SMED30034951

Overview
NameSMED30034951
Smed IDSMED30034951
Length (bp)1089
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 SMED30034951 (SMED30034951) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034951 (SMED30034951) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30034951 (SMED30034951) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034951 (SMED30034951) 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.
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




SMED30034951

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30034951SMESG000009367.1 SmedASXL_010460SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
zeta neoblastSMED30034951SMESG000009367.1 dd_Smed_v4_15071_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
SMED30034951 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002041:19277..24157 -5366
Homology
BLAST of SMED30034951 vs. TrEMBL
Match: A0A0L8GP07 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22030888mg PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.134e-11
Identity = 67/288 (23.26%), Postives = 122/288 (42.36%), Query Frame = 2
Query:   95 KPPECYKLLTACIHLSIYQMEVASEFLDYFKCLDGPDYITDSSQSFLFYSIRWIHKEQKLCFEDKWQIKFQYNLD---DQAILLIPGSEFIKIIMEDNSN---IFNVTSLDDLKSQINQ--SGHCVTIILI--DIQHEIXXXXXXXXNSKYGKLTXXXXXXXXXXXXXXHKICTVKMPNYIDA---------GKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSGG 901
            +P EC K +T  I   +         +  F   D  +        F+ Y + W  K   LC++ + Q+   +NLD      +++IP   F +++    +N   + NV+SLD     I     G+ V + +I  DI  ++ K      +S+      K    I   L I+    T+++ N  +                ++KA+G+K  K+  L SE  F F   +G +     N        +  +W+LQL++F+ +   + +AI  ++ TPK++F+A  K +    G
Sbjct:  183 QPKECLKSMTVVIDPGVVNQPGVGTAI--FSACDDLEVTYKIESQFMPYVVSW--KRTTLCYDTEDQVVKTWNLDVDEKDIVIMIPLDIFTEMLDHFKTNSMAMSNVSSLDQYAENIQSLYPGYSVMLAVIGSDIGSQVSKRSGSHQSSQR-----KAKNGIDDRLSIEEAFLTLQLKNLFNCQLIQSSSGITNLIKSFTKAVGEKPGKKDRLQSE--FSFHNAKGNNTHGSSN--------IQGMWKLQLQQFKNVSSDIANAIVFQYPTPKSLFEAYEKCSSEKEG 451          

HSP 2 Score: 44.669 bits (104), Expect = 2.134e-11
Identity = 19/40 (47.50%), Postives = 28/40 (70.00%), Query Frame = 3
Query:  951 EKEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTA 1070
            EKE I  + DI VRR  G++ +T+R+GKE A +IY  +T+
Sbjct:  448 EKEGIKVLEDITVRRHAGVLQSTKRIGKEAARRIYQLMTS 487          
BLAST of SMED30034951 vs. TrEMBL
Match: A0A267ELL5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009863g2 PE=4 SV=1)

HSP 1 Score: 48.9062 bits (115), Expect = 2.646e-8
Identity = 23/89 (25.84%), Postives = 42/89 (47.19%), Query Frame = 2
Query:  605 IDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDA 871
            +  GK     +KAI ++ FK   L S   F      G  C+++ +   G+  G+D++WR QL+ F  +   +   I   + +P ++  A
Sbjct:  243 VQLGKLVYCLTKAIAERPFKAARLESVFSFHVGAGVGAGCRLEESADGGSPAGIDELWRCQLQCFPLVTAEVARTIMRAYPSPGHLIRA 331          

HSP 2 Score: 38.891 bits (89), Expect = 2.646e-8
Identity = 14/39 (35.90%), Postives = 26/39 (66.67%), Query Frame = 3
Query:  954 KEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTA 1070
            +EA+  +AD++V +G G +   RR+G E+  +IY F ++
Sbjct:  339 EEAVKLVADLQVCKGTGPLSTARRLGPELGKRIYAFYSS 377          
BLAST of SMED30034951 vs. TrEMBL
Match: A0A267H2G5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009863g3 PE=4 SV=1)

HSP 1 Score: 48.9062 bits (115), Expect = 2.942e-8
Identity = 23/89 (25.84%), Postives = 42/89 (47.19%), Query Frame = 2
Query:  605 IDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDA 871
            +  GK     +KAI ++ FK   L S   F      G  C+++ +   G+  G+D++WR QL+ F  +   +   I   + +P ++  A
Sbjct:  243 VQLGKLVYCLTKAIAERPFKAARLESVFSFHVGAGVGAGCRLEESADGGSPAGIDELWRCQLQCFPLVTAEVARTIMRAYPSPGHLIRA 331          

