SMED30021900

Overview
NameSMED30021900
Smed IDSMED30021900
Length (bp)885
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30021900 (SMED30021900) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021900 (SMED30021900) 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



SMED30021900

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30021900SMESG000043279.1 Contig3176newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021900SMESG000043279.1 Contig3176uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021900SMESG000001368.1 SMESG000001395.1 Contig3176newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021900SMESG000001368.1 SMESG000001395.1 Contig3176uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30021900SMESG000043279.1 SmedASXL_070492SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30021900SMESG000043279.1 dd_Smed_v4_13818_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30021900SMESG000043279.1 dd_Smed_v6_13818_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30021900SMESG000043279.1 Contig13482newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30021900SMESG000043279.1 Contig13482uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Category 4 cellSMED30021900SMESG000043279.1 dd_Smed_v4_13818_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
SMED30021900 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017174:57..3684 +3081
Homology
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BLAST of SMED30021900 vs. Planmine SMEST
Match: SMESG000043279.1 (SMESG000043279.1)

HSP 1 Score: 318.161 bits (814), Expect = 1.162e-110
Identity = 167/167 (100.00%), Postives = 167/167 (100.00%), Query Frame = 2 
Query:  239 LDEFIIDCDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVCEKIIQCTRXXXXXXXXXXXXRCSQCKMVIKWLENSLRTDGPITEMKNTLNKFCHLWTEPRDCRQLISTANIQAVFDGISSVIACQYLSFCPS 739
            LDEFIIDCDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVCEKIIQCTRNVNIHSIVSISSRCSQCKMVIKWLENSLRTDGPITEMKNTLNKFCHLWTEPRDCRQLISTANIQAVFDGISSVIACQYLSFCPS
Sbjct:   15 LDEFIIDCDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVCEKIIQCTRNVNIHSIVSISSRCSQCKMVIKWLENSLRTDGPITEMKNTLNKFCHLWTEPRDCRQLISTANIQAVFDGISSVIACQYLSFCPS 181
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BLAST of SMED30021900 vs. Planmine SMEST
Match: SMESG000019986.1 (SMESG000019986.1)

HSP 1 Score: 62.3882 bits (150), Expect = 1.281e-10
Identity = 39/172 (22.67%), Postives = 87/172 (50.58%), Query Frame = 2 
Query:  260 CDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVCEKIIQCTRXXXXX------------XXXXXXXRCSQCKMVIKWLENSLRTDGPITEMKNTLNKFCHLWTEPRD--CRQLISTANIQAVFDGISSVIACQYLSFC 733
            C+ C+N++  +  +++K+L+A  I N ++  C VF     +KC  ++   G+++++S+L +E  T VC+K+  C ++   H            + ++ + +C  C++ I+ +E        + +M+  ++ FC ++  P +  C+Q      ++ V + +     CQ L FC
Sbjct:  291 CNLCKNMIKLLEISVNKTLNATNIQNRVLYACTVFTSPAKDKCIKFYQGLGLEVIKSVLVDEDPTKVCKKLTICLKHAQHHESYQFLDLLNTFTTINSNEKCKICRIHIQLIERIYNRSKTLEQMQAVVDDFCGIFNCPYEYPCKQFYVKVGLE-VREKVLPRTVCQKLEFC 461

HSP 2 Score: 49.2914 bits (116), Expect = 2.324e-6
Identity = 24/74 (32.43%), Postives = 40/74 (54.05%), Query Frame = 2 
Query:  260 CDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVCEKIIQC 481
            C +C  ++ +     + S SA++I   L++ C +F++     C  YF   G +I+ES+LK E    VCEK+  C
Sbjct:  590 CQSCITMIKFEEKNFNNSKSAVEIQGKLLEYCSIFQQKFANICVEYFNSTGFEIIESILKKENPKKVCEKLHYC 663

