SMED30029161

Overview
NameSMED30029161
Smed IDSMED30029161
Length (bp)1007
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30029161 (SMED30029161) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029161 (SMED30029161) in cells (dots) of each of the 12 neoblast clusters.

 

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




SMED30029161

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cephalic gangliaSMED30029161h1SMcG0000812 dd_Smed_v4_5464_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029161h1SMcG0000812 dd_Smed_v4_5464_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30029161h1SMcG0000812 dd_Smed_v4_5464_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
SMED30029161 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008149:15327..16322 -4830
Homology
BLAST of SMED30029161 vs. TrEMBL
Match: A0A267F178 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig029604g1 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 6.162e-11
Identity = 16/34 (47.06%), Postives = 25/34 (73.53%), Query Frame = -2
Query:  656 IHLDWVYVPEQGDIFILVDAGTNWVEAILCKDRT 757
            +H+DW YV   G+I ++VD+ + W+EA  C+DRT
Sbjct:  842 VHMDWAYVKGAGNILVIVDSFSGWIEAFPCRDRT 875          

HSP 2 Score: 45.0542 bits (105), Expect = 6.162e-11
Identity = 58/195 (29.74%), Postives = 85/195 (43.59%), Query Frame = -1
Query:  162 R*NTFRTVFNCLSNLFFRSGTPNCVVMDNTPEFKS--IKL*LEAKGCNVLYSTTEW-------QRDVQTIKN---NHNNRLIHI----FLKYHLI--RAFSGTFNNSTAERLMRRKLNLSLIHP*KLMQSFHIRTVI*KLRSRQHS-------T*LQNASYINLNDELTLASNEEIS--KATPIE*KSEHEKETN 665
            R  T  +V  CL  +F R G P  VV DN PEF +  +   L A G   L S T +       +R VQT+K+     + ++ H+    FL+  L+  R  + +     AE L  R+L + ++   +   S     VI    S           T  QN ++I  +D L LAS  +++     P E K E E ETN
Sbjct:  872 RDRTADSVIQCLRTVFTRFGVPELVVSDNAPEFTTEVLTSWLRANGAKKLESPTYYPQANGAAERAVQTVKSALRAWSEKITHMEFSRFLQKVLLHHRNSASSRGCCPAEILFGRRLRVPVVTNFEQGDS-----VIYAPSSSSVGNPAKFVMTAGQNTAWILADDGLRLASTNQLAPMATRPSEFKMEDEDETN 1061          

HSP 3 Score: 22.7126 bits (47), Expect = 6.162e-11
Identity = 8/32 (25.00%), Postives = 16/32 (50.00%), Query Frame = -1
Query:  852 IKQYVIKQTQDTHTGLKQTANKLCTN*W*PSI 947
            +++       DTHTG+    + + T+ W P +
Sbjct:  773 LRKAAFDAIHDTHTGMHAAHSLMSTSCWWPGM 804          
BLAST of SMED30029161 vs. TrEMBL
Match: A0A267GGK0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig029604g6 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 1.421e-10
Identity = 16/34 (47.06%), Postives = 25/34 (73.53%), Query Frame = -2
Query:  656 IHLDWVYVPEQGDIFILVDAGTNWVEAILCKDRT 757
            +H+DW YV   G+I ++VD+ + W+EA  C+DRT
Sbjct:  999 VHMDWAYVKGAGNILVIVDSFSGWIEAFPCRDRT 1032          

HSP 2 Score: 44.2838 bits (103), Expect = 1.421e-10
Identity = 58/200 (29.00%), Postives = 89/200 (44.50%), Query Frame = -1
Query:  144 R*NTFRTVFNCLSNLFFRSGTPNCVVMDNTPEFKS--IKL*LEAKGCNVLYSTTEW-------QRDVQTIKN---NHNNRLIHI----FLKYHLI--RAFSGTFNNSTAERLMRRKLNLSLIHP*KLMQSFHIRTVI*KLRSRQHS-------T*LQNASYINLNDELTLASNEEISKATPIE*K-SEHEKETNEETNQI 665
            R  T  +V  CL  +F R G P  VV DN PEF +  +   L A G   L S T +       +R VQT+K+     + ++ H+    FL+  L+  R  + +     AE L  R+L + ++   +   S     VI    S           T  QN ++I  +D L LAS  +++   P+  + SE E E  +ETN +
Sbjct: 1029 RDRTADSVIQCLRTVFTRFGVPELVVSDNAPEFTTEVLTSWLRANGAKKLESPTYYPQANGAAERAVQTVKSALRAWSEKITHMEFSRFLQKVLLHHRNSASSRGCCPAEILFGRRLRVPVVTNFEQGDS-----VIYAPSSSSVGNPAKFVMTAGQNTAWILADDGLRLASTNQLA---PMATRPSEFEMEDEDETNSV 1220          

