SMED30020820

Overview
NameSMED30020820
Smed IDSMED30020820
Length (bp)1096
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



SMED30020820

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 cellSMED30020820 SmedASXL_050429SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020820 SmedASXL_050429SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020820 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001224:22688..23781 +5364
Homology
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BLAST of SMED30020820 vs. Planmine SMEST
Match: SMESG000077598.1 (SMESG000077598.1)

HSP 1 Score: 49.6766 bits (117), Expect = 2.010e-6
Identity = 47/135 (34.81%), Postives = 67/135 (49.63%), Query Frame = 2 
Query:  224 LVFVLEESDNTSIKVLNLLSETSLN-KSFLT*LETRNFKIITFRKPLTSPVYDINEKP--------ISKTNKTIK*HQSLIVQPIMNIVAET------NISELEFSEFIGTMLP*NKQTDTVNELSTKHSLKLAL 583
            + F  ++ +NTS K+L+  + T+ N +     LETR FKI T  KPLT+ +   N  P        IS+ N TI            NI A+T       I+ L+F+E I   L  +KQ +T+ EL   HSLKL +
Sbjct:  175 IGFFSKKVENTSNKILSFRTRTACNARRNRNQLETRKFKIYTDHKPLTNAMQMKNPSPRQIRQLNYISQFNCTI------------NIAADTLSRIDTEINALDFNELIEADLIKSKQAETLKELPATHSLKLKI 297
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BLAST of SMED30020820 vs. Planmine SMEST
Match: SMESG000000071.1 (SMESG000000071.1)

HSP 1 Score: 45.4394 bits (106), Expect = 3.280e-6
Identity = 43/115 (37.39%), Postives = 59/115 (51.30%), Query Frame = 2 
Query:  299 KSFLT*LETRNFKIITFRKPLTSPVYDINEKP--------ISKTNKTIK*HQSLIVQPIMNIVAET------NISELEFSEFIGTMLP*NKQTDTVNELSTKHSLKLALKIHQIY 601
            K F   LE RNFKI T  KPL + +   N           IS+ N+TI       V    NIVA+T      +I+ +EF E I T     KQ++T+ EL  KHSL+L  KI++++
Sbjct:   45 KHFQHLLEARNFKIYTDHKPLINAMEMKNPSSKQIRQLNFISQFNRTIN-----YVTGATNIVADTLSRIGKDINTIEFCEIIKTEQIKTKQSETLKELPAKHSLQLE-KINELW 153

HSP 2 Score: 23.8682 bits (50), Expect = 3.280e-6
Identity = 12/19 (63.16%), Postives = 13/19 (68.42%), Query Frame = 1 
Query:  583 ENSSNL*LLKEFRNTCKAK 639
            ENS  L L  EFRNTC +K
Sbjct:  159 ENSPRLLLPIEFRNTCISK 177
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BLAST of SMED30020820 vs. Planmine SMEST
Match: SMESG000007179.1 (SMESG000007179.1)

HSP 1 Score: 48.9062 bits (115), Expect = 3.762e-6
Identity = 47/123 (38.21%), Postives = 63/123 (51.22%), Query Frame = 2 
Query:  275 LLSETSLNKSFLT*LETRNFKIITFRKPLTSPVYDINEKP--------ISKTNKTIK*HQSLIVQPIMNIVA------ETNISELEFSEFIGTMLP*NKQTDTVNELSTKHSLKLALKIHQIY 601
            LL+     K F   LE RNFKI T  KPL + +   N           IS+ N TI       V    NIVA      ET+I+ +EF E I T    N+Q++T+ EL TKHSL+L  KI++++
Sbjct:   92 LLAIHEAKKHFQHLLEARNFKIYTGHKPLINSMEMKNPSSRQIRQLNFISQFNCTIN-----YVIGATNIVADTLSRIETDINTIEFCEIIETAQIKNEQSETLKELPTKHSLQLQ-KINELW 208
The following BLAST results are available for this feature:
BLAST of SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 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 SMED30020820 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000077598.12.010e-634.81SMESG000077598.1[more]
SMESG000000071.13.280e-637.39SMESG000000071.1[more]
SMESG000007179.13.762e-638.21SMESG000007179.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020820 ID=SMED30020820|Name=SMED30020820|organism=Schmidtea mediterranea sexual|type=transcript|length=1096bp
AAATTACATCACCACACAGGTAAGGTGTGTGTATGTGTCTCTATAATGTA
ACGTTATTGATTTTTCATTTTATTACTGTAGTTGCTATTTAGCTGAAACA
GGTGTATTACAAATCCAGCAATTGCATCATTAGTCTTTATGTTAGAGTAA
AATGTAATGCAATTCGATTTGCAGGATGTTACAACACCATTTCGGTGTTT
TCTGGAGCAAACTTTTAAATAAATTAGTTTTTGTTCTCGAAGAAAGTGAT
AACACATCAATTAAAGTACTCAATCTTTTATCTGAAACTTCTCTCAATAA
ATCATTTCTAACATAACTGGAAACCAGAAATTTCAAAATCATAACATTTC
GTAAGCCACTAACAAGCCCGGTATACGATATAAATGAGAAACCCATCTCC
AAGACAAATAAGACAATTAAATGACATCAAAGTTTAATTGTACAACCAAT
TATGAACATTGTAGCAGAAACAAACATAAGCGAACTTGAATTTAGCGAAT
TCATTGGAACGATGTTGCCTTAAAACAAACAGACGGATACGGTCAATGAA
TTATCTACAAAACATAGCTTGAAATTGGCATTGAAAATTCATCAAATTTA
TAACTATTAAAGGAGTTCCGAAACACATGCAAAGCAAAATTCACAAAATC
AACTACCAAGGAAACAACGCAAAAAGCTAGTAGCCTAAAGTAGCCAACTA
TTTAAAATATAAAACCACTGCTTACAATAGAAATATCAGAAGGCCACATT
TAAATAATGTAAACGGACACAAATTGTTTAGAGCCACTACCGAAAGTGTT
ACCGGATCAAGAAATACTTGAAACTCTACCATCTCAAAAACCAGCAGATA
ACAGCATTCAAACAAAAAATACCTAAAAAAAGAATTCGAATATAAAAACA
GAGGACGTAACAGATGACTACGTATTAAAAAGACAGAAGATTTTAAAGTA
AAGTACAACACTAGATAAATCAATTCTCACACAAAAATATGAAAAATTTT
ACCTACATACAAGAAACTGTATAGTGATCGTTTCAAATAATACACAAACA
TCCAATCAATAAAAACAAATATTACTCGAGGAAATTATTTTCTCTG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell