IAP domain containing-1

Overview
NameIAP domain containing-1
Smed IDSMED30001255
Length (bp)951
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 IAP domain containing-1 (SMED30001255) t-SNE clustered cells

Violin plots show distribution of expression levels for IAP domain containing-1 (SMED30001255) 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 IAP domain containing-1 (SMED30001255) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for IAP domain containing-1 (SMED30001255) 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.
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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




SMED30001255

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior sideSMED30001255h1SMcG0001569 dd_Smed_v4_4082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30001255h1SMcG0001569 dd_Smed_v4_4082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30001255h1SMcG0001569 dd_Smed_v6_4082_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of IAP domain containing-1 vs. TrEMBL
Match: I1ZIH9 (IAP domain containing-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 7.264e-7
Identity = 25/48 (52.08%), Postives = 35/48 (72.92%), Query Frame = 1
Query:  625 LFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            L LTC+ C+ NQVS+LY PC H+V+C +CF S+ + C+ C V I +YH
Sbjct:    5 LCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNVPIHQYH 52          
BLAST of IAP domain containing-1 vs. Planmine SMEST
Match: SMESG000031926.1 (SMESG000031926.1)

HSP 1 Score: 394.815 bits (1013), Expect = 3.222e-140
Identity = 192/194 (98.97%), Postives = 192/194 (98.97%), Query Frame = 1
Query:  187 MPLKNQIHDKIKYCTQTKYSTKVTDDFKDIDITSDKWCLTFSIIEKFLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNMNLVFWSCMEFRVGQYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            MPLKNQIHDKIKYCTQTKYSTKVTDDFKDI ITSDKWCLTFSIIEKFLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFN NLVFWSCMEFRVGQYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH
Sbjct:    1 MPLKNQIHDKIKYCTQTKYSTKVTDDFKDIGITSDKWCLTFSIIEKFLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNTNLVFWSCMEFRVGQYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 194          

HSP 2 Score: 72.7886 bits (177), Expect = 5.446e-15
Identity = 34/36 (94.44%), Postives = 35/36 (97.22%), Query Frame = -1
Query:    7 MPLKNQIHDKIKYCTQTKYSTKVTDDFKDIDITSDR 114
            MPLKNQIHDKIKYCTQTKYSTKVTDDFKDI ITSD+
Sbjct:    1 MPLKNQIHDKIKYCTQTKYSTKVTDDFKDIGITSDK 36          
BLAST of IAP domain containing-1 vs. Planmine SMEST
Match: SMESG000031958.1 (SMESG000031958.1)

HSP 1 Score: 122.094 bits (305), Expect = 1.829e-33
Identity = 62/142 (43.66%), Postives = 87/142 (61.27%), Query Frame = 1
Query:  346 FDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNMNLVFWSCMEFRVGQY-QKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            + L  + K  KS  +E I  LS+ FGYN ++LKL+S +I  N++K  D N+N +FW CME R  +   K+I   M   D ++  IN+ +K+     LTCS C   QVSVLYLPCGH+V CS C +ST   C +C + I+E+H
Sbjct:   45 WPLKMMRKFIKSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDEIEIEINNIVKKQNESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFH 186          
BLAST of IAP domain containing-1 vs. Planmine SMEST
Match: SMESG000031949.1 (SMESG000031949.1)

HSP 1 Score: 120.553 bits (301), Expect = 7.364e-33
Identity = 57/146 (39.04%), Postives = 88/146 (60.27%), Query Frame = 1
Query:  334 STNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNMNLVFWSCMEFRVG-QYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            S    D IFL KL KSFN   I+     FGY+  +LKL S +++  +IK    NMN +FW+CME R+  +Y+  I  +++N + L+    +K +     +L C  C+  QVS+LYLPCGH+++C+ CF+  T+ C+ C + I+E H
Sbjct:   44 SFENLDFIFLGKLLKSFNEPLIQYFHDTFGYDKPLLKLVSFILNSYEIKVNKDNMNFLFWTCMELRLDFEYRSEINKWISNFEQLKLKAQEKFQNIASFYLKCFLCKIQQVSILYLPCGHLILCTKCFQRNTKYCQICQILIEEAH 189          
BLAST of IAP domain containing-1 vs. Planmine SMEST
Match: SMESG000067789.1 (SMESG000067789.1)

HSP 1 Score: 118.242 bits (295), Expect = 7.997e-32
Identity = 61/155 (39.35%), Postives = 98/155 (63.23%), Query Frame = 1
Query:  310 SIIEKFLSSTNGF-DLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNMNLVFWSCMEFRVG-QYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            S +E F+++ + F D   +N L K F + SIE L  +F Y+  +LKLSS ++ L+     + ++N  FW CME R+  +Y +L + ++   D ++  + +KL +  + +LTCS C+ NQVSVLYLPCGH++VCS C     R+C++C+  I+EYH
Sbjct:   54 STVEDFINTYDTFTDKEIINIL-KIFKNPSIEYLIDIFNYDKCILKLSSYLMYLDKTGMDNDSLNEYFWDCMELRLNPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKCQDKNNRKCQACSAPINEYH 207          
BLAST of IAP domain containing-1 vs. Planmine SMEST
Match: SMESG000032006.1 (SMESG000032006.1)

