SMED30023023

Overview
NameSMED30023023
Smed IDSMED30023023
Length (bp)316
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



SMED30023023

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
X2 cellSMED30023023 SmedASXL_077182SmedAsxl_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
SMED30023023 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003311:33565..33880 -1346
v31.000191:98421..98736 +1337
v31.000027:316350..316665 +1265
v31.023764:7259..7574 +1256
v31.000933:7737..8052 -1229
v31.039777:634..949 -1202
Homology
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BLAST of SMED30023023 vs. Planmine SMEST
Match: SMESG000002835.1 (SMESG000002835.1)

HSP 1 Score: 152.91 bits (385), Expect = 2.665e-44
Identity = 83/105 (79.05%), Postives = 90/105 (85.71%), Query Frame = -2 
Query:    1 YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLELDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRRCLPTDMDAE 315
            YQEFE+S  DPDI YAPRILFSSPPASIHINLVDE+NE   L+++LSDLELD +E A L   VPN+GPRGEIAGPSSRRDED RG PP YRPPKRRCLPTDMDAE
Sbjct: 1417 YQEFESSEFDPDICYAPRILFSSPPASIHINLVDEENEPPQLIRSLSDLELDLEEIATLMWEVPNIGPRGEIAGPSSRRDEDSRGDPPPYRPPKRRCLPTDMDAE 1521
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BLAST of SMED30023023 vs. Planmine SMEST
Match: SMESG000002835.1 (SMESG000002835.1)

HSP 1 Score: 152.91 bits (385), Expect = 2.881e-44
Identity = 83/105 (79.05%), Postives = 90/105 (85.71%), Query Frame = -2 
Query:    1 YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLELDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRRCLPTDMDAE 315
            YQEFE+S  DPDI YAPRILFSSPPASIHINLVDE+NE   L+++LSDLELD +E A L   VPN+GPRGEIAGPSSRRDED RG PP YRPPKRRCLPTDMDAE
Sbjct: 1436 YQEFESSEFDPDICYAPRILFSSPPASIHINLVDEENEPPQLIRSLSDLELDLEEIATLMWEVPNIGPRGEIAGPSSRRDEDSRGDPPPYRPPKRRCLPTDMDAE 1540
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BLAST of SMED30023023 vs. Planmine SMEST
Match: SMESG000071901.1 (SMESG000071901.1)

HSP 1 Score: 132.494 bits (332), Expect = 8.946e-41
Identity = 70/105 (66.67%), Postives = 81/105 (77.14%), Query Frame = -2 
Query:    1 YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLELDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRRCLPTDMDAE 315
            Y+EFE  G DPDI YAP+++FSSPP SIHINLVDED E   +++ L  L LD  E AVLTG V N+GPRGEIAGPSSR +++ RG PP YRP KRRCL TDMDAE
Sbjct:   54 YREFEALGFDPDILYAPQVMFSSPPESIHINLVDEDIEPPQMIRTLGRLGLDSGEIAVLTGEVLNLGPRGEIAGPSSRENDEHRGDPPPYRPTKRRCL-TDMDAE 157
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BLAST of SMED30023023 vs. Planmine SMEST
Match: SMESG000049314.1 (SMESG000049314.1)

HSP 1 Score: 118.242 bits (295), Expect = 4.110e-32
Identity = 58/96 (60.42%), Postives = 73/96 (76.04%), Query Frame = -2 
Query:   28 YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLELDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRR 315
            Y+EFE  G+DPDI YAPR++FSSPP SIHINLVDED E+  ++QAL  L LD +E A+LTG V NVG + EIAGPS+  + + + +PP YRP KRR
Sbjct:   41 YREFEIPGLDPDICYAPRVIFSSPPRSIHINLVDEDLESPQVVQALDRLGLDTNEIAILTGEVSNVGSQCEIAGPSTSTEGNHQANPPPYRPAKRR 136
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BLAST of SMED30023023 vs. Planmine SMEST
Match: SMESG000041233.1 (SMESG000041233.1)

HSP 1 Score: 115.546 bits (288), Expect = 1.995e-31
Identity = 57/105 (54.29%), Postives = 72/105 (68.57%), Query Frame = -2 
Query:    1 YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLELDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRRCLPTDMDAE 315
            YQEFE  G DPD+ YAP ++F SP  SIHINLVDE++E+  + QAL  L+LD  E A+L G VP +    E AGPS+R +     +PP YRP KRRCLPTD+D +
Sbjct:  399 YQEFEIPGFDPDVLYAPSVVFHSPARSIHINLVDEESESPRINQALDHLDLDLSEIAILMGNVPRISSPSEEAGPSTRTEVSYNTNPPPYRPAKRRCLPTDIDVD 503
The following BLAST results are available for this feature:
BLAST of SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 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 SMED30023023 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002835.12.665e-4479.05SMESG000002835.1[more]
SMESG000002835.12.881e-4479.05SMESG000002835.1[more]
SMESG000071901.18.946e-4166.67SMESG000071901.1[more]
SMESG000049314.14.110e-3260.42SMESG000049314.1[more]
SMESG000041233.11.995e-3154.29SMESG000041233.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023023 ID=SMED30023023|Name=SMED30023023|organism=Schmidtea mediterranea sexual|type=transcript|length=316bp
TTCCGCGTCCATATCCGTCGGGAGACATCTCCGTTTCGGCGGTCGGTATG
ATGGAGGATGGCCTCGAGGATCCTCGTCTCTCCGCGAGGAGGGTCCAGCT
ATTTCACCACGGGGGCCGACGTTGGGGACCGTTCCCGTGAGTACAGCATT
CTCATCGAAGTCCAACTCAAGGTCGCTTAGCGCCTGCATCAACGGGTGAG
CTTCATTATCCTCATCCACCAGGTTGATATGTATAGAAGCTGGGGGAGAG
GAGAATAGGATTCGCGGAGCATATCTGATGTCCGGGTCCATTCCCGAGTT
TTCGAACTCTTGGTAA
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protein sequence of SMED30023023-orf-1

>SMED30023023-orf-1 ID=SMED30023023-orf-1|Name=SMED30023023-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
YQEFENSGMDPDIRYAPRILFSSPPASIHINLVDEDNEAHPLMQALSDLE
LDFDENAVLTGTVPNVGPRGEIAGPSSRRDEDPRGHPPSYRPPKRRCLPT
DMDAE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell