SMED30018197

Overview
NameSMED30018197
Smed IDSMED30018197
Length (bp)313
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30018197

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30018197h1SMcG0000290 SmedASXL_004439SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30018197h1SMcG0000290 SmedASXL_019869SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30018197h1SMcG0000290 SmedASXL_003018SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30018197h1SMcG0000290 SmedASXL_001008SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
gutSMED30018197h1SMcG0000290 dd_Smed_v4_22938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018197h1SMcG0000290 dd_Smed_v4_22938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018197h1SMcG0000290 dd_Smed_v4_39554_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018197h1SMcG0000290 dd_Smed_v4_12726_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018197h1SMcG0000290 dd_Smed_v4_35838_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018197h1SMcG0000290 dd_Smed_v4_22938_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30018197h1SMcG0000290 SMED_05003_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30018197h1SMcG0000290 SMED_05003_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018197 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001732:6776..7136 -1538
v31.001732:6133..6431 -658
v31.001732:5676..5999 -531
v31.001732:7187..7500 -441
Homology
[Close]
BLAST of SMED30018197 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 198.364 bits (503), Expect = 3.056e-60
Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS
Sbjct:  259 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 361

HSP 2 Score: 129.798 bits (325), Expect = 2.916e-36
Identity = 84/132 (63.64%), Postives = 89/132 (67.42%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENS----------------NSERSILSEIPP---KLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN                 +SERSILSEIP     L PINSS I+I+ LS +S
Sbjct:  478 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQS 609

HSP 3 Score: 77.7962 bits (190), Expect = 5.649e-18
Identity = 54/103 (52.43%), Postives = 62/103 (60.19%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N+   +N    S +    + +REM                   P KL PINSSSIDIQHLSNRS
Sbjct:  380 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSII----NEYREM-------------------PSKLSPINSSSIDIQHLSNRS 459

HSP 4 Score: 65.855 bits (159), Expect = 9.211e-14
Identity = 42/67 (62.69%), Postives = 46/67 (68.66%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTN 173
            ISNEFIE RNQSNIIDS LINKSQ+S R  +S+KTFVL N          SI NEN +M SKL H N
Sbjct:  622 ISNEFIEYRNQSNIIDSVLINKSQTSIRYSESDKTFVLSNAEDGQNISDKSIINENSKMSSKLSHKN 688

HSP 5 Score: 43.8986 bits (102), Expect = 4.863e-6
Identity = 23/32 (71.88%), Postives = 29/32 (90.62%), Query Frame = 3 
Query:  219 NSERSILSE-IPPKLPPINSSSIDIQHLSNRS 311
            N+++SI++E +P KL PINSSSIDIQHLSNRS
Sbjct:  209 NADKSIINENMPSKLHPINSSSIDIQHLSNRS 240
[Close]
BLAST of SMED30018197 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 198.364 bits (503), Expect = 3.056e-60
Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS
Sbjct:  260 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 362

HSP 2 Score: 129.798 bits (325), Expect = 2.944e-36
Identity = 84/132 (63.64%), Postives = 89/132 (67.42%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENS----------------NSERSILSEIPP---KLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN                 +SERSILSEIP     L PINSS I+I+ LS +S
Sbjct:  479 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQS 610

HSP 3 Score: 77.7962 bits (190), Expect = 5.705e-18
Identity = 54/103 (52.43%), Postives = 62/103 (60.19%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N+   +N    S +    + +REM                   P KL PINSSSIDIQHLSNRS
Sbjct:  381 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSII----NEYREM-------------------PSKLSPINSSSIDIQHLSNRS 460

HSP 4 Score: 65.855 bits (159), Expect = 9.211e-14
Identity = 42/67 (62.69%), Postives = 46/67 (68.66%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTN 173
            ISNEFIE RNQSNIIDS LINKSQ+S R  +S+KTFVL N          SI NEN +M SKL H N
Sbjct:  623 ISNEFIEYRNQSNIIDSVLINKSQTSIRYSESDKTFVLSNAEDGQNISDKSIINENSKMSSKLSHKN 689

