E3 ubiquitin-protein ligase XIAP

Overview
NameE3 ubiquitin-protein ligase XIAP
Smed IDSMED30015020
Length (bp)797
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of E3 ubiquitin-protein ligase XIAP (SMED30015020) t-SNE clustered cells

Violin plots show distribution of expression levels for E3 ubiquitin-protein ligase XIAP (SMED30015020) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of E3 ubiquitin-protein ligase XIAP (SMED30015020) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for E3 ubiquitin-protein ligase XIAP (SMED30015020) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30015020

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30015020SMESG000031958.1 Contig778GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015020SMESG000031958.1 Contig51160newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015020SMESG000031958.1 Contig51160uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30015020SMESG000031958.1 dd_Smed_v6_2104_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015020SMESG000031958.1 dd_Smed_v6_2104_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30015020SMESG000031958.1 dd_Smed_v6_2104_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
intestinal phagocyteSMED30015020SMESG000031958.1 dd_Smed_v6_2104_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30015020SMESG000031958.1 dd_Smed_v6_2104_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30015020SMESG000031958.1 dd_Smed_v4_2104_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of E3 ubiquitin-protein ligase XIAP vs. TrEMBL
Match: I1ZIH9 (IAP domain containing-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 9.431e-6
Identity = 27/55 (49.09%), Postives = 34/55 (61.82%), Query Frame = 3 
Query:  498 TESLL--TCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIY 656
            TE LL  TC+ C K QVS+LY PC HVV C  C  S+   C  C + I ++H+IY
Sbjct:    1 TERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNVPIHQYHLIY 55
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Match: SMESG000031958.1 (SMESG000031958.1)

HSP 1 Score: 359.377 bits (921), Expect = 3.248e-127
Identity = 187/190 (98.42%), Postives = 188/190 (98.95%), Query Frame = 3 
Query:   90 MINSARENGIGLIVKKNDQIFKKEISLVEIVKNTLLNFQLDLEKWPLKMMRKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDXXXXXXXXXVKKQTESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF 659
            MINSARENGIGLIV KNDQIFKKEISLVEIVKNTLLNFQLDLEKWPLKMMRKFI+SLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDEIEIEINNIVKKQ ESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF
Sbjct:    1 MINSARENGIGLIVNKNDQIFKKEISLVEIVKNTLLNFQLDLEKWPLKMMRKFIKSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDEIEIEINNIVKKQNESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF 190
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Match: SMESG000032006.1 (SMESG000032006.1)

HSP 1 Score: 127.102 bits (318), Expect = 5.568e-36
Identity = 66/167 (39.52%), Postives = 97/167 (58.08%), Query Frame = 3 
Query:  159 EISLVEIVKNTLLNFQLDLEKWPLKMMRKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDXXXXXXXXXVKKQTESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF 659
            ++S    ++N + +F  + E  PLK +++ ++S  NE++  L E FGY  S+LKLAS +I  N++    E +N+IFW CM LR DK C KII   M   D I +++  I  K ++  LTC  C    VS+LYLPCG +V CS C+  +   C  C   ++E H IYF
Sbjct:   18 QLSTQHSIENEIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF 184
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Match: SMESG000031926.1 (SMESG000031926.1)

HSP 1 Score: 119.013 bits (297), Expect = 8.766e-33
Identity = 63/145 (43.45%), Postives = 89/145 (61.38%), Query Frame = 3 
Query:  222 WPLKMMRKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDXXXXXXXXXVKKQTESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIY 656
            + L  + K  +S  +E I  LS+ FGYN ++LKL+S +I  N++K  D N N +FW CME R  +   K+I   M   D ++  IN+ +K+ T   LTCS C   QVSVLYLPCGH+V CS C +ST   C +C + I+E+H +Y
Sbjct:   54 FDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNTNLVFWSCMEFRVGQY-QKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYHFVY 197
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Match: SMESG000067789.1 (SMESG000067789.1)

HSP 1 Score: 112.849 bits (281), Expect = 2.895e-30
Identity = 67/188 (35.64%), Postives = 105/188 (55.85%), Query Frame = 3 
Query:   99 SARENGIGLIVKKNDQIFKKEISLVEIV--KNTLLNFQLDLEKWPLKMMRKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDXXXXXXXXXVKKQTESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIY 656
            S  EN +     KN  I  ++   +E +  K+T+ +F    + +  K +   ++  KN  I  L + F Y+  ILKL+S+++  ++   D+++LN+ FW CMELR + E  ++    +RK+D IE ++   +    +  LTCSIC + QVSVLYLPCGHV+ CS+C       C AC   I E+H IY
Sbjct:   26 SENENSVKT---KNKTIISEQKPSMEFIEFKSTVEDFINTYDTFTDKEIINILKIFKNPSIEYLIDIFNYDKCILKLSSYLMYLDKTGMDNDSLNEYFWDCMELRLNPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKCQDKNNRKCQACSAPINEYHAIY 210
[Close]
BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Match: SMESG000067788.1 (SMESG000067788.1)