HSP 1 Score: 117.087 bits (292), Expect = 1.100e-31
Identity = 57/149 (38.26%), Postives = 91/149 (61.07%), Query Frame = 1
Query:  325 FLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNMNLVFWSCMEFRVGQY-QKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYH 768
            FL +     L  + ++ KSF +E +E L + FGY  ++LKL+SCVIS+N I  +   MN +FW CM  R+ +   K+I+ +M N+D +  ++     + ++ +LTC  C+ N VS+LYLPCG IV+CS C+  +  +C+ C   +DE H
Sbjct:   32 FLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMH 180          
The following BLAST results are available for this feature:
BLAST of IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIH97.264e-752.08IAP domain containing-1 (Fragment) OS=Schmidtea me... [more]
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BLAST of IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 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 IAP domain containing-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031926.13.222e-14098.97SMESG000031926.1[more]
SMESG000031958.11.829e-3343.66SMESG000031958.1[more]
SMESG000031949.17.364e-3339.04SMESG000031949.1[more]
SMESG000067789.17.997e-3239.35SMESG000067789.1[more]
SMESG000032006.11.100e-3138.26SMESG000032006.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001255 ID=SMED30001255|Name=IAP domain containing-1|organism=Schmidtea mediterranea sexual|type=transcript|length=951bp
TTCCGATCTATCCGAAGTAATGTCTATGTCCTTAAAATCATCTGTAACTT
TGGTTGAATATTTTGTCTGAGTACAATATTTAATTTTATCATGAATTTGA
TTCTTTAACGGCATTAGCCAGTTTTTTAAAATATTTTGAAATTTAAATGT
TATATAATCTTTAAAAATATTTTAAAAAACTGGCTAATGCCGTTAAAGAA
TCAAATTCATGATAAAATTAAATATTGTACTCAGACAAAATATTCAACCA
AAGTTACAGATGATTTTAAAGACATAGACATTACTTCGGATAAATGGTGT
TTAACATTTTCGATTATTGAAAAATTTCTCTCATCAACTAATGGATTTGA
TCTTATTTTTCTCAACAAACTTAACAAATCATTTAATCATGAATCTATTG
AAAATCTTTCTAAATTGTTTGGATACAACCATGCGATGCTGAAATTATCG
AGTTGCGTAATAAGTTTAAATGATATTAAACCTACTGATTTCAACATGAA
CTTGGTTTTCTGGTCGTGTATGGAGTTCAGAGTAGGACAATATCAAAAAC
TTATTCAATATTTCATGGCAAATGTTGATAATTTACAACAAAATATCAAC
GATAAATTGAAAGAAGCAACTCGATTGTTTCTCACGTGCTCATGTTGTGA
AACCAATCAAGTTTCGGTTTTATATTTGCCATGTGGCCACATAGTTGTTT
GTTCGTCTTGTTTCAAAAGCACTACTCGAAGGTGTGAATCGTGTGCTGTG
GATATCGATGAATATCATTTTGTGTATCTGTAGTTCGTCTTTTATTATGA
GTTCATTTTTTTGTTATTTAACAGGATGTTTCATTTTTGAATTATTATTT
GTTTCTTTTTCTTAAGCTATATAACAAAGAATCTGATTTGTCGAAAATTT
GAAAATTAATAAAAATTTGTGTTGAATATTTAATAATAAATACTAGACTG
G
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protein sequence of SMED30001255-orf-1

>SMED30001255-orf-1 ID=SMED30001255-orf-1|Name=SMED30001255-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=199bp
MPLKNQIHDKIKYCTQTKYSTKVTDDFKDIDITSDKWCLTFSIIEKFLSS
TNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPT
DFNMNLVFWSCMEFRVGQYQKLIQYFMANVDNLQQNINDKLKEATRLFLT
CSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYHFVYL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR017066E3ligase_BOI-like
IPR013083Znf_RING/FYVE/PHD
IPR001841Znf_RING
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR017066E3 ubiquitin-protein ligase BOI-likePIRSFPIRSF036836SBP1_RNase_bindcoord: 109..188
e-value: 8.4E-7
score: 26.6
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 127..198
e-value: 9.2E-10
score: 39.9
NoneNo IPR availablePFAMPF13920zf-C3HC4_3coord: 150..191
e-value: 1.9E-7
score: 30.8
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 151..186
score: 8.742