HSP 5 Score: 43.8986 bits (102), Expect = 4.863e-6
Identity = 23/32 (71.88%), Postives = 29/32 (90.62%), Query Frame = 3 
Query:  219 NSERSILSE-IPPKLPPINSSSIDIQHLSNRS 311
            N+++SI++E +P KL PINSSSIDIQHLSNRS
Sbjct:  210 NADKSIINENMPSKLHPINSSSIDIQHLSNRS 241
[Close]
BLAST of SMED30018197 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 198.364 bits (503), Expect = 3.056e-60
Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS
Sbjct:  264 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 366

HSP 2 Score: 130.183 bits (326), Expect = 2.698e-36
Identity = 84/132 (63.64%), Postives = 89/132 (67.42%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENS----------------NSERSILSEIPP---KLPPINSSSIDIQHLSNRS 311
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN                 +SERSILSEIP     L PINSS I+I+ LS +S
Sbjct:  483 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQS 614

HSP 3 Score: 77.7962 bits (190), Expect = 5.650e-18
Identity = 54/103 (52.43%), Postives = 62/103 (60.19%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLSNRS 311
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N+   +N    S +    + +REM                   P KL PINSSSIDIQHLSNRS
Sbjct:  385 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSII----NEYREM-------------------PSKLSPINSSSIDIQHLSNRS 464

HSP 4 Score: 65.855 bits (159), Expect = 9.034e-14
Identity = 42/67 (62.69%), Postives = 46/67 (68.66%), Query Frame = 3 
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTN 173
            ISNEFIE RNQSNIIDS LINKSQ+S R  +S+KTFVL N          SI NEN +M SKL H N
Sbjct:  627 ISNEFIEYRNQSNIIDSVLINKSQTSIRYSESDKTFVLSNAEDGQNISDKSIINENSKMSSKLSHKN 693

HSP 5 Score: 43.8986 bits (102), Expect = 4.770e-6
Identity = 23/32 (71.88%), Postives = 29/32 (90.62%), Query Frame = 3 
Query:  219 NSERSILSE-IPPKLPPINSSSIDIQHLSNRS 311
            N+++SI++E +P KL PINSSSIDIQHLSNRS
Sbjct:  214 NADKSIINENMPSKLHPINSSSIDIQHLSNRS 245
The following BLAST results are available for this feature:
BLAST of SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 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 SMED30018197 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000065696.13.056e-60100.00SMESG000065696.1[more]
SMESG000065696.13.056e-60100.00SMESG000065696.1[more]
SMESG000065696.13.056e-60100.00SMESG000065696.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018197 ID=SMED30018197|Name=SMED30018197|organism=Schmidtea mediterranea sexual|type=transcript|length=313bp
CAATTTCCAATGAATTTATTGAAAATCGAAATCAATCGAATATTATTGAC
TCAGGACTGATCAATAAATCGCAATCATCAAAGCGATCTTTTCAATCCAA
TAAAACGTTTGTATTGCGTAATTCAATTCCAAATGAAAACCCAGAAATGC
TATCAAAATTGCCCCACACAAATTCTGCTTTTAGAGAAATGCAGTCCATT
AGTTTGAATGAGAACTCCAATTCTGAAAGATCGATTTTATCTGAAATTCC
ACCAAAATTGCCCCCAATAAATTCATCTAGTATCGACATTCAACATTTAT
CCAATAGATCACC
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protein sequence of SMED30018197-orf-1

>SMED30018197-orf-1 ID=SMED30018197-orf-1|Name=SMED30018197-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEML
SKLPHTNSAFREMQSISLNENSNSERSILSEIPPKLPPINSSSIDIQHLS
NRS
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 81..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 86..103