HSP 3 Score: 22.3274 bits (46), Expect = 1.421e-10
Identity = 8/23 (34.78%), Postives = 13/23 (56.52%), Query Frame = -1
Query:  852 QDTHTGLKQTANKLCTN*W*PSI 920
             DTHTG+    + + T+ W P +
Sbjct:  939 HDTHTGMHAAHSLMSTSCWWPGM 961          
BLAST of SMED30029161 vs. TrEMBL
Match: A0A267G4H6 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig029604g7 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 4.873e-10
Identity = 16/34 (47.06%), Postives = 25/34 (73.53%), Query Frame = -2
Query:  656 IHLDWVYVPEQGDIFILVDAGTNWVEAILCKDRT 757
            +H+DW YV   G+I ++VD+ + W+EA  C+DRT
Sbjct:  999 VHMDWAYVKGAGNILVIVDSFSGWIEAFPCRDRT 1032          

HSP 2 Score: 41.9726 bits (97), Expect = 4.873e-10
Identity = 58/200 (29.00%), Postives = 88/200 (44.00%), Query Frame = -1
Query:  144 R*NTFRTVFNCLSNLFFRSGTPNCVVMDNTPEFKS--IKL*LEAKGCNVLYSTTEW-------QRDVQTIKN---NHNNRLIHI----FLKYHLI--RAFSGTFNNSTAERLMRRKLNLSLIHP*KLMQSFHIRTVI*KLRSRQHS-------T*LQNASYINLNDELTLASNEEISKATPIE*K-SEHEKETNEETNQI 665
            R  T  +V  CL  +F R G P  VV DN PEF +  +   L A G   L S T +       +R VQT+K+     + ++ H+    FL+  L+  R    +     AE L  R+L + ++   +   S     VI    S           T  QN ++I  +D L LAS  +++   P+  + SE E E  +ETN +
Sbjct: 1029 RDRTADSVIQCLRAVFTRFGVPELVVSDNAPEFTTEVLTSWLRANGAKKLESPTYYPQANGAAERAVQTVKSALRAWSEKVTHMEFSRFLQKVLLHHRNSVSSRGCCPAEILFGRRLRVPVVTNFEQGDS-----VIYAPSSSSVGNPAKFVMTAGQNTAWILADDGLRLASTNQLA---PMATRPSEFEMEDEDETNSV 1220          

HSP 3 Score: 22.7126 bits (47), Expect = 4.873e-10
Identity = 8/32 (25.00%), Postives = 16/32 (50.00%), Query Frame = -1
Query:  852 IKQYVIKQTQDTHTGLKQTANKLCTN*W*PSI 947
            +++       DTHTG+    + + T+ W P +
Sbjct:  930 LRKAAFDAIHDTHTGMHAAHSLMSTSCWWPGM 961          
BLAST of SMED30029161 vs. TrEMBL
Match: A0A267ENZ4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig029604g4 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 6.874e-10
Identity = 16/34 (47.06%), Postives = 25/34 (73.53%), Query Frame = -2
Query:  656 IHLDWVYVPEQGDIFILVDAGTNWVEAILCKDRT 757
            +H+DW YV   G+I ++VD+ + W+EA  C+DRT
Sbjct:  999 VHMDWAYVKGAGNILVIVDSFSGWIEAFPCRDRT 1032          