HSP 3 Score: 47.7506 bits (112), Expect = 7.140e-6
Identity = 56/245 (22.86%), Postives = 103/245 (42.04%), Query Frame = 2 
Query:   50 NQCQEYFSSTDEEAVMNSNEFVKSLCHRFEGANVKRCFQYFSLKNSLSEISFIGNDVKPKNLKLDEFIIDCDTCENLVDYIGNTIDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETSTFVC------------EKIIQCTRXXXXXXXXXXXXRCSQCKMVIKWLENSLRTDGPITEMKNTLNKFCHLWTE--PRDCRQLISTANIQAVFDGISSV---IACQYLSFC 733
            N C EYF+ST         E ++S+  +     V     Y   +NS  E S     +  +  K DE   DC  C+  V++   +I+KSL+   I   +I  C ++K  +   C  ++   G D+++++L N  ST +C            E   Q    + + +      +C  C   + WLE ++  +     ++  + + C +  +   R C +  ST  +Q + D ++ V   ++CQ    C
Sbjct:  630 NICVEYFNST-------GFEIIESILKKENPKKVCEKLHYCHQRNSQGEESQDLLTLFYRKEK-DE---DCKLCKKRVEFYKISINKSLNPAVIQQKMIAGCAIYKLSLKTLCVFFYNTAGFDVIKAVLTNGESTTICKLMDFCLVDSEIEGSHQFLDLLQMLTSGKSEKKCQLCISSVTWLEENVNKENSSKFVQELMFEICSVLYQRYQRMCVKYFSTRGLQLIKDVLNDVDPNVSCQTQKLC 863
The following BLAST results are available for this feature:
BLAST of SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 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 SMED30021900 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000043279.11.162e-110100.00SMESG000043279.1[more]
SMESG000019986.11.281e-1022.67SMESG000019986.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021900 ID=SMED30021900|Name=SMED30021900|organism=Schmidtea mediterranea sexual|type=transcript|length=885bp
AATGAAATATTTATTAATAAACACGATTTTATTTATTAGTTTCTCTTGTA
ATCAATGCCAAGAATATTTTAGTTCTACCGATGAAGAAGCAGTTATGAAT
TCTAATGAATTCGTAAAATCGTTGTGCCATCGTTTTGAGGGAGCCAATGT
TAAAAGATGTTTCCAGTATTTTTCTTTGAAGAATTCTTTATCCGAGATTT
CATTTATTGGAAATGATGTGAAACCAAAAAATTTGAAACTGGATGAATTT
ATTATCGATTGTGACACATGTGAAAATCTCGTTGATTATATCGGAAATAC
GATTGACAAATCACTTTCAGCAATCCAAATATTAAATACCCTTATAGACG
TCTGCTTTGTATTTAAAAGAATAATTCATGAAAAGTGTTGTAGCTATTTC
TACTGGAAGGGTATGGACATTGTGGAGTCAATGTTAAAGAATGAAACTTC
TACTTTTGTTTGTGAGAAAATTATCCAGTGCACCAGAAATGTCAACATTC
ATTCAATAGTTTCAATTTCCTCACGATGTAGTCAATGCAAAATGGTAATA
AAATGGCTTGAAAACTCTTTGAGAACTGATGGTCCAATAACGGAAATGAA
AAATACATTAAACAAGTTTTGTCATTTATGGACAGAGCCTAGAGACTGTA
GACAGCTAATTTCTACAGCCAATATTCAGGCGGTTTTTGATGGAATTTCA
TCCGTTATTGCGTGCCAATATCTCAGCTTTTGTCCAAGCTAGGTTTGCGT
CATGAAATCCGATTCAAAGCAATCTGGTTGTCAGAGACCAGAGATCAAAT
TTTTCATTTTAAACATCATCGGCACGATTTTTGTGAATTCGTGTTCTTTT
TTATTTCTCAATTCATTTAGCATTTTAAAAAAAAA
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protein sequence of SMED30021900-orf-1

>SMED30021900-orf-1 ID=SMED30021900-orf-1|Name=SMED30021900-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=247bp
MKYLLINTILFISFSCNQCQEYFSSTDEEAVMNSNEFVKSLCHRFEGANV
KRCFQYFSLKNSLSEISFIGNDVKPKNLKLDEFIIDCDTCENLVDYIGNT
IDKSLSAIQILNTLIDVCFVFKRIIHEKCCSYFYWKGMDIVESMLKNETS
TFVCEKIIQCTRNVNIHSIVSISSRCSQCKMVIKWLENSLRTDGPITEMK
NTLNKFCHLWTEPRDCRQLISTANIQAVFDGISSVIACQYLSFCPS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000070intestinal phagocyte
PLANA:0000418head
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR011001Saposin-like
IPR008139SaposinB_dom
Vocabulary: cellular component
TermDefinition
GO:0005764lysosome
Vocabulary: biological process
TermDefinition
GO:0006629lipid metabolic process
GO:0006665sphingolipid metabolic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.225.10coord: 84..162
e-value: 1.4E-6
score: 30.7
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..16
score: 5.0
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.6
IPR008139Saposin B type domainPROSITEPS50015SAP_Bcoord: 83..164
score: 11.234
IPR011001Saposin-likeSUPERFAMILYSSF47862Saposincoord: 86..161