SMED30035458

Overview
NameSMED30035458
Smed IDSMED30035458
Length (bp)526
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 SMED30035458 (SMED30035458) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035458 (SMED30035458) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30035458 (SMED30035458) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035458 (SMED30035458) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30035458

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30035458SMESG000021176.1 SmedASXL_005990SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035458 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000718:108740..109317 +2463
Homology
[Close]
BLAST of SMED30035458 vs. Ensembl Human
Match: TRIAP1 (TP53 regulated inhibitor of apoptosis 1 [Source:HGNC Symbol;Acc:HGNC:26937])

HSP 1 Score: 43.8986 bits (102), Expect = 6.212e-6
Identity = 24/63 (38.10%), Postives = 35/63 (55.56%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFP-KFLSGD-KNDPCGDKLAVYVSCVRKDLEKLNLDIKELD 292
            M S  + C   K+ YD CF+ +F  KFL GD   DPC D    Y  CV+K +++  + I+ L+
Sbjct:    1 MNSVGEACTDMKREYDQCFNRWFAEKFLKGDSSGDPCTDLFKRYQQCVQKAIKEKEIPIEGLE 63
[Close]
BLAST of SMED30035458 vs. Ensembl Celegans
Match: mdmh-35 (MitochonDrial interMembrane space protein Homolog [Source:RefSeq peptide;Acc:NP_495651])

HSP 1 Score: 46.595 bits (109), Expect = 3.455e-7
Identity = 27/75 (36.00%), Postives = 38/75 (50.67%), Query Frame = 2 
Query:  104 RHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKN-----DPCGDKLAVYVSCVRKDL---EKLNLDIKELDQSKL 304
            RHM S   ECD  K+ YD CF+EFF KF++ +       +PC     VY  CV + L       +D+ E+ +  L
Sbjct:    4 RHMSSIFPECDHLKQIYDKCFTEFFQKFITPNYRHQYAVNPCERLHDVYKRCVEERLATQRPFEIDLDEIRKEYL 78
[Close]
BLAST of SMED30035458 vs. Ensembl Fly
Match: CG30108 (gene:FBgn0050108 transcript:FBtr0273298)

HSP 1 Score: 47.7506 bits (112), Expect = 1.483e-7
Identity = 22/63 (34.92%), Postives = 40/63 (63.49%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFP-KFLSGDKND-PCGDKLAVYVSCVRKDLEKLNLDIKELD 292
            M S  ++C++ K+ YDACF+ +F  +FL G  +D  C     VY  CV++ +++  +D++E+D
Sbjct:    1 MSSVGEDCNELKQQYDACFNSWFSERFLKGQMDDSACAPIFRVYQECVKRAIKEKKIDLQEID 63
[Close]
BLAST of SMED30035458 vs. Ensembl Fly
Match: CG30109 (gene:FBgn0050109 transcript:FBtr0340271)

HSP 1 Score: 44.669 bits (104), Expect = 2.263e-6
Identity = 21/62 (33.87%), Postives = 38/62 (61.29%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPK-FLSGDKNDP-CGDKLAVYVSCVRKDLEKLNLDIKEL 289
            M S  ++C++ KK YDACF+ +F + FL G  +D  C     VY  CV++ + +  ++++E+
Sbjct:    1 MNSIGEDCNELKKQYDACFNSWFSEGFLKGQTDDSGCAPIFRVYQECVKRAMREQKIELREV 62
[Close]
BLAST of SMED30035458 vs. Ensembl Zebrafish
Match: triap1 (TP53 regulated inhibitor of apoptosis 1 [Source:ZFIN;Acc:ZDB-GENE-050417-161])

HSP 1 Score: 43.8986 bits (102), Expect = 3.306e-6
Identity = 22/63 (34.92%), Postives = 40/63 (63.49%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFP-KFLSGDKN-DPCGDKLAVYVSCVRKDLEKLNLDIKELD 292
            M S  + C + K+ YD CF+ +F  KFL GD++ DPC +    Y +CV+K +++ ++ I+ ++
Sbjct:    1 MNSVGEGCTELKREYDQCFNRWFAEKFLKGDRSADPCSELFNKYHTCVQKAIKEKDIPIEGVE 63
[Close]
BLAST of SMED30035458 vs. Ensembl Mouse
Match: Triap1 (TP53 regulated inhibitor of apoptosis 1 [Source:MGI Symbol;Acc:MGI:1916326])

HSP 1 Score: 43.8986 bits (102), Expect = 4.583e-6
Identity = 24/63 (38.10%), Postives = 35/63 (55.56%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFP-KFLSGD-KNDPCGDKLAVYVSCVRKDLEKLNLDIKELD 292
            M S  + C   K+ YD CF+ +F  KFL GD   DPC D    Y  CV+K +++  + I+ L+
Sbjct:    1 MNSVGEACTDMKREYDQCFNRWFAEKFLKGDGSGDPCTDLFKRYQQCVQKAIKEKEIPIEGLE 63
[Close]
BLAST of SMED30035458 vs. UniProt/SwissProt
Match: sp|P45967|MIS35_CAEEL (Uncharacterized protein mdmh-35 OS=Caenorhabditis elegans OX=6239 GN=mdmh-35 PE=3 SV=1)

HSP 1 Score: 46.595 bits (109), Expect = 4.394e-6
Identity = 27/75 (36.00%), Postives = 38/75 (50.67%), Query Frame = 2 
Query:  104 RHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKN-----DPCGDKLAVYVSCVRKDL---EKLNLDIKELDQSKL 304
            RHM S   ECD  K+ YD CF+EFF KF++ +       +PC     VY  CV + L       +D+ E+ +  L
Sbjct:    4 RHMSSIFPECDHLKQIYDKCFTEFFQKFITPNYRHQYAVNPCERLHDVYKRCVEERLATQRPFEIDLDEIRKEYL 78
[Close]
BLAST of SMED30035458 vs. TrEMBL
Match: A0A183A0W5 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS600 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 2.243e-17
Identity = 36/65 (55.38%), Postives = 43/65 (66.15%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKL 304
            + S   ECD  K  YDACF EFFPKFL G  NDPCG KL  Y  C+R  LE + +D+KELD S++
Sbjct:   26 LGSLVPECDSVKSAYDACFQEFFPKFLRGSTNDPCGPKLKAYQQCLRGTLESMGIDMKELDASRV 90
[Close]
BLAST of SMED30035458 vs. TrEMBL
Match: A0A504YH30 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_09350 PE=4 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 1.183e-16
Identity = 34/65 (52.31%), Postives = 42/65 (64.62%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKL 304
            + S + ECD  K  YDACF EFFPKFL G   DPCG KL  Y  C+R  LE + +D+ ELD S++
Sbjct:   29 LGSLAPECDSVKSAYDACFQEFFPKFLRGSTADPCGPKLRAYQQCLRGTLESIGIDMTELDASRM 93
[Close]
BLAST of SMED30035458 vs. TrEMBL
Match: A0A2H1C2G1 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_11419 PE=4 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 1.360e-16
Identity = 34/65 (52.31%), Postives = 42/65 (64.62%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKL 304
            + S + ECD  K  YDACF EFFPKFL G   DPCG KL  Y  C+R  LE + +D+ ELD S++
Sbjct:   29 LGSLAPECDSVKSAYDACFQEFFPKFLRGSTADPCGPKLRAYQQCLRGTLESIGIDMTELDASRM 93
[Close]
BLAST of SMED30035458 vs. TrEMBL
Match: A0A5J4NHL6 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0009325 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 6.120e-15
Identity = 33/68 (48.53%), Postives = 42/68 (61.76%), Query Frame = 2 
Query:  101 QRHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKL 304
            Q  +PS + ECD  K  YDACF +FF KFL G   DPCG KL  Y  C+R  L  L +D+ E+D S++
Sbjct:   53 QTKLPSLAPECDPLKAAYDACFQDFFQKFLHGSTTDPCGPKLKAYQKCLRSTLVSLGIDLTEVDASRM 120
[Close]
BLAST of SMED30035458 vs. TrEMBL
Match: G7YGS6 (Uncharacterized protein T09A5.7 OS=Clonorchis sinensis OX=79923 GN=T09A5.7 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 2.478e-12
Identity = 31/65 (47.69%), Postives = 39/65 (60.00%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKL 304
            + S + ECD  K  YDACF EFF KFL G   DPCG KL  Y  C+R  L  L LD+ ++D + +
Sbjct:   24 LRSLAPECDSLKAAYDACFQEFFEKFLHGYSVDPCGQKLKAYQKCLRGALSNLGLDMTKIDSTHM 88
[Close]
BLAST of SMED30035458 vs. Ensembl Nematostella
Match: EDO32160 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SVU1])

HSP 1 Score: 48.9062 bits (115), Expect = 1.489e-8
Identity = 25/70 (35.71%), Postives = 42/70 (60.00%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFPK-FLSGDK-NDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKLLRG 313
            M S  +EC++ K+ YDACF+ ++   FL GD+   PC +    Y +CV K +++ N+ I E++ + L  G
Sbjct:    1 MNSVGEECNELKREYDACFNVWYTDYFLKGDRQTTPCKEMFEKYRTCVMKAIKEKNISIDEINDNTLGTG 70
[Close]
BLAST of SMED30035458 vs. Ensembl Medaka
Match: triap1 (TP53 regulated inhibitor of apoptosis 1 [Source:NCBI gene;Acc:101164329])

HSP 1 Score: 43.1282 bits (100), Expect = 6.611e-6
Identity = 21/59 (35.59%), Postives = 35/59 (59.32%), Query Frame = 2 
Query:  110 MPSFSKECDQYKKTYDACFSEFFP-KFLSGDK-NDPCGDKLAVYVSCVRKDLEKLNLDI 280
            M S  + C + K+ YD CF+ +F  KFL GD+  DPC +    Y  CV+K +++ ++ +
Sbjct:    1 MNSVGEACTELKREYDQCFNRWFAEKFLKGDRSGDPCTETFRRYQRCVQKAIKEKDIPV 59
[Close]
BLAST of SMED30035458 vs. Planmine SMEST
Match: SMESG000021176.1 (SMESG000021176.1)

HSP 1 Score: 179.104 bits (453), Expect = 6.261e-59
Identity = 91/103 (88.35%), Postives = 91/103 (88.35%), Query Frame = 2 
Query:   23 MQCNSXXXXXXXXXXXADKKPTNIADQRHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKLLRGDRSDIK 331
            MQCN            ADKKPTNIADQRHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKLLRGDRSDIK
Sbjct:    1 MQCN------------ADKKPTNIADQRHMPSFSKECDQYKKTYDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSKLLRGDRSDIK 91
The following BLAST results are available for this feature:
BLAST of SMED30035458 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
TRIAP16.212e-638.10TP53 regulated inhibitor of apoptosis 1 [Source:HG... [more]
back to top
BLAST of SMED30035458 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
mdmh-353.455e-736.00MitochonDrial interMembrane space protein Homolog ... [more]
back to top
BLAST of SMED30035458 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
CG301081.483e-734.92gene:FBgn0050108 transcript:FBtr0273298[more]
CG301092.263e-633.87gene:FBgn0050109 transcript:FBtr0340271[more]
back to top
BLAST of SMED30035458 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
triap13.306e-634.92TP53 regulated inhibitor of apoptosis 1 [Source:ZF... [more]
back to top
BLAST of SMED30035458 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035458 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Triap14.583e-638.10TP53 regulated inhibitor of apoptosis 1 [Source:MG... [more]
back to top
BLAST of SMED30035458 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P45967|MIS35_CAEEL4.394e-636.00Uncharacterized protein mdmh-35 OS=Caenorhabditis ... [more]
back to top
BLAST of SMED30035458 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183A0W52.243e-1755.38Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A504YH301.183e-1652.31Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A2H1C2G11.360e-1652.31Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A5J4NHL66.120e-1548.53Uncharacterized protein OS=Paragonimus westermani ... [more]
G7YGS62.478e-1247.69Uncharacterized protein T09A5.7 OS=Clonorchis sine... [more]
back to top
BLAST of SMED30035458 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035458 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035458 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035458 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO321601.489e-835.71Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
back to top
BLAST of SMED30035458 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
triap16.611e-635.59TP53 regulated inhibitor of apoptosis 1 [Source:NC... [more]
back to top
BLAST of SMED30035458 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000021176.16.261e-5988.35SMESG000021176.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035458 ID=SMED30035458|Name=SMED30035458|organism=Schmidtea mediterranea sexual|type=transcript|length=526bp
TTTGAGTATCATCGAAAATGCAATGCAATGTAATTCAATCATCCAATNAA
TCTNTATAAATCTTATATNGGCGGACAAAAAACCAACAAATATCGCGGAT
CAAAGACATATGCCGAGTTTCAGCAAAGAATGCGACCAATACAAAAAAAC
GTATGATGCATGTTTTTCGGAATTTTTCCCGAAATTTCTGTCCGGGGACA
AAAATGATCCATGCGGGGATAAATTAGCGGTTTATGTGAGTTGTGTACGG
AAAGATTTGGAAAAACTCAATTTAGATATAAAAGAACTAGATCAGAGCAA
ATTGTTACGAGGCGATCGATCCGATATTAAGTGAAATGTGCTCAATTATT
ATTGTGTATATTAAATATATAGTCATTTATATATATTATTGGTCTTTCTA
TTGTTATTATTTATATATGTGTGTTTGAGGCATACCAGTCATTTATAATT
TGTTTTTTGGAATATCTGGGAAATGCTTTTGGATATTTGTACTGTTGTGA
TTGGATTAAAATTTATGTATTTTAGA
back to top

protein sequence of SMED30035458-orf-1

>SMED30035458-orf-1 ID=SMED30035458-orf-1|Name=SMED30035458-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
LSIIENAMQCNSIIQXIXINLIXADKKPTNIADQRHMPSFSKECDQYKKT
YDACFSEFFPKFLSGDKNDPCGDKLAVYVSCVRKDLEKLNLDIKELDQSK
LLRGDRSDIK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR007918MDM35_apoptosis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 43..63
IPR007918Mitochondrial distribution/morphology family 35/apoptosisPFAMPF05254UPF0203coord: 3..60
e-value: 9.3E-14
score: 51.4