HSP 2 Score: 41.2022 bits (95), Expect = 6.874e-10
Identity = 57/200 (28.50%), Postives = 88/200 (44.00%), Query Frame = -1
Query:  144 R*NTFRTVFNCLSNLFFRSGTPNCVVMDNTPEFKS--IKL*LEAKGCNVLYSTTEW-------QRDVQTIKN---NHNNRLIHI----FLKYHLI--RAFSGTFNNSTAERLMRRKLNLSLIHP*KLMQSFHIRTVI*KLRSRQHS-------T*LQNASYINLNDELTLASNEEISKATPIE*K-SEHEKETNEETNQI 665
            R  T  +V  CL  +F R G P  VV DN PEF +  +   L A G   L S T +       +R VQT+K+     + ++ H+    FL+  L+  R  + +     AE    R+L + ++   +   S     VI    S           T  QN ++I  +D L LAS  +++   P+  + SE E E  +ETN +
Sbjct: 1029 RDRTADSVIQCLRTVFTRFGVPELVVSDNAPEFTTEVLTSWLRANGAKKLESPTYYPQANGAAERAVQTVKSALRAWSEKITHMEFSRFLQKVLLHHRNSASSRGCCPAEIPFGRRLRVPVVTNFEQGDS-----VIYAPSSSSVGNPAKFVMTAGQNTAWILADDGLRLASTNQLA---PMATRPSEFEMEDEDETNSV 1220          

HSP 3 Score: 22.7126 bits (47), Expect = 6.874e-10
Identity = 8/32 (25.00%), Postives = 16/32 (50.00%), Query Frame = -1
Query:  852 IKQYVIKQTQDTHTGLKQTANKLCTN*W*PSI 947
            +++       DTHTG+    + + T+ W P +
Sbjct:  930 LRKAAFNAIHDTHTGMHAAHSLMSTSCWWPGM 961          
BLAST of SMED30029161 vs. TrEMBL
Match: A0A267ESH1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig029604g2 PE=4 SV=1)

HSP 1 Score: 46.2098 bits (108), Expect = 2.632e-9
Identity = 16/34 (47.06%), Postives = 25/34 (73.53%), Query Frame = -2
Query:  656 IHLDWVYVPEQGDIFILVDAGTNWVEAILCKDRT 757
            +H+DW YV   G+I ++VD+ + W+EA  C+DRT
Sbjct:  525 VHMDWAYVKGAGNILVIVDSFSGWIEAFPCRDRT 558          

HSP 2 Score: 41.5874 bits (96), Expect = 2.632e-9
Identity = 57/195 (29.23%), Postives = 84/195 (43.08%), Query Frame = -1
Query:  162 R*NTFRTVFNCLSNLFFRSGTPNCVVMDNTPEFKSIKL--*LEAKGCNVLYSTTEW-------QRDVQTIKN---NHNNRLIHI----FLKYHLI--RAFSGTFNNSTAERLMRRKLNLSLIHP*KLMQSFHIRTVI*KLRSRQHS-------T*LQNASYINLNDELTLASNEEISKAT--PIE*KSEHEKETN 665
            R  T  +V  CL  +F R G P  VV DN PEF +  L   L A G   L   T +       +R VQT+K+     + ++ H+    FL+  L+  R  + +     AE L  R+L + ++   +   S     VI    S           T  QN ++I  +D L LAS  +++     P E + E E ETN
Sbjct:  555 RDRTADSVIQCLRTVFTRFGVPELVVSDNAPEFTTEVLTSWLRANGAKKLELPTYYPQANGAAERAVQTVKSALRAWSEKITHMEFSRFLQKVLLHHRNSASSRGCCPAEILFGRRLRVPVVTNFEQGDS-----VIYAPSSSSVGNPAKFVMTAGQNTAWILADDGLRLASTNQLAPMATQPSEFEMEDEDETN 744          

HSP 3 Score: 22.7126 bits (47), Expect = 2.632e-9
Identity = 8/32 (25.00%), Postives = 16/32 (50.00%), Query Frame = -1
Query:  852 IKQYVIKQTQDTHTGLKQTANKLCTN*W*PSI 947
            +++       DTHTG+    + + T+ W P +
Sbjct:  456 LRKAAFDAIHDTHTGMHAAHSLMSTSCWWPGM 487          
BLAST of SMED30029161 vs. Planmine SMEST
Match: SMESG000069762.1 (SMESG000069762.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.045e-20
Identity = 27/34 (79.41%), Postives = 32/34 (94.12%), Query Frame = -1
Query:  168 NASYINLNDELTLASNEEISKATPIE*KSEHEKE 269
            NASYIN++D+L LASNE+ISKATPIE KSEHEK+
Sbjct:   41 NASYINIDDDLMLASNEQISKATPIEKKSEHEKK 74          

