SMED30006074

Overview
NameSMED30006074
Smed IDSMED30006074
Length (bp)339
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30006074 (SMED30006074) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006074 (SMED30006074) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30006074

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006074 Contig51224newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006074 Contig51224uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30006074 dd_Smed_v6_177_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30006074 dd_Smed_v4_177_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30006074 dd_Smed_v6_177_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30006074 dd_Smed_v6_177_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30006074 dd_Smed_v4_177_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
SMED30006074 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004658:9748..10122 +1428
Homology
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BLAST of SMED30006074 vs. Planmine SMEST
Match: SMESG000019341.1 (SMESG000019341.1)

HSP 1 Score: 98.2117 bits (243), Expect = 5.721e-28
Identity = 58/96 (60.42%), Postives = 63/96 (65.62%), Query Frame = 1 
Query:   49 MEFNVDDSKTDMGNQMRXEAINTIXGGFTKXRXNNXSREEYLCSXFXKXFXRXYIILSGIVXMGXRNXGSSVTHEKGTLIYGTTGDYGXMLWKAGQ 336
            MEFNVDDSKTDMGNQMR EAINTI         NN  +   +C+   K F   +      V MG +  GSSVTHEKGTLIYGTTGDYG MLWKAGQ
Sbjct:    1 MEFNVDDSKTDMGNQMREEAINTIMEALQNEENNNQEKN--ICAQIRKKFDELHYPQWHCV-MG-KKFGSSVTHEKGTLIYGTTGDYGLMLWKAGQ 92
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BLAST of SMED30006074 vs. Planmine SMEST
Match: SMESG000003270.1 (SMESG000003270.1)

HSP 1 Score: 80.1073 bits (196), Expect = 6.346e-21
Identity = 44/95 (46.32%), Postives = 58/95 (61.05%), Query Frame = 1 
Query:   49 MEFNVDDSKTDMGNQMRXEAINTIXGGFTKXRXNNXSREEYLCSXFXKXFXRXYIILSGIVXMGXRNXGSSVTHEKGTLIYGTTGDYGXMLWKAG 333
            MEF VD+SKTDM + MR EA+  I   F     +N  +E+ +C+   K F   +      + MG +  GSSV+HEKGTL+YG  GD+G MLWKAG
Sbjct:    1 MEFIVDESKTDMTDSMRIEALEAIRSAF--YNEDNNGQEKNICAEIRKKFDALHFPQWHCI-MG-KKFGSSVSHEKGTLLYGACGDHGLMLWKAG 91
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BLAST of SMED30006074 vs. Planmine SMEST
Match: SMESG000043382.1 (SMESG000043382.1)

HSP 1 Score: 44.669 bits (104), Expect = 5.412e-7
Identity = 27/97 (27.84%), Postives = 44/97 (45.36%), Query Frame = 1 
Query:   49 MEFNVDDSKTDMGNQMRXEAINTIXGGFTKXRXNNXSREEYLC--SXFXKXFXRXYIILSGIVXMGXRNXGSSVTHEKGTLIYGTTGDYGXMLWKAG 333
            M + ++  +TDM   ++  A   I    +  +  N  R   L         F   +  + G      +  G+S+THEK +L+Y TT DYG +L+K G
Sbjct:    1 MIYQIEIEQTDMPENVKNAAAKIIEQAVSNPKNQNVERNIALEIREKMNLDFKPQWQCIVG------KKYGTSITHEKESLMYATTNDYGILLFKGG 91
The following BLAST results are available for this feature:
BLAST of SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 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 SMED30006074 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000019341.15.721e-2860.42SMESG000019341.1[more]
SMESG000003270.16.346e-2146.32SMESG000003270.1[more]
SMESG000043382.15.412e-727.84SMESG000043382.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006074 ID=SMED30006074|Name=SMED30006074|organism=Schmidtea mediterranea sexual|type=transcript|length=339bp
AACTATTTAAATCGAATATCAACANGAGATTTCAATAATCATAGCAAAAT
GGAGTTTAATGTTGATGACAGTAAAACCGATATGGGCAATCAAATGAGGG
ANGAAGCCATCAATACAATCNATGGAGGCTTTACAAAANTGAGGNAAAAC
AATAANTCAAGAGAAGAATATTTGTGCTCAGNATTCGNCAAGAANTTTNG
ACGAANTTACATTATCCTCAGTGGCATTGTGTNGATGGGNNAAAGAAATT
NCGGAAGTAGTGTAACCCATGAAAAGGGTACTTTGATTTACGGAACTACC
GGAGATTACGGTTNGATGTTGTGGAAAGCCGGACAGTAA
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protein sequence of SMED30006074-orf-1

>SMED30006074-orf-1 ID=SMED30006074-orf-1|Name=SMED30006074-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
NYLNRISTXDFNNHSKMEFNVDDSKTDMGNQMRXEAINTIXGGFTKXRXN
NXSREEYLCSXFXKXFXRXYIILSGIVXMXXRNXGSSVTHEKGTLIYGTT
GDYGXMLWKAGQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000240body wall musculature
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR037177DLC_sf
IPR019763Dynein_light_1/2_CS
IPR001372Dynein_light_chain_typ-1/2
Vocabulary: cellular component
TermDefinition
GO:0005875microtubule associated complex
GO:0030286dynein complex
Vocabulary: biological process
TermDefinition
GO:0007017microtubule-based process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001372Dynein light chain, type 1/2SMARTSM01375Dynein_light_2coord: 16..106
e-value: 1.2E-21
score: 88.0
IPR001372Dynein light chain, type 1/2PFAMPF01221Dynein_lightcoord: 25..105
e-value: 1.3E-24
score: 86.3
IPR001372Dynein light chain, type 1/2PANTHERPTHR11886DYNEIN LIGHT CHAINcoord: 24..107
IPR037177Dynein light chain superfamilyGENE3DG3DSA:3.30.740.10coord: 24..107
e-value: 1.1E-24
score: 88.3
IPR037177Dynein light chain superfamilySUPERFAMILYSSF54648DLCcoord: 24..106
NoneNo IPR availablePANTHERPTHR11886:SF35DYNEIN LIGHT CHAIN 2, CYTOPLASMICcoord: 24..107
IPR019763Dynein light chain, type 1/2, conserved sitePROSITEPS01239DYNEIN_LIGHT_1coord: 73..87