SMED30029711

Overview
NameSMED30029711
Smed IDSMED30029711
Length (bp)1185
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30029711 (SMED30029711) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029711 (SMED30029711) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30029711 (SMED30029711) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029711 (SMED30029711) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30029711

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



PAGE Curations: 22

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30029711SMESG000039804.1 SMESG000039803.1 SmedASXL_005532SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30029711SMESG000039803.1 SmedASXL_006515SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30029711SMESG000039803.1 dd_Smed_v4_3788_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029711SMESG000039804.1 Contig54709newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029711SMESG000039804.1 Contig54709uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029711SMESG000039803.1 Contig42186newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029711SMESG000039803.1 Contig42186uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30029711SMESG000039804.1 dd_Smed_v6_5259_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30029711SMESG000039803.1 dd_Smed_v6_3788_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30029711SMESG000039804.1 dd_Smed_v4_5259_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029711SMESG000039803.1 dd_Smed_v4_3788_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
SMED30029711 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003798:33151..34423 -5805
Homology
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BLAST of SMED30029711 vs. Ensembl Human
Match: DYDC1 (DPY30 domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23460])

HSP 1 Score: 47.3654 bits (111), Expect = 1.362e-6
Identity = 22/42 (52.38%), Postives = 28/42 (66.67%), Query Frame = -1 
Query:   64 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVEN 189
            E+ +L  H+G  L  GLA +   RP DPIEYLA ++YKY EN
Sbjct:    2 ESIYLQKHLGACLTQGLAEVARVRPVDPIEYLALWIYKYKEN 43
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BLAST of SMED30029711 vs. Ensembl Human
Match: DYDC1 (DPY30 domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23460])

HSP 1 Score: 47.3654 bits (111), Expect = 6.854e-6
Identity = 22/42 (52.38%), Postives = 28/42 (66.67%), Query Frame = -1 
Query:   64 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVEN 189
            E+ +L  H+G  L  GLA +   RP DPIEYLA ++YKY EN
Sbjct:    2 ESIYLQKHLGACLTQGLAEVARVRPVDPIEYLALWIYKYKEN 43
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BLAST of SMED30029711 vs. TrEMBL
Match: A7RSS0 (Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g92230 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.844e-6
Identity = 27/45 (60.00%), Postives = 32/45 (71.11%), Query Frame = -1 
Query:   55 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENY 189
            ++E+L  HVG AL LGLA I   RP DPIEYLA +L KYVEN  +
Sbjct:    2 DSEYLKKHVGEALSLGLAEIVNKRPVDPIEYLAFWLRKYVENTEF 46
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BLAST of SMED30029711 vs. TrEMBL
Match: V4A1N7 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_229340 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 3.702e-6
Identity = 22/46 (47.83%), Postives = 34/46 (73.91%), Query Frame = -1 
Query:   43 FLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQV 180
            FL  HVG +L + LA +   RPKDPIEY+ ++L+ +++N+ +QKQV
Sbjct:    5 FLRKHVGESLVICLAEVAEKRPKDPIEYIGQWLHNHIKNQQHQKQV 50
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BLAST of SMED30029711 vs. TrEMBL
Match: A0A2B4RW87 (DPY30 domain-containing protein 1 OS=Stylophora pistillata OX=50429 GN=Dydc1 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 4.811e-6
Identity = 28/47 (59.57%), Postives = 33/47 (70.21%), Query Frame = -1 
Query:   46 AEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQ 186
            +E+L  HVG AL  GLA I   RP DPIEYLA +L KYVENE + K+
Sbjct:    3 SEYLKKHVGKALASGLAEIAEKRPVDPIEYLAHWLRKYVENEEFAKK 49
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BLAST of SMED30029711 vs. TrEMBL
Match: A0A3M6TVQ4 (Uncharacterized protein OS=Pocillopora damicornis OX=46731 GN=pdam_00024773 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 5.395e-6
Identity = 28/49 (57.14%), Postives = 34/49 (69.39%), Query Frame = -1 
Query:   40 AEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQVM 186
            +E+L  HVG AL  GLA I   RP DPIEYLA +L KYVENE + K+ +
Sbjct:    3 SEYLKKHVGKALASGLAEIAEKRPVDPIEYLAHWLRKYVENEEFAKKEL 51
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BLAST of SMED30029711 vs. Ensembl Nematostella
Match: EDO45464 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RSS0])

HSP 1 Score: 55.8398 bits (133), Expect = 2.549e-10
Identity = 27/45 (60.00%), Postives = 32/45 (71.11%), Query Frame = -1 
Query:   55 EAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENY 189
            ++E+L  HVG AL LGLA I   RP DPIEYLA +L KYVEN  +
Sbjct:    2 DSEYLKKHVGEALSLGLAEIVNKRPVDPIEYLAFWLRKYVENTEF 46
[Close]
BLAST of SMED30029711 vs. Planmine SMEST
Match: SMESG000039804.1 (SMESG000039804.1)

