SMED30013138

Overview
NameSMED30013138
Smed IDSMED30013138
Length (bp)1088
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 SMED30013138 (SMED30013138) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013138 (SMED30013138) 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 SMED30013138 (SMED30013138) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013138 (SMED30013138) 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



SMED30013138

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30013138SMESG000004029.1 SmedASXL_010638SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30013138SMESG000004029.1 dd_Smed_v4_4798_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013138SMESG000004029.1 Contig34165newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013138SMESG000004029.1 Contig34165uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30013138SMESG000004029.1 dd_Smed_v6_4798_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30013138SMESG000004029.1 OX_Smed_1.0.22018ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30013138SMESG000004029.1 Contig34165newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30013138SMESG000004029.1 Contig34165uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30013138SMESG000004029.1 dd_Smed_v4_4798_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
Alignments
SMED30013138 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010937:585..8597 +3403
Homology
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BLAST of SMED30013138 vs. TrEMBL
Match: A0A267F248 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig027449g2 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 6.079e-13
Identity = 41/103 (39.81%), Postives = 56/103 (54.37%), Query Frame = 1 
Query:  319 RMSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITV 627
            RMSVI  SGK +A R      K K    + +  T   VNSY+P+    VWN  L G   SIAL KD+ E+WC+D L+ T+     T + +DF +   K RI++
Sbjct:   32 RMSVIFSSGKSAAARM--KEGKKKKPTKVARPRTAMPVNSYMPTSETAVWNTKLHGVNYSIALSKDSLELWCNDQLLQTVSDFSDTGSTLDFELDGQKGRISI 132
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BLAST of SMED30013138 vs. TrEMBL
Match: A0A267FI76 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig027449g1 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 7.152e-13
Identity = 41/103 (39.81%), Postives = 56/103 (54.37%), Query Frame = 1 
Query:  319 RMSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITV 627
            RMSVI  SGK +A R      K K    + +  T   VNSY+P+    VWN  L G   SIAL KD+ E+WC+D L+ T+     T + +DF +   K RI++
Sbjct:   45 RMSVIFSSGKSAAARM--KEGKKKKPTKVARPRTAMPVNSYMPTAETAVWNTKLQGVNYSIALSKDSLELWCNDQLLQTVSDFSDTGSTLDFELDGQKGRISI 145
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BLAST of SMED30013138 vs. TrEMBL
Match: A0A1I8GCJ2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig018185g1 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.195e-12
Identity = 39/125 (31.20%), Postives = 72/125 (57.60%), Query Frame = 1 
Query:  322 MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRA 696
            MS++L SGK +A +F+  + K + +K +++ +  A  + YLP+D+  VWN  + G   S+AL K++ ++WC+D +I+     + T +KM+F +     R  +     S+     LT+DG  +P+A
Sbjct:    1 MSILLSSGKGAASKFRDGAKKGRPEK-VKRAANDAQFHPYLPTDATVVWNTKISGVDYSLALDKESLDLWCNDNVIDAECDFNDTGSKMEFQLAGK--RACLKMQPSSRGTKYRLTLDGAKVPKA 122
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BLAST of SMED30013138 vs. TrEMBL
Match: A0A504YQW5 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_07595 PE=4 SV=1)

HSP 1 Score: 75.485 bits (184), Expect = 1.447e-12
Identity = 43/105 (40.95%), Postives = 58/105 (55.24%), Query Frame = 1 
Query:  319 RMSVILMSGKKSAQRFKGSSNKDKDKKTIEKLS-TVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVS 630
            +MS +  SGKKSA   +GSS     KK   + S T    NSY+PS++V VWN  +   P+S A CKD   +W  D L+ T E       + DF +M HK ++TVS
Sbjct:   28 KMSAVFTSGKKSAAVVRGSSEGSTLKKKASQGSDTNLPANSYVPSENVIVWNVTMDHMPLSFAYCKDTASLWVGDELVQTREHKLEDFVQHDFCIMDHKAQLTVS 132
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BLAST of SMED30013138 vs. TrEMBL
Match: A0A1I8HSG9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig023001g1 PE=4 SV=1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.534e-12
Identity = 44/134 (32.84%), Postives = 70/134 (52.24%), Query Frame = 1 
Query:  322 MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITV-SFDKHSKHPISVLTIDGEII-----PRAVPI 705
            MS+IL SGK +A + +    K    K + +  T   V+SYLP++   VWN  + G   S+AL KD  E+WC+D L+ T +      + +DF + S K RI +    + +K+     T+DG  +     PR +P+
Sbjct:    1 MSIILTSGKSAASKLRQPKQK---PKKVARPRTAMPVDSYLPTEETAVWNVRVDGVHFSVALSKDTLEVWCNDQLMETTDDFSDMGSTVDFDLGSKKARIWILPGPRGTKY---KFTLDGATVAAAKPPRQLPL 128
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BLAST of SMED30013138 vs. Planmine SMEST
Match: SMESG000004029.1 (SMESG000004029.1)

