTTTTATACATGGTTTAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q93034	Cullin-5 OS=Homo sapiens OX=9606 GN=CUL5 PE=1 SV=4
Q9JJ31	Cullin-5 OS=Rattus norvegicus OX=10116 GN=Cul5 PE=1 SV=3
Q5RB36	Cullin-5 OS=Pongo abelii OX=9601 GN=CUL5 PE=2 SV=3

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
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR036317 all species →	Homologous_superfamily	Cullin homology domain superfamily	Interproscan
IPR016158 all species →	Domain	Cullin homology domain	Interproscan
IPR016159 all species →	Homologous_superfamily	Cullin repeat-like-containing domain superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR019559 all species →	Domain	Cullin protein, neddylation domain	Interproscan
IPR045093 all species →	Family	Cullin	Interproscan
IPR001373 all species →	Domain	Cullin, N-terminal	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11932 all species →	CULLIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
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:0031466 all species →	Cellular Component	Cul5-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
GO:0003676 all species →	Molecular Function	nucleic acid 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

No KEGG orthology assignment for g4833.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g4833.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

96.1Max TPM

34.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	32.60	96.09
whole organisms · low pH treatment	15	15	36.76	82.61
whole organisms · extra low pH treatment pH treatment	12	12	34.64	79.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	96.09
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	64.76
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	60.94
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	46.96
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	41.37
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	37.40
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	36.82
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	35.89
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	34.63
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	33.16
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	30.71
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	29.71
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	29.09
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	20.20
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	18.33
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	15.51
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	15.13
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	13.97
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	12.14
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	5.94
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	5.87
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	82.61
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	79.89
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	55.39
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	48.10
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	41.15
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	37.46
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	36.17
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	32.58
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	31.65
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	28.61
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	27.05
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	25.87
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	12.03
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.49
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.31
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	79.19
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	64.55
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	55.64
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	45.22
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	35.23
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	31.39
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	29.38
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	25.99
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	24.87
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	12.40
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	7.20
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	4.69

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.