SMED30001667

Overview
NameSMED30001667
Smed IDSMED30001667
Length (bp)602
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



SMED30001667

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
parenchymaSMED30001667SMESG000003539.1 SMESG000057219.1 dd_Smed_v4_8541_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
body wall musculatureSMED30001667SMESG000003539.1 SMESG000057219.1 dd_Smed_v4_8541_1_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30001667SMESG000003539.1 SMESG000057219.1 dd_Smed_v4_8541_1_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
SMED30001667 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009842:2205..2804 +2820
v31.012739:578..1177 +2802
v31.000590:138466..139043 -2711
v31.000550:102235..102734 +1635
Homology
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BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000057219.1 (SMESG000057219.1)

HSP 1 Score: 209.149 bits (531), Expect = 1.460e-67
Identity = 99/102 (97.06%), Postives = 100/102 (98.04%), Query Frame = -2 
Query:    2 MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI 307
            MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNS+KE NSWQH QAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI
Sbjct:    1 MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSNKELNSWQHGQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI 102
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BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000001175.1 (SMESG000001175.1)

HSP 1 Score: 202.986 bits (515), Expect = 2.364e-64
Identity = 115/191 (60.21%), Postives = 145/191 (75.92%), Query Frame = -2 
Query:    8 RFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 580
            RFSD+QVL+ F+IN +G + +IWS WNRLRTQLTPC  D  Y    YI  L++GE  + W HPGA +L   ILTDATYRLALADLDTLA ++QG+  + +PQHA RCW RVRRTARWPNS+TCRYID +L GN  +  N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N  YA
Sbjct:   20 RFSDSQVLIDFIINKKGIKLDIWSSWNRLRTQLTPCASDPNYNIMKYISSLISGECIDNWWHPGAYKLATDILTDATYRLALADLDTLAKILQGSLSIWDPQHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 210
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BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000011541.1 (SMESG000011541.1)

HSP 1 Score: 205.682 bits (522), Expect = 1.877e-61
Identity = 112/191 (58.64%), Postives = 148/191 (77.49%), Query Frame = -2 
Query:    8 RFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 580
            R+SDAQVL+ F++N +G + +IWS WNRLRTQLTPC  D  Y   +YI GL++G+  + W HPGA +L   ILTDATYRLALADLD+LA ++QG+  + +PQHA RCW RVRRTARWPNS+TCRY+D +L GN D+  N W H QA++++RMLTI+LA+SFK DK++++GN+ Y + LI RK DY+N  YA
Sbjct:   29 RYSDAQVLIEFIMNEKGIKLDIWSSWNRLRTQLTPCASDPNYNIMNYISGLVSGDCVDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPQHAARCWYRVRRTARWPNSRTCRYVDSFLKGNLDELPNKWLHGQALSMLRMLTISLAKSFKPDKDLRIGNDLYNAPLIYRKNDYMNAQYA 219
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BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000037845.1 (SMESG000037845.1)

HSP 1 Score: 201.06 bits (510), Expect = 2.050e-59
Identity = 113/190 (59.47%), Postives = 144/190 (75.79%), Query Frame = -2 
Query:    8 FSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 577
            FSDAQVL+ F++N +G + +IWS WNRLRTQLTPC  DS Y    YI  L++GE  + W HPGA +L   ILTDATYRLALADLD+LA ++QG+  + +P HA RCW RVRRTARWPNS+TCRYID +L GN  +  N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N  YA
Sbjct:  552 FSDAQVLIDFIMNKKGIKLDIWSSWNRLRTQLTPCASDSNYIIIKYISSLISGECIDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPHHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 741
[Close]
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000037845.1 (SMESG000037845.1)

HSP 1 Score: 200.675 bits (509), Expect = 2.524e-59
Identity = 113/190 (59.47%), Postives = 144/190 (75.79%), Query Frame = -2 
Query:    8 FSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 577
            FSDAQVL+ F++N +G + +IWS WNRLRTQLTPC  DS Y    YI  L++GE  + W HPGA +L   ILTDATYRLALADLD+LA ++QG+  + +P HA RCW RVRRTARWPNS+TCRYID +L GN  +  N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N  YA
Sbjct:  552 FSDAQVLIDFIMNKKGIKLDIWSSWNRLRTQLTPCASDSNYIIIKYISSLISGECIDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPHHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 741
The following BLAST results are available for this feature:
BLAST of SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 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 SMED30001667 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057219.11.460e-6797.06SMESG000057219.1[more]
SMESG000001175.12.364e-6460.21SMESG000001175.1[more]
SMESG000011541.11.877e-6158.64SMESG000011541.1[more]
SMESG000037845.12.050e-5959.47SMESG000037845.1[more]
SMESG000037845.12.524e-5959.47SMESG000037845.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001667 ID=SMED30001667|Name=SMED30001667|organism=Schmidtea mediterranea sexual|type=transcript|length=602bp
AGATGTCCGCATAGTTTTTATTCAAGTAATCAGTTTTTCTTTCGATCAAA
GATGATTTATAAAAATTATTACCCAGTTTAATATTTTTGTCATATTTAAA
TGACCTAGCAAGATTTATTGTGAGCATCCTGATCAGGTTAATTGCCTGAC
TATGTTGCCAGCTGTTGAATTCTTTGTCGCTGTTGCCGTGGAGGTACTTG
TCAATGTACCGGCAAGTCTTTGAGTTGGGCCATCTTGCAGTGCGACGCAC
CCGGAGCCAGCATCTGATTGCATGCTGGGGATTCATCATTTCTCCAGTTC
CTTGCATTAAGGAAGCCAGCGTGTCTAAATCGGCCAGCGCCAGTCTATAG
GTAGCATCAGTCAAGATGCAGTTTCCCAGTTCAATGGCACCTGGGTGTAT
CCATGGGTTTGACTTTTCGCCATTCAACAAGCCATCTATATAACTGTATG
GGTAATAACAAGAATCAAGTTCACATGGAGTCAGCTGCGTCCTGAGGCGG
TTCCAGATGCTCCATATGTTTGATCTGTTACCCTCAAAATTTATTAAAAA
AGCCACCAGCACTTGGGCATCAGAAAATCTTTTTTTTTTTTTTTTTTTTT
TT
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protein sequence of SMED30001667-orf-1

>SMED30001667-orf-1 ID=SMED30001667-orf-1|Name=SMED30001667-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=200bp
KKKKKKKRFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYY
PYSYIDGLLNGEKSNPWIHPGAIELGNCILTDATYRLALADLDTLASLMQ
GTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQH
SQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000240body wall musculature