HSP 1 Score: 105.531 bits (262), Expect = 1.712e-27
Identity = 64/149 (42.95%), Postives = 87/149 (58.39%), Query Frame = 3 
Query:  210 DLEKWPLKMMRKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDXXXXXXXXXVKKQTESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIY 656
            +  K   K++ + ++  KN  I    ETFGYN  ILKL S+++  N++  + ENLND FW  M L               + D IE E+  IVK++ + LLTC  C K  VS+LYLPCGHVV C++C+Q +   C ACG  IEEFH+IY
Sbjct:   75 NYAKLNSKILLEILKLFKNSSIKFCHETFGYNKKILKLCSFLMERNKVNINHENLNDYFWSFMNLS--------------QLDGIEKEMCEIVKERNKQLLTCMGCQKNSVSILYLPCGHVVMCNKCYQISTKHCQACGSSIEEFHVIY 209
The following BLAST results are available for this feature:
BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIH99.431e-649.09IAP domain containing-1 (Fragment) OS=Schmidtea me... [more]
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of E3 ubiquitin-protein ligase XIAP vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031958.13.248e-12798.42SMESG000031958.1[more]
SMESG000032006.15.568e-3639.52SMESG000032006.1[more]
SMESG000031926.18.766e-3343.45SMESG000031926.1[more]
SMESG000067789.12.895e-3035.64SMESG000067789.1[more]
SMESG000067788.11.712e-2742.95SMESG000067788.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015020 ID=SMED30015020|Name=E3 ubiquitin-protein ligase XIAP|organism=Schmidtea mediterranea sexual|type=transcript|length=797bp
CAAATTATTAGTAAAAATCATTTGACTAAAATTTGCACTTCAAAATCAAT
ATTTATTTCAATTAAAAGTCTGAAGTGGCACATATTTGAATGATAAATAG
TGCTAGAGAGAATGGCATAGGCTTGATTGTGAAAAAAAACGATCAAATTT
TCAAGAAAGAAATCTCATTGGTTGAAATTGTCAAAAATACTCTATTAAAT
TTCCAATTGGATTTAGAAAAATGGCCTCTAAAGATGATGAGGAAATTTAT
AAGATCATTAAAAAATGAATTTATTTTCAAATTATCAGAAACATTTGGAT
ACAATCCTTCGATTCTGAAATTAGCAAGCTGGATTATTTGTTTTAATGAA
ATGAAAAATGATGATGAAAATCTAAATGACATTTTCTGGATTTGTATGGA
GTTGAGATTCGATAAAGAGTGTTGGAAAATTATAGATATTTTGATGAGAA
AAACTGATGAAATTGAAATTGAGATTAACAATATTGTTAAAAAACAAACT
GAAAGCCTTTTGACATGTAGCATTTGTATGAAGGAGCAGGTTTCTGTGTT
GTATTTGCCCTGTGGCCATGTGGTCGCATGTTCCCGCTGTCATCAGAGCA
CCTTCCATTCATGTTTGGCGTGTGGTATTAAAATTGAGGAATTTCATATT
ATTTATTTTTAATCTCCTTAACTTTATTATCGCACTAGGAAAATGGTAAA
CCTGTGAGAAATAGCATAAAATGGAAATTGTTTTACTGAATAGCATTTTA
TAATTGATTTTGTTATTGTTATTAAACCAAATAAATACTAATTAACT
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protein sequence of SMED30015020-orf-1

>SMED30015020-orf-1 ID=SMED30015020-orf-1|Name=SMED30015020-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=191bp
MINSARENGIGLIVKKNDQIFKKEISLVEIVKNTLLNFQLDLEKWPLKMM
RKFIRSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFW
ICMELRFDKECWKIIDILMRKTDEIEIEINNIVKKQTESLLTCSICMKEQ
VSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004869cysteine-type endopeptidase inhibitor activity
GO:0016740transferase activity
GO:0030414peptidase inhibitor activity
GO:0043027cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0046872metal ion binding
GO:0008270zinc ion binding
GO:0005515protein binding
Vocabulary: cellular component
TermDefinition
GO:0005737cytoplasm
Vocabulary: biological process
TermDefinition
GO:0006915apoptotic process
GO:0007275multicellular organism development
GO:0010466negative regulation of peptidase activity
GO:0016055Wnt signaling pathway
GO:0016567protein ubiquitination
GO:0043066negative regulation of apoptotic process
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045861negative regulation of proteolysis
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000018Category 4 cell
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000070intestinal phagocyte
PLANA:0002032epidermal cell
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR017066E3ligase_BOI-like
IPR013083Znf_RING/FYVE/PHD
IPR001841Znf_RING
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePFAMPF13920zf-C3HC4_3coord: 142..184
e-value: 1.9E-9
score: 37.2
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 138..188
IPR017066E3 ubiquitin-protein ligase BOI-likePIRSFPIRSF036836SBP1_RNase_bindcoord: 115..189
e-value: 4.1E-7
score: 27.7
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 126..190
e-value: 9.4E-12
score: 46.1
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 143..178
score: 8.639