X1.A.G7.1

Overview
NameX1.A.G7.1
Smed IDSMED30001543
Length (bp)989
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 X1.A.G7.1 (SMED30001543) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30001543) 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 X1.A.G7.1 (SMED30001543) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30001543) 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



SMED30001543

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30001543SMESG000046822.1 SmedASXL_010397SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30001543SMESG000046822.1 dd_Smed_v4_7962_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001543SMESG000046822.1 dd_Smed_v4_7962_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30001543SMESG000046822.1 dd_Smed_v4_7962_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30001543SMESG000046822.1 dd_Smed_v4_7962_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001543SMESG000046822.1 dd_Smed_v4_7962_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001543SMESG000046822.1 Contig41695newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001543SMESG000046822.1 Contig41695uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30001543SMESG000046822.1 dd_Smed_v6_7962_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30001543SMESG000046822.1 OX_Smed_1.0.16207ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of X1.A.G7.1 vs. TrEMBL
Match: V9XRT9 (X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 3.699e-6
Identity = 55/198 (27.78%), Postives = 89/198 (44.95%), Query Frame = 2 
Query:  194 GYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVASFAQSTNNCEVMNCLISGPYVRSLPALGXXXXXXXXXXXXXXXWDSSLKCGDVCC 787
            G + DQ     P    QP +  +  T  + + +  GP  + + +             SK H I+G + I  G  ++ IDPLLP + +Y +SI   G+FM+ISGI SI   +R  K  L+ +   NI A I I  G ++ +L  +      N  ++  +  G    SL  L              +I++S+L C ++CC
Sbjct:    7 GDIYDQLSSSPPEYSQQPTNLLINSTGIHSDQVQDGPVRLVL-LESKEIRSGSKFINSKSHRIFGYILIACGIFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAILYGTAFYHRQNGILIFTVFYGILTMSLLVL--------------LIFNSALICKEICC 189
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BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046822.1 (SMESG000046822.1)

HSP 1 Score: 360.918 bits (925), Expect = 9.312e-127
Identity = 189/193 (97.93%), Postives = 191/193 (98.96%), Query Frame = 2 
Query:   65 MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVASFAQSTN 643
            MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSIILGGIIMIIDPLLPAIFQYIYSIFCVGLFMMISGICSILGSR+QNKCCLVASLTFNIF SILIFAGYVIGLLVASFAQ+T 
Sbjct:    1 MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSIILGGIIMIIDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRKQNKCCLVASLTFNIFGSILIFAGYVIGLLVASFAQTTK 193
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BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046822.1 (SMESG000046822.1)

HSP 1 Score: 304.294 bits (778), Expect = 5.900e-105
Identity = 160/161 (99.38%), Postives = 161/161 (100.00%), Query Frame = 2 
Query:   65 MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCL 547
            MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSIILGGIIMIIDPLLPAIFQYIYSIFCVGLFMMISGICSILGSR+QNKCCL
Sbjct:    1 MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQTEKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSIILGGIIMIIDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRKQNKCCL 161
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BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046819.1 (SMESG000046819.1)

HSP 1 Score: 121.709 bits (304), Expect = 1.334e-32
Identity = 90/216 (41.67%), Postives = 136/216 (62.96%), Query Frame = 2 
Query:  185 ANPGYVSDQ------TEKHMPINYN--QPPSYT-VAQTPFNQNIILVGPSNIQ-MAMNQVNTEQIYD--MRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVAS----FAQSTNNCEVMNCLISGPYVRSLPALGXXXXXXXXXXXXXXXWDSSLKCGDVC 784
            +N G+ +++      +++H    +    PP+Y  + ++P     + + P   + +A+    TE+  +  +RY ++HLIYGT+S++LGGI + IDP+LP+IFQY YS++  GLFM+ISG+CSI GSR+ NKC L+ASL FNI A I+IF  Y+IG+L ++    F    N    +       Y   +  L IFN +FG+I+FV +IWDSSLKCGDVC
Sbjct:    4 SNAGFTTEEYAIILNSDRHNLQTFEPLSPPNYNDIVKSPLTGPTLSIPPPQYEGIAVPPQTTEESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGILASNQSGFFFTPCNQYNAICYPSVSFYTEGVKGLAIFNVVFGMILFVLMIWDSSLKCGDVC 219
[Close]
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046815.1 (SMESG000046815.1)

HSP 1 Score: 120.553 bits (301), Expect = 3.424e-32
Identity = 91/219 (41.55%), Postives = 136/219 (62.10%), Query Frame = 2 
Query:  185 ANPGYVSDQ------TEKHMPINYN--QPPSYT-VAQTPFNQNIILVGPSNIQ-MAMNQVNTEQIYD--MRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVAS----FAQSTNNCEVMNCLISGPYVRSLPALGXXXXXXXXXXXXXXXWDSSLKCGDVCCIK 793
            +N G+ +++      +++H    +    PP+Y  + ++P     + + P   + +A+    TE+  +  +RY ++HLIYGT+S++LGGI + IDP+LP+IFQY YS++  GLFM+ISG+CSI GSR+ NKC L+ASL FNI A I+IF  Y+IG+L ++    F    N    +       Y   +    IFN +FGII+FV +IWDSSLKCGDVC  K
Sbjct:    4 SNAGFTTEEYAIILNSDRHNLQTFEPLSPPNYNDIVKSPLTGPTLSIPPPQYEGIAVPPQTTEESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGILASNQSGFFFTPCNQYNAICYPSVSFYTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKK 222
[Close]
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046812.1 (SMESG000046812.1)