HSP 2 Score: 38.891 bits (89), Expect = 2.942e-8
Identity = 14/39 (35.90%), Postives = 26/39 (66.67%), Query Frame = 3
Query:  954 KEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTA 1070
            +EA+  +AD++V +G G +   RR+G E+  +IY F ++
Sbjct:  339 EEAVKLVADLQVCKGTGPLSTARRLGPELGKRIYAFYSS 377          
BLAST of SMED30034951 vs. TrEMBL
Match: A0A267ER68 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009863g1 PE=4 SV=1)

HSP 1 Score: 48.9062 bits (115), Expect = 3.297e-8
Identity = 23/89 (25.84%), Postives = 42/89 (47.19%), Query Frame = 2
Query:  605 IDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDA 871
            +  GK     +KAI ++ FK   L S   F      G  C+++ +   G+  G+D++WR QL+ F  +   +   I   + +P ++  A
Sbjct:  243 VQLGKLVYCLAKAIAERPFKAARLESVFSFHVGAGVGAGCRLEESADGGSPAGIDELWRCQLQCFPLVTAEVARTIMRAYPSPGHLIRA 331          

HSP 2 Score: 38.891 bits (89), Expect = 3.297e-8
Identity = 14/39 (35.90%), Postives = 26/39 (66.67%), Query Frame = 3
Query:  954 KEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTA 1070
            +EA+  +AD++V +G G +   RR+G E+  +IY F ++
Sbjct:  339 EEAVRLVADLQVCKGTGPLSTARRLGPELGKRIYAFYSS 377          
BLAST of SMED30034951 vs. TrEMBL
Match: A0A444SHJ0 (Crossover junction endonuclease EME1 OS=Armadillidium vulgare OX=13347 GN=Avbf_15409 PE=4 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 9.090e-8
Identity = 20/43 (46.51%), Postives = 31/43 (72.09%), Query Frame = 3
Query:  942 SLVEKEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTA 1070
            S+ E E +  +ADI VRRG+G++ NTR++G E+++KIY F   
Sbjct:  468 SIPEAEGLKLLADIPVRRGVGVLVNTRKIGPELSSKIYRFFMC 510          

HSP 2 Score: 35.8094 bits (81), Expect = 9.090e-8
Identity = 25/95 (26.32%), Postives = 43/95 (45.26%), Query Frame = 2
Query:  620 FAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCP--DGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSG 898
            F    +KAI +K FK      +   +FS +       ++NC   D + GG+  +W  QL++F  +      AI +K+ +P+ +      I E  G
Sbjct:  387 FVAQVAKAIAEKPFK----LEKARTNFSWHIES---YNVNCVKIDKSGGGLLKLWHQQLRQFNNVGPEAAQAIAKKYPSPQALIKVYRSIPEAEG 474          
BLAST of SMED30034951 vs. Planmine SMEST
Match: SMESG000009367.1 (SMESG000009367.1)

HSP 1 Score: 516.153 bits (1328), Expect = 0.000e+0
Identity = 274/274 (100.00%), Postives = 274/274 (100.00%), Query Frame = 2
Query:   77 YIDKSIKPPECYKLLTACIHLSIYQMEVASEFLDYFKCLDGPDYITDSSQSFLFYSIRWIHKEQKLCFEDKWQIKFQYNLDDQAILLIPGSEFIKIIMEDNSNIFNVTSLDDLKSQINQSGHCVTIILIDIQHEIXXXXXXXXNSKYGKLTXXXXXXXXXXXXXXHKICTVKMPNYIDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSG 898
            YIDKSIKPPECYKLLTACIHLSIYQMEVASEFLDYFKCLDGPDYITDSSQSFLFYSIRWIHKEQKLCFEDKWQIKFQYNLDDQAILLIPGSEFIKIIMEDNSNIFNVTSLDDLKSQINQSGHCVTIILIDIQHEILKLKKLKLNSKYGKLTEKIIEKILIDLQIDHKICTVKMPNYIDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSG
Sbjct:   22 YIDKSIKPPECYKLLTACIHLSIYQMEVASEFLDYFKCLDGPDYITDSSQSFLFYSIRWIHKEQKLCFEDKWQIKFQYNLDDQAILLIPGSEFIKIIMEDNSNIFNVTSLDDLKSQINQSGHCVTIILIDIQHEILKLKKLKLNSKYGKLTEKIIEKILIDLQIDHKICTVKMPNYIDAGKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGGVDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSG 295          

