SMED30032309

Overview
NameSMED30032309
Smed IDSMED30032309
Length (bp)394
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.
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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




SMED30032309

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 cellSMED30032309h1SMcG0000290 SmedASXL_004439SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30032309h1SMcG0000290 SmedASXL_019869SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30032309h1SMcG0000290 SmedASXL_003018SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30032309h1SMcG0000290 SmedASXL_001008SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
gutSMED30032309h1SMcG0000290 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 gangliaSMED30032309h1SMcG0000290 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 neoblastSMED30032309h1SMcG0000290 dd_Smed_v4_39554_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30032309h1SMcG0000290 dd_Smed_v4_12726_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30032309h1SMcG0000290 dd_Smed_v4_35838_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30032309h1SMcG0000290 dd_Smed_v4_22938_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30032309h1SMcG0000290 SMED_05003_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30032309h1SMcG0000290 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
SMED30032309 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001732:6008..7136 -1925
v31.001732:6069..6431 -678
v31.001732:5608..5999 -531
v31.001732:6367..6725 -506
Homology
BLAST of SMED30032309 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 161.384 bits (407), Expect = 7.965e-47
Identity = 120/140 (85.71%), Postives = 121/140 (86.43%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHPLINLDXXXXXXXXXXXXXXXXXXXXXXXXEIETLSEQSPVKNSLLL 392
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN SK NDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL
Sbjct:  483 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL 622          

HSP 2 Score: 141.354 bits (355), Expect = 1.029e-39
Identity = 74/84 (88.10%), Postives = 77/84 (91.67%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHP 254
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENS+    I++   P
Sbjct:  264 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPP 347          

HSP 3 Score: 65.4698 bits (158), Expect = 3.527e-13
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 4 Score: 60.8474 bits (146), Expect = 1.219e-11
Identity = 43/77 (55.84%), Postives = 50/77 (64.94%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSIS 203
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N          SI NE  EM SKL   NS+  ++Q +S
Sbjct:  385 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSIINEYREMPSKLSPINSSSIDIQHLS 461          

HSP 5 Score: 53.9138 bits (128), Expect = 2.933e-9
Identity = 29/41 (70.73%), Postives = 34/41 (82.93%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNS 125
            ISNEFIEN NQS+IIDS LIN SQ+S R  +S+KTFVL N+
Sbjct:  711 ISNEFIENLNQSDIIDSVLINNSQTSIRYLESDKTFVLSNA 751          
BLAST of SMED30032309 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 161.384 bits (407), Expect = 8.121e-47
Identity = 120/140 (85.71%), Postives = 121/140 (86.43%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHPLINLDXXXXXXXXXXXXXXXXXXXXXXXXEIETLSEQSPVKNSLLL 392
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN SK NDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL
Sbjct:  479 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL 618          

HSP 2 Score: 141.354 bits (355), Expect = 9.896e-40
Identity = 74/84 (88.10%), Postives = 77/84 (91.67%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHP 254
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENS+    I++   P
Sbjct:  260 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPP 343          

HSP 3 Score: 65.4698 bits (158), Expect = 3.526e-13
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 4 Score: 60.8474 bits (146), Expect = 1.196e-11
Identity = 43/77 (55.84%), Postives = 50/77 (64.94%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSIS 203
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N          SI NE  EM SKL   NS+  ++Q +S
Sbjct:  381 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSIINEYREMPSKLSPINSSSIDIQHLS 457          

HSP 5 Score: 54.299 bits (129), Expect = 2.877e-9
Identity = 29/41 (70.73%), Postives = 34/41 (82.93%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNS 125
            ISNEFIEN NQS+IIDS LIN SQ+S R  +S+KTFVL N+
Sbjct:  707 ISNEFIENLNQSDIIDSVLINNSQTSIRYLESDKTFVLSNA 747          
BLAST of SMED30032309 vs. Planmine SMEST
Match: SMESG000065696.1 (SMESG000065696.1)

HSP 1 Score: 161.384 bits (407), Expect = 8.861e-47
Identity = 120/140 (85.71%), Postives = 121/140 (86.43%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHPLINLDXXXXXXXXXXXXXXXXXXXXXXXXEIETLSEQSPVKNSLLL 392
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN          SIPNENPE+  KL   NS FREMQSI LNEN SK NDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL
Sbjct:  478 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSDEGQNVADKSIPNENPEITYKLSRENSTFREMQSIRLNENPSKINDIINNSHPLINLDSERSILSEIPEIISILSPINSSGIEIETLSEQSPVKNSLLL 617          

HSP 2 Score: 140.969 bits (354), Expect = 1.049e-39
Identity = 74/84 (88.10%), Postives = 77/84 (91.67%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSSKTNDIINNSHP 254
            ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENS+    I++   P
Sbjct:  259 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEMLSKLPHTNSAFREMQSISLNENSNSERSILSEIPP 342          

HSP 3 Score: 65.4698 bits (158), Expect = 3.595e-13
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 4 Score: 60.8474 bits (146), Expect = 1.243e-11
Identity = 43/77 (55.84%), Postives = 50/77 (64.94%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRN----------SIPNENPEMLSKLPHTNSAFREMQSIS 203
            ISNEFIEN NQSNI DS LINKSQ+S R  +S+KTFVL N          SI NE  EM SKL   NS+  ++Q +S
Sbjct:  380 ISNEFIENLNQSNINDSVLINKSQTSIRYLESDKTFVLSNAEDGQNIADKSIINEYREMPSKLSPINSSSIDIQHLS 456          

HSP 5 Score: 53.9138 bits (128), Expect = 2.933e-9
Identity = 29/41 (70.73%), Postives = 34/41 (82.93%), Query Frame = 3
Query:    3 ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNS 125
            ISNEFIEN NQS+IIDS LIN SQ+S R  +S+KTFVL N+
Sbjct:  706 ISNEFIENLNQSDIIDSVLINNSQTSIRYLESDKTFVLSNA 746          
The following BLAST results are available for this feature:
BLAST of SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 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 SMED30032309 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000065696.17.965e-4785.71SMESG000065696.1[more]
SMESG000065696.18.121e-4785.71SMESG000065696.1[more]
SMESG000065696.18.861e-4785.71SMESG000065696.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032309 ID=SMED30032309|Name=SMED30032309|organism=Schmidtea mediterranea sexual|type=transcript|length=394bp
CAATTTCCAATGAATTTATTGAAAATCGAAATCAATCGAATATTATTGAC
TCAGGACTGATCAATAAATCGCAATCATCAAAGCGATCTTTTCAATCCAA
TAAAACGTTTGTATTGCGTAATTCAATTCCAAATGAAAACCCAGAAATGC
TATCAAAATTGCCCCACACAAATTCTGCTTTTAGAGAAATGCAGTCCATT
AGTTTGAATGAGAACTCCAGTAAAACAAATGATATAATCAATAATTCACA
TCCACTAATCAATCTAGATTCTGAAAGATCGATTTTATCTGAAATTCCAG
AAATTATATCAATATTGTCCCCGATAAATTCATCCGGTATTGAAATTGAA
ACTTTATCCGAACAATCGCCGGTGAAAAATTCTTTACTTCTTCC
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protein sequence of SMED30032309-orf-1

>SMED30032309-orf-1 ID=SMED30032309-orf-1|Name=SMED30032309-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
ISNEFIENRNQSNIIDSGLINKSQSSKRSFQSNKTFVLRNSIPNENPEML
SKLPHTNSAFREMQSISLNENSSKTNDIINNSHPLINLDSERSILSEIPE
IISILSPINSSGIEIETLSEQSPVKNSLLL
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