Detailed information of OS493_026045-T1 in Lophelia pertusa

Genomic Location: scaffold_131:1106451...1118441
NR annotation: KAJ7356286.1, E3 ubiquitin-protein ligase sh3rf3 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8TEJ3E3 ubiquitin-protein ligase SH3RF3 OS=Homo sapiens OX=9606 GN=SH3RF3 PE=1 SV=2
Q6NRD3E3 ubiquitin-protein ligase SH3RF1 OS=Xenopus laevis OX=8355 GN=sh3rf1 PE=1 SV=1
Q28E95E3 ubiquitin-protein ligase SH3RF1 OS=Xenopus tropicalis OX=8364 GN=sh3rf1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006413 (this species only) · gene tree & orthology
Ubiquitin familyE3|E3 activity RING|RING · all ubiquitin genes in this species
Ubiquitin familyUBD|Other|SH3 · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14604
all species →		SH3_9Variant SH3 domainDomainInterproscan
PF00097
all species →		zf-C3HC4Zinc finger, C3HC4 type (RING finger)DomainInterproscan
PF00018
all species →		SH3_1SH3 domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001452
all species →		DomainSH3 domainInterproscan
IPR017907
all species →		Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR036028
all species →		Homologous_superfamilySH3-like domain superfamilyInterproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR018957
all species →		DomainZinc finger, C3HC4 RING-typeInterproscan
IPR035816
all species →		DomainSH3RF1/SH3RF3, fourth SH3 domainInterproscan
IPR050384
all species →		FamilyEndophilin/SH3RFInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR028502
all species →		DomainE3 ubiquitin-protein ligase SH3RF3, RING finger, HC subclassInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14167
all species →		SH3 DOMAIN-CONTAININGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0046872
all species →		Molecular Functionmetal ion bindingInterproscan
GO:0016567
all species →		Biological Processprotein ubiquitinationInterproscan
GO:0032436
all species →		Biological Processpositive regulation of proteasomal ubiquitin-dependent protein catabolic processInterproscan
GO:0046330
all species →		Biological Processpositive regulation of JNK cascadeInterproscan
GO:0061630
all species →		Molecular Functionubiquitin protein ligase activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K12171SH3RF, POSH; E3 ubiquitin-protein ligase SH3RFEC:2.3.2.27
Ubiquitin systemko04121deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_026045-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples
110TPM > 0
7Conditions
57.4Max TPM
16.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
polyp at pH7 9 18 18 10.43 18.57
polyp at pH7 6 18 18 11.92 16.94
coral polyp · control treatment 16 16 18.74 31.01
coral polyp · oil and dispersant treatment 16 16 31.97 57.36
coral polyp · oil treatment 16 16 16.35 24.79
coral polyp · dispersant treatment 16 16 19.94 49.88
Polyp 10 10 6.14 8.40

