SMED30004033

Overview
NameSMED30004033
Smed IDSMED30004033
Length (bp)562
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 SMED30004033 (SMED30004033) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004033 (SMED30004033) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30004033 (SMED30004033) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004033 (SMED30004033) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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



SMED30004033

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30004033 dd_Smed_v4_33434_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
SMED30004033 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007562:22589..23150 +2747
v31.014737:1986..2547 -2729
v31.002207:42819..43365 +2103
v31.004339:30716..31264 +2050
v31.006600:24830..25366 -2019
v31.002336:9660..10186 +1838
v31.000128:7126..7654 -1703
v31.000197:165215..165729 +1553
Homology
[Close]
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000058576.1 (SMESG000058576.1)

HSP 1 Score: 164.851 bits (416), Expect = 1.523e-50
Identity = 77/108 (71.30%), Postives = 90/108 (83.33%), Query Frame = 2 
Query:   17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEH 340
            PS AI  + GRNPA EA Q AEFSLYRLE+LV KFQWKV+MA+RRL++INA I   E+ STDGYAPDYG+ FELK+P L +M+A TNIILPAKLFNG +R+RNRRDEH
Sbjct:  162 PSIAINHKLGRNPAEEARQHAEFSLYRLEELVLKFQWKVRMARRRLEQINAAIASGEILSTDGYAPDYGISFELKNPALTRMQALTNIILPAKLFNGSMRHRNRRDEH 269
[Close]
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1)

HSP 1 Score: 139.428 bits (350), Expect = 3.203e-42
Identity = 69/101 (68.32%), Postives = 77/101 (76.24%), Query Frame = 2 
Query:   20 SFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYR 322
            S AIKREP RN ARE  Q AEFSLYRLE+LVRKFQWKV+M QR L +INA I   E+PSTDGYA DYG+ FEL DP L QM   TN ILPA+LFN  IR++
Sbjct:   57 SLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYAQDYGLLFELNDPVLTQMH--TNAILPAQLFNERIRHQ 155
[Close]
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 120.553 bits (301), Expect = 1.689e-33
Identity = 59/85 (69.41%), Postives = 71/85 (83.53%), Query Frame = 2 
Query:  137 MAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEH-YQYQYTTKPEHDRYMR 388
            MA+RRL+RINAVI   E+PSTDGYAPDYGV FEL+DP  A+M+APTNI+LP  LFNGPIR+R+RRDEH YQ Q+ TK E ++Y R
Sbjct:    1 MARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDP--ARMKAPTNIVLPVNLFNGPIRHRDRRDEHSYQCQHPTKKERNQYRR 83

HSP 2 Score: 110.923 bits (276), Expect = 8.088e-30
Identity = 55/116 (47.41%), Postives = 76/116 (65.52%), Query Frame = 2 
Query:   17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEHYQYQYTTK 364
            PS AIKREPG NPAREA Q AE++  + E+L RK+Q K  +A++RL ++N  I    +PSTDG+ P+YGV FEL DP L QM APT +++P KL    +R R    +   + Y ++
Sbjct:  140 PSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQTGDHTYASR 255
[Close]
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 112.849 bits (281), Expect = 3.030e-31
Identity = 54/102 (52.94%), Postives = 71/102 (69.61%), Query Frame = 2 
Query:   17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYR 322
            PS AIKREPG NPAREA Q AE++  ++E+L RK+  K  +A++RL ++N  I    +PSTDG+ P+YGV FEL DP L QM APT ++LP KL    +R R
Sbjct:   87 PSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNR 188
[Close]
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 117.857 bits (294), Expect = 1.203e-30
Identity = 59/131 (45.04%), Postives = 82/131 (62.60%), Query Frame = 2 
Query:   17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEHYQYQYTTKPEHDRYMRPLQDRRS 409
            PS AIKREPG NPAREA Q A+++  ++E+L RK+  K   A++RL ++N  I    +PSTDG+ P+YGV FEL DP L QM APT +++P KL    +  RN+   H    +T    H ++   L +RRS
Sbjct: 1697 PSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTL--RNQLGSHQTGDHTYASRHPQWNSKLNNRRS 1825
The following BLAST results are available for this feature:
BLAST of SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 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 SMED30004033 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058576.11.523e-5071.30SMESG000058576.1[more]
SMESG000026733.13.203e-4268.32SMESG000026733.1[more]
SMESG000004883.11.689e-3369.41SMESG000004883.1[more]
SMESG000027782.13.030e-3152.94SMESG000027782.1[more]
SMESG000057533.11.203e-3045.04SMESG000057533.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004033 ID=SMED30004033|Name=SMED30004033|organism=Schmidtea mediterranea sexual|type=transcript|length=562bp
GAGAATTCCAGACAAGCCAAGCTTCGCTATCAAACGCGAACCTGGCCGAA
ATCCGGCTCGAGAAGCGAGCCAGAGCGCGGAATTTTCACTCTATCGACTG
GAGAAACTCGTAAGGAAGTTCCAATGGAAGGTTAAGATGGCCCAAAGAAG
GTTGGATCGAATCAATGCCGTCATCAAATATGAAGAGGTCCCCAGTACGG
ACGGATACGCGCCGGATTATGGCGTATTTTTCGAGCTAAAGGATCCGACA
CTGGCACAAATGCGAGCACCCACCAACATAATCCTTCCGGCCAAACTGTT
CAATGGACCGATACGATACCGAAATCGGAGGGATGAACACTACCAATATC
AATATACAACTAAACCGGAGCATGATCGGTACATGAGACCCCTCCAAGAT
AGAAGATCCAGAGGACCTTATTAAATACAAACTGGAAATTTGACAAAAAA
CCGCTTTTAATGATTAACAGATGTTAACTTAGTGGGAAGACTTATTTTAT
TGAATGGTTAAAAAACATAAAGTAACTTCTCTAATAAAGAATATTAAATA
ACTCTTAATTTA
back to top

protein sequence of SMED30004033-orf-1

>SMED30004033-orf-1 ID=SMED30004033-orf-1|Name=SMED30004033-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
RIPDKPSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRR
LDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLF
NGPIRYRNRRDEHYQYQYTTKPEHDRYMRPLQDRRSRGPY*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell