SMED30000288

Overview
NameSMED30000288
Smed IDSMED30000288
Length (bp)307
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



SMED30000288

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30000288h1SMcG0013723 Contig54038newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000288h1SMcG0013723 Contig54038uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30000288h1SMcG0013723 dd_Smed_v4_9081_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30000288h1SMcG0013723 dd_Smed_v4_9081_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000288h1SMcG0013723 dd_Smed_v4_9081_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30000288h1SMcG0013723 dd_Smed_v4_9081_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000288 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001422:78704..79010 +1265
v31.022492:10270..10574 -1202
v31.004345:16838..17139 -1195
v31.010544:15203..15500 -1024
v31.012562:9900..10164 +781
v31.007204:17722..18081 -726
Homology
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BLAST of SMED30000288 vs. Planmine SMEST
Match: SMESG000054890.1 (SMESG000054890.1)

HSP 1 Score: 90.8929 bits (224), Expect = 1.027e-24
Identity = 46/59 (77.97%), Postives = 49/59 (83.05%), Query Frame = 1 
Query:  130 MKGRPSVVIKIQNQEMDCLLDSVATVNAMSLNQFKKFNNIELMKTADILRSTNDNELET 306
            MKGR SVVIKIQNQE+DCL DS AT   +SLNQFKK NNIEL+KTA ILR  NDNELET
Sbjct:    1 MKGRLSVVIKIQNQEIDCLFDSGATECILSLNQFKKINNIELIKTASILRCANDNELET 59
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BLAST of SMED30000288 vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 75.0998 bits (183), Expect = 4.242e-17
Identity = 40/105 (38.10%), Postives = 68/105 (64.76%), Query Frame = 1 
Query:    1 VEKVNRFVQKNFEVIERCENL---EQRSAEILSIDKMRSNIIRYDTMKGRPSVVIKIQNQEMDCLLDSVATVNAMSLNQFKKFNNIELMKTADILRSTNDNELET 306
            +EK+ +F++KN +V   C N    + R   ILS+++ +S  I Y+ M+GRPS  + IQ +++DCLLD+ A +N M+ +   +  NIE+++T + LR  N++ LET
Sbjct: 2503 IEKIYKFLKKNGDV---CINEIVEDTREQNILSVEEQKSPAITYNIMQGRPSTTLDIQGRKVDCLLDTGARINVMAKSVIDRLENIEILETRESLRCANNSRLET 2604
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BLAST of SMED30000288 vs. Planmine SMEST
Match: SMESG000006000.1 (SMESG000006000.1)

HSP 1 Score: 65.4698 bits (158), Expect = 1.178e-14
Identity = 32/44 (72.73%), Postives = 36/44 (81.82%), Query Frame = 1 
Query:  175 MDCLLDSVATVNAMSLNQFKKFNNIELMKTADILRSTNDNELET 306
            M  LLDS ATVN MSLNQ+K+F NIELMKTA+IL+  NDNELE 
Sbjct:    1 MGSLLDSGATVNVMSLNQYKRFINIELMKTANILKCGNDNELEA 44
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BLAST of SMED30000288 vs. Planmine SMEST
Match: SMESG000053025.1 (SMESG000053025.1)

HSP 1 Score: 48.9062 bits (115), Expect = 5.348e-8
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 1 
Query:  175 MDCLLDSVATVNAMSLNQFKKFNNIELMKTADILRSTNDNELET 306
            M+CLLD+ A VN MS ++F+   +IEL+ T DILR  N+  LET
Sbjct:    1 MECLLDTGAKVNVMSWSKFENLKDIELIATTDILRCANNFVLET 44
[Close]
BLAST of SMED30000288 vs. Planmine SMEST
Match: SMESG000077872.1 (SMESG000077872.1)

HSP 1 Score: 47.3654 bits (111), Expect = 1.744e-7
Identity = 33/89 (37.08%), Postives = 53/89 (59.55%), Query Frame = 1 
Query:   55 ENLEQRSAEILSI----DKMRS--NIIRYDTMKGRPSVVIKIQNQEMDCLLDSVATVNAMSLNQFKKFNNIELMKTADI-LRSTNDNEL 300
            +NL + S E L +    DK +   +II+YD +KGRPS+ + I  +   CLLD+ A ++ + LN   K N +  +KT++I +R  ND+ L
Sbjct:   66 DNLNEISFEKLLVMNKNDKFKEIESIIKYDIIKGRPSINVTIDGKCCRCLLDTGANISVLDLNLIGK-NQMNKIKTSNIKVRCANDSPL 153
The following BLAST results are available for this feature:
BLAST of SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 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 SMED30000288 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054890.11.027e-2477.97SMESG000054890.1[more]
SMESG000029259.14.242e-1738.10SMESG000029259.1[more]
SMESG000006000.11.178e-1472.73SMESG000006000.1[more]
SMESG000053025.15.348e-852.27SMESG000053025.1[more]
SMESG000077872.11.744e-737.08SMESG000077872.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000288 ID=SMED30000288|Name=SMED30000288|organism=Schmidtea mediterranea sexual|type=transcript|length=307bp
GTTGAAAAAGTTAATAGGTTTGTTCAAAAGAACTTTGAGGTGATTGAGAG
ATGTGAAAATTTGGAACAGAGAAGTGCGGAGATATTGTCAATAGATAAAA
TGAGGTCGAATATTATCAGGTATGACACAATGAAAGGTAGACCTAGTGTA
GTAATCAAAATTCAAAATCAGGAAATGGATTGTTTACTTGATTCTGTAGC
AACAGTAAACGCAATGAGCTTGAACCAGTTCAAAAAATTTAATAATATAG
AGCTTATGAAGACGGCAGATATTTTAAGATCCACAAATGATAATGAATTG
GAAACAA
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protein sequence of SMED30000288-orf-1

>SMED30000288-orf-1 ID=SMED30000288-orf-1|Name=SMED30000288-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
VEKVNRFVQKNFEVIERCENLEQRSAEILSIDKMRSNIIRYDTMKGRPSV
VIKIQNQEMDCLLDSVATVNAMSLNQFKKFNNIELMKTADILRSTNDNEL
ET
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