HSP 1 Score: 119.013 bits (297), Expect = 1.307e-31
Identity = 88/191 (46.07%), Postives = 120/191 (62.83%), Query Frame = 2 
Query:  245 PPSYT-VAQTPFNQNIILVGP---SNIQMAMNQVNTEQIYDMRYSKLHLIYGTMSXXXXXXXXXXDPLLPAIFQYIYSIFCVGLFMMISGICSILGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVASFAQ-STNNCEVMNCLI---SGPYVRSLPALGXXXXXXXXXXXXXXXWDSSLKCGDVCCIK 793
            PP+Y  + ++P N   + + P     I +        Q   +RY ++HLIYGT+ ++LGGI + IDP+LP+IFQY YS++  GLFM+ISG+CSI GSR+ NKC L+ASL FNI A I+IF  Y+IG+L  + +  S   C   N +       Y   +    IFN +FGII+FV +IWDSSLKCGDVC  K
Sbjct:   32 PPNYNDIVKSPLNGPTLSIPPPQYEGIVVPPQTTEESQNSMLRYKRMHLIYGTIYVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILAMIVIFTNYIIGILALNQSGFSFTPCNQYNSICYPSVSFYTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKK 222
The following BLAST results are available for this feature:
BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRT93.699e-627.78X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=... [more]
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BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046822.19.312e-12797.93SMESG000046822.1[more]
SMESG000046822.15.900e-10599.38SMESG000046822.1[more]
SMESG000046819.11.334e-3241.67SMESG000046819.1[more]
SMESG000046815.13.424e-3241.55SMESG000046815.1[more]
SMESG000046812.11.307e-3146.07SMESG000046812.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001543 ID=SMED30001543|Name=X1.A.G7.1|organism=Schmidtea mediterranea sexual|type=transcript|length=989bp
TTTTAAATTACTGGATTTTTTAATTATAAGATTATATTTATATATTATAG
GTTAAAAAATTACAATGGAAAATCCTAATTCGGTTGTTCCTGGTTCACAG
CCTCCTCCGTATATCTATGCTGATCCCAATAATGGTGGGAACTACAATCA
AATGCCAACTCAAACTTATTCTTATTTGCCATACGCAAATCCTGGATATG
TATCTGATCAAACGGAAAAGCATATGCCTATTAATTACAACCAACCTCCA
AGTTACACTGTAGCACAAACACCATTCAACCAAAATATAATCTTAGTTGG
TCCGTCAAACATTCAAATGGCAATGAATCAAGTCAACACTGAACAGATTT
ACGATATGAGATACTCGAAACTGCACCTGATTTATGGGACGATGTCAATC
ATTCTCGGGGGAATAATAATGATAATTGACCCCCTTTTGCCGGCGATTTT
TCAATACATTTATTCAATATTTTGTGTTGGCTTGTTCATGATGATCAGCG
GAATTTGTTCAATCCTTGGGAGCAGGAGGCAGAATAAATGCTGTTTGGTA
GCCTCTCTGACTTTCAATATTTTTGCATCTATACTGATTTTTGCAGGATA
CGTAATCGGATTATTGGTTGCGTCATTTGCCCAGAGCACTAACAATTGTG
AAGTTATGAATTGTCTAATAAGTGGGCCGTATGTGAGATCTCTTCCTGCT
TTGGGAATTTTCAATAGTATCTTTGGGATAATTATCTTTGTTTTTATTAT
TTGGGATTCGAGCCTGAAATGTGGAGACGTTTGCTGCATCAAAATGATTA
CAAGAGCAATTGCAAGTAGTCCCAACATCGAGGTGATCAACAATGTTTCG
TAGGGCCCCCAGAGCATTAATATAATATCAAGATGACTTATATTTTATTA
GATCTGACTATAAACTGTTATTTTTGAATTAGTTCTTGACACCTTCAACA
CTATTGTGCATTGATATTAAACAATTTATTTAATAAAAC
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protein sequence of SMED30001543-orf-1

>SMED30001543-orf-1 ID=SMED30001543-orf-1|Name=SMED30001543-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
MLWGPYETLLITSMLGLLAIALVIILMQQTSPHFRLESQIIKTKIIIPKI
LLKIPKAGRDLTYGPLIRQFITSQLLVLWANDATNNPITYPAKISIDAKI
LKVREATKQHLFCLLLPRIEQIPLIIMNKPTQNIE*
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protein sequence of SMED30001543-orf-2

>SMED30001543-orf-2 ID=SMED30001543-orf-2|Name=SMED30001543-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=263bp
MENPNSVVPGSQPPPYIYADPNNGGNYNQMPTQTYSYLPYANPGYVSDQT
EKHMPINYNQPPSYTVAQTPFNQNIILVGPSNIQMAMNQVNTEQIYDMRY
SKLHLIYGTMSIILGGIIMIIDPLLPAIFQYIYSIFCVGLFMMISGICSI
LGSRRQNKCCLVASLTFNIFASILIFAGYVIGLLVASFAQSTNNCEVMNC
LISGPYVRSLPALGIFNSIFGIIIFVFIIWDSSLKCGDVCCIKMITRAIA
SSPNIEVINNVS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR007237CD20-like