HSP 1 Score: 304.294 bits (778), Expect = 1.419e-104
Identity = 148/148 (100.00%), Postives = 148/148 (100.00%), Query Frame = 1 
Query:  322 MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH 765
            MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH
Sbjct:    1 MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH 148
[Close]
BLAST of SMED30013138 vs. Planmine SMEST
Match: SMESG000004029.1 (SMESG000004029.1)

HSP 1 Score: 295.049 bits (754), Expect = 5.644e-101
Identity = 143/143 (100.00%), Postives = 143/143 (100.00%), Query Frame = 1 
Query:  337 MSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH 765
            MSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH
Sbjct:    1 MSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYH 143
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BLAST of SMED30013138 vs. Planmine SMEST
Match: SMESG000064469.1 (SMESG000064469.1)

HSP 1 Score: 65.855 bits (159), Expect = 7.185e-13
Identity = 42/139 (30.22%), Postives = 69/139 (49.64%), Query Frame = 1 
Query:  322 MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHS-------------KHPISVLTIDGEIIPRAV 699
            MSV+L SG+  +++ K +  +  D      +    + +SY PSD+++VWNC++ G  +SIAL K+  EIWC+D L+ T            F + +H  R+ ++    S             K  I+ L ID +I+P  V
Sbjct:    1 MSVLLNSGQNKSKKPKPAPAQASDP-----VIQCESFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVV 134
The following BLAST results are available for this feature:
BLAST of SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267F2486.079e-1339.81Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267FI767.152e-1339.81Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8GCJ21.195e-1231.20Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A504YQW51.447e-1240.95Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A1I8HSG91.534e-1232.84Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 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 SMED30013138 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000004029.11.419e-104100.00SMESG000004029.1[more]
SMESG000004029.15.644e-101100.00SMESG000004029.1[more]
SMESG000064469.17.185e-1330.22SMESG000064469.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013138 ID=SMED30013138|Name=SMED30013138|organism=Schmidtea mediterranea sexual|type=transcript|length=1088bp
CAGAAACCAACAAACAACACGTCTAACATTTGTGTTAACGAGAGAACTAT
TTATTAACTGTAGCTATTTATTAGAGAAGCCATTTTCAATTTTTCTATTA
CAAACCGATTTTGGTAGCATTTTAGTCTCCCAGTTACAGAGACAACAGTT
TTAAATGTGTATTTTATATCAAATTCCACGTGGATTTAAGTCGGCGTGTA
TCCAATCATAGATGTGATTATCAGAAATATAATATTTCAAATAAAAAGAA
TACTTGAATAGTAAAAATAGTAGGAGTTTGAATTATTTAGAAACGTTATA
TAGTTTTTATCGATTATTAGAATGTCTGTCATTTTGATGTCTGGTAAAAA
ATCTGCACAGAGGTTTAAAGGAAGCTCTAATAAAGATAAAGACAAGAAAA
CAATTGAAAAGCTTTCCACAGTCGCTACAGTTAATTCTTATTTACCATCA
GATAGTGTTGACGTGTGGAACTGTGTTTTGGGAGGTTCACCAGTAAGCAT
TGCTCTCTGCAAAGATAATTTCGAGATTTGGTGTGATGACGTTCTAATAA
ATACAATCGAAACACTGGATGCTACAGAAACAAAAATGGATTTTGTAATG
ATGTCACATAAAATGAGGATAACCGTTTCGTTTGACAAGCACTCAAAACA
CCCGATTTCAGTTCTAACAATCGACGGGGAAATCATTCCTCGTGCAGTTC
CGATAATTTCTAGCGCAAATCCTCATCCAACAGCTGACAGCAATATCAAC
AATCAAAATTATCATCCAATTCAGTAGATAATAATCAGGCCATAAAGATA
TATCATTTTTACTAAATATTCATTTACTATTGATATTGCTATTTTAGAAC
CTTCTATTGTTGGTGATTACTATAGATTATATATTATCATTATTATACTT
AGGAGGTTGTTGGAACGGATTGTACTTATCTATATACAGTGAAATCTGAT
TTCCGATAGCAGACTAGTTTAGAGGTTTTGGAATTCGCATTGGTATAAAA
AAACAAAATTATGGATATTCGGAATCACATAATAACGCTGTAAAATTAAT
TTAAATTCAAAAAGCAAAATATTGATTAAAAAGTTTGG
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protein sequence of SMED30013138-orf-1

>SMED30013138-orf-1 ID=SMED30013138-orf-1|Name=SMED30013138-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
MSVILMSGKKSAQRFKGSSNKDKDKKTIEKLSTVATVNSYLPSDSVDVWN
CVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRI
TVSFDKHSKHPISVLTIDGEIIPRAVPIISSANPHPTADSNINNQNYHPI
Q*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR038513FAIM1_dom_sf
IPR010695FAIM1
Vocabulary: biological process
TermDefinition
GO:0043066negative regulation of apoptotic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR038513FAIM1 domain superfamilyGENE3DG3DSA:2.40.128.180coord: 45..126
e-value: 5.7E-9
score: 37.7
IPR010695Fas apoptotic inhibitory molecule 1PFAMPF06905FAIM1coord: 45..123
e-value: 4.6E-6
score: 26.4
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..23