HSP 2 Score: 44.2838 bits (103), Expect = 1.045e-20
Identity = 23/31 (74.19%), Postives = 26/31 (83.87%), Query Frame = -3
Query:  286 KKIKSFANPSLKIDAIIPYKNSNMKAAIKAT 378
            +K+KS ANPSLKI   I YKNS+MKAAIKAT
Sbjct:    3 RKLKSLANPSLKIGKSIHYKNSDMKAAIKAT 33          

HSP 3 Score: 37.3502 bits (85), Expect = 1.045e-20
Identity = 18/32 (56.25%), Postives = 24/32 (75.00%), Query Frame = -2
Query:   80 KKKRMRKQIKY*KLKEQFIVQRDIWLRGANVI 175
            +KK ++ +IKY K KEQFI QR  W++ ANVI
Sbjct:   72 EKKPLKNKIKYRKRKEQFIAQRFTWIKDANVI 103          
The following BLAST results are available for this feature:
BLAST of SMED30029161 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 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 SMED30029161 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267F1786.162e-1147.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GGK01.421e-1047.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267G4H64.873e-1047.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267ENZ46.874e-1047.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267ESH12.632e-947.06Uncharacterized protein OS=Macrostomum lignano OX=... [more]
back to top
BLAST of SMED30029161 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 SMED30029161 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 SMED30029161 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 SMED30029161 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30029161 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000069762.11.045e-2079.41SMESG000069762.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029161 ID=SMED30029161|Name=SMED30029161|organism=Schmidtea mediterranea sexual|type=transcript|length=1007bp
GAATTTCCAATATTTATTTATTTACTAATATTTAAACAAAAATAATAATG
TATTTAAGCATATTAATATATATGAAATATATAACATTCGCACCTCTAAG
CCAAATATCTCTTTGGACGATGAATTGCTCTTTTAATTTTCAATATTTGA
TTTGTTTCCTCATTCGTTTCTTTTTCGTGTTCTGACTTTTATTCTATTGG
CGTGGCTTTTGAGATTTCTTCATTGCTAGCTAATGTTAACTCATCATTTA
GATTTATATACGAGGCGTTTTGCAATCAGGTACTATGTTGCCTTGATCGC
AGCTTTCATATTACTGTTCTTATATGGAATGATTGCATCAATTTTCAAGG
ATGGATTAGCGAAAGATTTAATTTTCTTCTCATTAGCCTTTCAGCAGTCG
AGTTATTGAATGTTCCAGAGAATGCTCTGATTAAATGATACTTTAAAAAG
ATATGAATCAAACGATTATTATGATTATTTTTTATGGTTTGTACGTCTCT
CTGCCACTCAGTTGTTGAGTATAAAACATTGCATCCTTTTGCTTCTAGTC
ATAACTTTATTGATTTAAATTCTGGAGTATTATCCATTACGACACAGTTA
GGTGTTCCGGATCTGAAAAATAGATTAGAAAGACAATTGAATACTGTCCT
AAATGTGTTCTATCTTTACACAATATTGCTTCAACCCAATTTGTACCGGC
ATCTACCAAAATGAATATATCACCCTGTTCTGGAACATATACCCAATCTA
AATGAATTATATCTCATTTATCTGGCGTGGGCAATTTGTCAGAACTACTT
ATTGATTTAAATTTGTAGGATTGACATATTTTATAGTTTTTTAAATATCA
AAATTGAAGGCTACCACTAATTTGTACACAACTTGTTCGCTGTCTGTTTT
AGTCCTGTATGCGTATCTTGCGTTTGTTTAATGACATATTGTTTAATGCC
TCACCTGTGTCGATTAGAATAAGAATCTCATTTGCCACTAAACCATCTAT
TACTTTA
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR012337RNaseH-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 52..71