HSP 1 Score: 251.136 bits (640), Expect = 1.424e-83
Identity = 120/121 (99.17%), Postives = 121/121 (100.00%), Query Frame = 3 
Query:  723 MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDNQNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW 1085
            MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISND+QNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW
Sbjct:    1 MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDSQNSCDNNKLYQTGCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFERIKIKNPEPVEQISEYNRRFVW 121
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BLAST of SMED30029711 vs. Planmine SMEST
Match: SMESG000039803.1 (SMESG000039803.1)

HSP 1 Score: 143.665 bits (361), Expect = 1.292e-40
Identity = 68/80 (85.00%), Postives = 73/80 (91.25%), Query Frame = -1 
Query:    4 MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQVMLSVIHVNS*ILV 243
            MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQ+ +   ++   IL+
Sbjct:    1 MSIGSRSATSYSQQTANKEAEFLIDHVGTALQLGLAAIQTYRPKDPIEYLARYLYKYVENENYQKQMEMDEYNLQQEILL 80
The following BLAST results are available for this feature:
BLAST of SMED30029711 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
DYDC11.362e-652.38DPY30 domain containing 1 [Source:HGNC Symbol;Acc:... [more]
DYDC16.854e-652.38DPY30 domain containing 1 [Source:HGNC Symbol;Acc:... [more]
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BLAST of SMED30029711 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 SMED30029711 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 SMED30029711 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 SMED30029711 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 SMED30029711 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 SMED30029711 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 SMED30029711 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A7RSS01.844e-660.00Predicted protein (Fragment) OS=Nematostella vecte... [more]
V4A1N73.702e-647.83Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A2B4RW874.811e-659.57DPY30 domain-containing protein 1 OS=Stylophora pi... [more]
A0A3M6TVQ45.395e-657.14Uncharacterized protein OS=Pocillopora damicornis ... [more]
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BLAST of SMED30029711 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 SMED30029711 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 SMED30029711 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 SMED30029711 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO454642.549e-1060.00Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30029711 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 SMED30029711 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000039804.11.424e-8399.17SMESG000039804.1[more]
SMESG000039803.11.292e-4085.00SMESG000039803.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029711 ID=SMED30029711|Name=SMED30029711|organism=Schmidtea mediterranea sexual|type=transcript|length=1185bp
TAAAACTAAAATTCAGGAATTGACATGAATGACTGATAACATTACTTGCT
TCTGATAATTTTCATTTTCAACATATTTGTAGAGATATCTCGCTAAGTAT
TCTATTGGATCTTTTGGCCGATACGTTTGGATAGCAGCTAATCCTAATTG
CAGAGCCGTACCGACGTGATCAATGAGAAATTCTGCTTCCTTGTTGGCTG
TTTGTTGAGAATAAGACGTAGCTGATCGCGAACCGATAGACATTTCAAAT
TATTTTTCGATTTTGACAGAGTATTTAAAAAATAACAAGCATATAGTCAA
TAACAACGCATTGATGCTTGTTGTCTTGGTGATTGTTATCGTATTGTGTC
CATGAACAATAGGCATGCAACACACACTATTGTGTATCGGTTTCACAATC
AATCTAAAAGCATCAAAAGATAATGGAATATCGCCTTGAAAAATTAATTC
CTGATTCATAATAAATTATACTTGATTAATATTTCTAAAAGATAAATATT
AAACTCCGAGAAAAAATTTAAGAATTTTACTTAATTAGTCTGTTGGATAT
TAGTATGATTTTGAAATTGTTCTTTAAATCAAATAGCCAATCAAAATTCA
GATCTGTGAAGTTGTTATGGCAACGATAACAGACTGATTTCAATTTTAAT
CGTTTTTAATTTCTATTACGATACTCGTCACTTTAATAAGATTTTTCAGT
AATTGATTGTAATTGAAAATCCATGGAATTATCACGATCAAAAGAGGTAA
AATTCAATGAGGAAATAATAGAACTGCCTGCCAGTCCTAGATTCAATTTA
TCCACAAGTCATAGAGAATTTATTTCCAATGATAATCAAAATTCCTGCGA
TAACAATAAATTATATCAAACTGGTTGTGTCGGTCGGACCCCACAAGAGA
TGGCAGGTATTATGGTCAATTATCCCGGAATAACAGAACATAAACGCCGC
TATAAATGGCCTCATGGAGACATTGAATTTGAAAGCATCATCAATCCCGG
CTATGAAGGTCTGTTTGAAAGAATCAAAATCAAAAACCCAGAGCCTGTGG
AACAAATATCGGAATATAATAGGAGATTTGTGTGGCCATAATGACCAATT
AACTATAAATACTTTACAAGGATATTTTGTTGTATTATTAGATTAATTGA
AATATCAATGAAATAAAATAAAAAGTGATGTTTTC
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protein sequence of SMED30029711-orf-1

>SMED30029711-orf-1 ID=SMED30029711-orf-1|Name=SMED30029711-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MELSRSKEVKFNEEIIELPASPRFNLSTSHREFISNDNQNSCDNNKLYQT
GCVGRTPQEMAGIMVNYPGITEHKRRYKWPHGDIEFESIINPGYEGLFER
IKIKNPEPVEQISEYNRRFVWP*
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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:0000099neuron
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR007858Dpy-30_motif