HSP 2 Score: 93.2041 bits (230), Expect = 4.696e-21
Identity = 46/46 (100.00%), Postives = 46/46 (100.00%), Query Frame = 3
Query:  951 EKEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTATTDDSG 1088
            EKEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTATTDDSG
Sbjct:  296 EKEAINSIADIEVRRGIGIVDNTRRVGKEIATKIYTFLTATTDDSG 341          
The following BLAST results are available for this feature:
BLAST of SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0L8GP072.134e-1123.26Uncharacterized protein OS=Octopus bimaculoides OX... [more]
A0A267ELL52.646e-825.84Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267H2G52.942e-825.84Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267ER683.297e-825.84Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A444SHJ09.090e-846.51Crossover junction endonuclease EME1 OS=Armadillid... [more]
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BLAST of SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 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 SMED30034951 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009367.14.696e-21100.00SMESG000009367.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034951 ID=SMED30034951|Name=SMED30034951|organism=Schmidtea mediterranea sexual|type=transcript|length=1089bp
GTATTTTGACTGAATGAATAAAGAAAATTTAAAAAAGCAAAAGGAAAATG
AAAAAATTAAAAAGAATTTAGAGAAATATATTGATAAATCTATTAAACCA
CCCGAATGTTATAAACTTTTGACCGCTTGTATTCATTTATCAATCTATCA
AATGGAAGTAGCATCGGAGTTTTTAGATTATTTCAAATGCCTCGATGGAC
CTGATTATATAACAGATAGTAGTCAAAGTTTTCTGTTTTATTCTATTCGC
TGGATTCACAAAGAACAAAAACTATGTTTTGAAGATAAATGGCAGATAAA
ATTTCAGTATAATTTAGACGATCAGGCTATTTTATTAATTCCTGGATCGG
AATTTATTAAAATAATTATGGAAGATAATTCTAACATTTTTAATGTAACC
TCTCTTGATGATCTAAAAAGTCAAATTAATCAATCGGGTCACTGTGTTAC
GATTATTTTGATAGATATTCAGCATGAAATTTTAAAATTGAAAAAATTAA
AACTCAATTCAAAATATGGAAAGTTAACCGAGAAAATTATTGAGAAAATA
TTGATCGATTTGCAAATCGATCATAAAATCTGCACGGTGAAAATGCCCAA
TTATATTGATGCGGGCAAATTTGCTATGGGGTATTCAAAAGCGATAGGTC
AAAAGAAATTTAAGGAGAAAATGCTTTTTTCAGAAGATTTATTCGATTTT
TCGTTAAATCAAGGTGGGAGTTGTCAAATCGATATGAACTGTCCAGATGG
TGCATTGGGTGGTGTAGACGATGTCTGGCGGCTACAGTTGAAGAAATTTA
GAGGAATCGAGCAACCAATGGTGGATGCGATTTTTGAAAAGTTTTCTACT
CCGAAAAATATGTTTGATGCTGTTATGAAAATTACCGAGTTATCCGGAGG
TTGATGGAATTGATTTCTCAATTATAGGATTTTTATGAATTTCATTGGTA
GAAAAAGAGGCAATTAACAGTATTGCCGATATTGAGGTGCGCCGAGGAAT
TGGTATTGTGGACAATACAAGAAGAGTGGGCAAAGAAATCGCAACGAAAA
TTTATACTTTTCTGACAGCAACTACTGATGATAGTGGAT
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protein sequence of SMED30034951-orf-1

>SMED30034951-orf-1 ID=SMED30034951-orf-1|Name=SMED30034951-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=297bp
MNKENLKKQKENEKIKKNLEKYIDKSIKPPECYKLLTACIHLSIYQMEVA
SEFLDYFKCLDGPDYITDSSQSFLFYSIRWIHKEQKLCFEDKWQIKFQYN
LDDQAILLIPGSEFIKIIMEDNSNIFNVTSLDDLKSQINQSGHCVTIILI
DIQHEILKLKKLKLNSKYGKLTEKIIEKILIDLQIDHKICTVKMPNYIDA
GKFAMGYSKAIGQKKFKEKMLFSEDLFDFSLNQGGSCQIDMNCPDGALGG
VDDVWRLQLKKFRGIEQPMVDAIFEKFSTPKNMFDAVMKITELSGG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR033310Mms4/EME1/EME2
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0048476Holliday junction resolvase complex
Vocabulary: biological process
TermDefinition
GO:0006281DNA repair
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 5..25
NoneNo IPR availableGENE3DG3DSA:3.40.50.10130coord: 31..221
e-value: 6.9E-7
score: 31.2
IPR033310Mms4/EME1/EME2PANTHERPTHR21077EME1 PROTEINcoord: 2..285