Per sample · hover a bar for the full sample record

Show the sample table (110 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11359523 polyp at pH7 9 not recorded not recorded not recorded - 18.57
SRR11359519 polyp at pH7 9 not recorded not recorded not recorded - 17.97
SRR11359522 polyp at pH7 9 not recorded not recorded not recorded - 17.92
SRR11359518 polyp at pH7 9 not recorded not recorded not recorded - 15.33
SRR11359520 polyp at pH7 9 not recorded not recorded not recorded - 14.33
SRR11359521 polyp at pH7 9 not recorded not recorded not recorded - 13.96
SRR11359497 polyp at pH7 9 not recorded not recorded not recorded - 10.71
SRR11359498 polyp at pH7 9 not recorded not recorded not recorded - 9.95
SRR11359496 polyp at pH7 9 not recorded not recorded not recorded - 9.54
SRR11359510 polyp at pH7 9 not recorded not recorded not recorded - 9.23
SRR11359511 polyp at pH7 9 not recorded not recorded not recorded - 8.26
SRR11359499 polyp at pH7 9 not recorded not recorded not recorded - 8.01
SRR11359495 polyp at pH7 9 not recorded not recorded not recorded - 7.28
SRR11359508 polyp at pH7 9 not recorded not recorded not recorded - 6.80
SRR11359494 polyp at pH7 9 not recorded not recorded not recorded - 6.57
SRR11359509 polyp at pH7 9 not recorded not recorded not recorded - 5.56
SRR11359507 polyp at pH7 9 not recorded not recorded not recorded - 4.73
SRR11359506 polyp at pH7 9 not recorded not recorded not recorded - 3.08
SRR11359524 polyp at pH7 6 not recorded not recorded not recorded - 16.94
SRR11359527 polyp at pH7 6 not recorded not recorded not recorded - 16.90
SRR11359525 polyp at pH7 6 not recorded not recorded not recorded - 16.59
SRR11359526 polyp at pH7 6 not recorded not recorded not recorded - 16.07
SRR11359515 polyp at pH7 6 not recorded not recorded not recorded - 13.50
SRR11359504 polyp at pH7 6 not recorded not recorded not recorded - 12.27
SRR11359505 polyp at pH7 6 not recorded not recorded not recorded - 11.92
SRR11359514 polyp at pH7 6 not recorded not recorded not recorded - 11.82
SRR11359528 polyp at pH7 6 not recorded not recorded not recorded - 11.72
SRR11359529 polyp at pH7 6 not recorded not recorded not recorded - 11.69
SRR11359517 polyp at pH7 6 not recorded not recorded not recorded - 11.50
SRR11359513 polyp at pH7 6 not recorded not recorded not recorded - 10.79
SRR11359516 polyp at pH7 6 not recorded not recorded not recorded - 10.36
SRR11359512 polyp at pH7 6 not recorded not recorded not recorded - 9.56
SRR11359500 polyp at pH7 6 not recorded not recorded not recorded - 9.06
SRR11359501 polyp at pH7 6 not recorded not recorded not recorded - 8.69
SRR11359502 polyp at pH7 6 not recorded not recorded not recorded - 7.74
SRR11359503 polyp at pH7 6 not recorded not recorded not recorded - 7.37
SRR16705990 coral polyp · control treatment coral polyp polyp control treatment SRP344271 31.01
SRR16705972 coral polyp · control treatment coral polyp polyp control treatment SRP344271 28.00
SRR16705974 coral polyp · control treatment coral polyp polyp control treatment SRP344271 24.13
SRR16705965 coral polyp · control treatment coral polyp polyp control treatment SRP344271 23.77
SRR16705960 coral polyp · control treatment coral polyp polyp control treatment SRP344271 20.48
SRR16705942 coral polyp · control treatment coral polyp polyp control treatment SRP344271 18.83
SRR16705943 coral polyp · control treatment coral polyp polyp control treatment SRP344271 18.20
SRR16705957 coral polyp · control treatment coral polyp polyp control treatment SRP344271 17.99
SRR16705971 coral polyp · control treatment coral polyp polyp control treatment SRP344271 17.55
SRR16705946 coral polyp · control treatment coral polyp polyp control treatment SRP344271 16.95
SRR16705989 coral polyp · control treatment coral polyp polyp control treatment SRP344271 16.29
SRR16705973 coral polyp · control treatment coral polyp polyp control treatment SRP344271 15.15
SRR16705991 coral polyp · control treatment coral polyp polyp control treatment SRP344271 13.97
SRR16705975 coral polyp · control treatment coral polyp polyp control treatment SRP344271 13.69
SRR16705970 coral polyp · control treatment coral polyp polyp control treatment SRP344271 12.29
SRR16705992 coral polyp · control treatment coral polyp polyp control treatment SRP344271 11.59
SRR16705996 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 57.36
SRR16705978 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 52.72
SRR16705979 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 43.91
SRR16705945 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 40.21
SRR16705995 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 39.00
SRR16706004 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 36.96
SRR16705993 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 33.18
SRR16705947 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 33.05
SRR16705944 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 32.29
SRR16705982 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 27.38
SRR16705976 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 22.83
SRR16706005 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 22.40
SRR16705977 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 19.67
SRR16705994 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 19.10
SRR16705948 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 18.55
SRR16705997 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 12.94
SRR16705981 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 24.79
SRR16705983 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 24.32
SRR16705999 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 22.22
SRR16705984 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 19.20
SRR16705949 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 18.39
SRR16705952 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 17.95
SRR16705963 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 17.39
SRR16705961 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 16.63
SRR16706000 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 16.28
SRR16705998 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 16.08
SRR16706001 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 15.55
SRR16705980 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 15.50
SRR16705951 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 14.91
SRR16705962 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 8.63
SRR16705950 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 8.34
SRR16705964 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 5.48
SRR16705987 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 49.88
SRR16705968 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 29.65
SRR16706002 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 26.17
SRR16705955 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 24.03
SRR16705969 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 23.41
SRR16705959 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 22.26
SRR16705988 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 21.98
SRR16705966 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 20.84
SRR16705958 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 18.43
SRR16705967 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 17.28
SRR16706003 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 16.99
SRR16705956 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 16.75
SRR16705954 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 14.41
SRR16705986 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 11.50
SRR16705985 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 4.04
SRR16705953 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 1.46
SRR23025713 Polyp not recorded not recorded not recorded - 8.40
SRR23025710 Polyp not recorded not recorded not recorded - 8.33
SRR23025711 Polyp not recorded not recorded not recorded - 7.99
SRR23025708 Polyp not recorded not recorded not recorded - 7.88
SRR23025712 Polyp not recorded not recorded not recorded - 5.66
SRR7746667 Polyp not recorded not recorded not recorded - 5.25
SRR7746666 Polyp not recorded not recorded not recorded - 5.04
SRR23025709 Polyp not recorded not recorded not recorded - 4.73
SRR7746668 Polyp not recorded not recorded not recorded - 4.59
SRR7746669 Polyp not recorded not recorded not recorded - 3.50

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.

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