SMED30005383

Overview
NameSMED30005383
Smed IDSMED30005383
Length (bp)1476
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30005383 (SMED30005383) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005383 (SMED30005383) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30005383

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30005383SMESG000040671.1 SmedASXL_048918SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30005383SMESG000040671.1 SmedASXL_079463SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005383SMESG000040671.1 SmedASXL_079463SmedAsxl_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
SMED30005383 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000850:41292..42684 -6519
Homology
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BLAST of SMED30005383 vs. Planmine SMEST
Match: SMESG000040682.1 (SMESG000040682.1)

HSP 1 Score: 226.483 bits (576), Expect = 1.220e-71
Identity = 108/124 (87.10%), Postives = 114/124 (91.94%), Query Frame = 1 
Query: 1105 EARSQEYAEMQKLYKKNISSATEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA*TEISTAEIFLAIR*MGKTAPGPDCIKYTKLKDNILSMAILFNTCLLTSFLP 1476
            EAR QEYAEMQKLYKKNISSA EKVIDGKW LRNE+Q+HSN++LIEAWRPIL+APPF+DCRPIEDQRN  Y   EISTAEIFLAIR MGKTAPGPD IKYTKLKDNILSMAILFNTCLLTSFLP
Sbjct:   55 EARKQEYAEMQKLYKKNISSAAEKVIDGKWSLRNEEQMHSNEELIEAWRPILDAPPFNDCRPIEDQRNTGYDLMEISTAEIFLAIRAMGKTAPGPDGIKYTKLKDNILSMAILFNTCLLTSFLP 178
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BLAST of SMED30005383 vs. Planmine SMEST
Match: SMESG000030694.1 (SMESG000030694.1)

HSP 1 Score: 229.95 bits (585), Expect = 6.619e-66
Identity = 139/258 (53.88%), Postives = 170/258 (65.89%), Query Frame = 1 
Query:  709 DINK-LSEKFTNRTMGSIKSKRTKDKIYHEMVRIDLLTSKENQSNEENRNIKGNDN-TDESKKEVLNYLEILLATNKEE*WLTPTLKEAAKLAVRGMKEEASKKLNEYASKTLFPGLXXXXXXXXXXXXXXXXXEARSQEYAEMQKLYKKNISSATEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA*TEISTAEIFLAIR*MGKTAPGPDCIKYTKLKDNILSMAILFNTCLLTSFLP 1476
            DINK L+E F NRTMGSIKSKRTKDK Y ++V++ + T  EN  NE + N    +N + +++KEV NYL +LL +N EE WLT TLKEAA LA++G K EAS+KLNEYASKTLFPGLK  +Q RKR+ K   + E R QEYAE+QKLYKKNISSA EK I+GKW ++ E++ H+NKDLI+AW+PILEAPPFSD                                            ++NI SMAILFNTCLLTSFLP
Sbjct:  129 DINKKLAEIFPNRTMGSIKSKRTKDKEYQDLVKLTMQTISENPDNETDFNTSNTENNSTDAEKEVKNYLNMLLLSNNEEEWLTSTLKEAATLALQGKKTEASEKLNEYASKTLFPGLKITNQTRKREKKISKR-ETRRQEYAEIQKLYKKNISSAAEKAINGKWSIKPEEEYHNNKDLIKAWKPILEAPPFSDS-------------------------------------------QENIQSMAILFNTCLLTSFLP 342

HSP 2 Score: 107.457 bits (267), Expect = 2.457e-24
Identity = 55/80 (68.75%), Postives = 69/80 (86.25%), Query Frame = 3 
Query:  366 EKAAPLRKLRWT*--KEIIIGAEIRILKEGSIKEQQEMNKILATKITGRTQDGIAKIRQKQEHRAEIQR*LNRTIATSET 599
            EKAAP +KLRWT   KEI+I +EI+I+KEGS+KEQ E+NKILA+++ GR+QDGIAKIRQKQEH+AEIQR L+ T+ T ET
Sbjct:    5 EKAAPTKKLRWTDEEKEILIESEIKIIKEGSLKEQHEINKILASRMPGRSQDGIAKIRQKQEHKAEIQRRLHGTVTTDET 84
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BLAST of SMED30005383 vs. Planmine SMEST
Match: SMESG000040671.1 (SMESG000040671.1)

HSP 1 Score: 182.956 bits (463), Expect = 3.954e-56
Identity = 94/110 (85.45%), Postives = 101/110 (91.82%), Query Frame = 1 
Query:  991 MKEEASKKLNEYASKTLFPGLXXXXXXXXXXXXXXXXXEARSQEYAEMQKLYKKNISSATEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA 1320
            MKEEASKKLNEYASKTLFPGLKT  +++++    P + EARSQ+YAEMQKLYKKNISSA EKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA
Sbjct:    1 MKEEASKKLNEYASKTLFPGLKTSQKRKRKLKSPPKR-EARSQQYAEMQKLYKKNISSAAEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA 109
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BLAST of SMED30005383 vs. Planmine SMEST
Match: SMESG000032594.1 (SMESG000032594.1)

HSP 1 Score: 102.449 bits (254), Expect = 8.404e-26
Identity = 51/55 (92.73%), Postives = 51/55 (92.73%), Query Frame = 1 
Query: 1309 MDYA*TEISTAEIFLAIR*MGKTAPGPDCIKYTKLKDNILSMAILFNTCLLTSFL 1473
            MDYA  EISTAEIFLAIR MGKTAPGPD IKYTKLKDNILSMAILFNTCLLTSFL
Sbjct:    1 MDYALMEISTAEIFLAIRAMGKTAPGPDGIKYTKLKDNILSMAILFNTCLLTSFL 55
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BLAST of SMED30005383 vs. Planmine SMEST
Match: SMESG000032556.1 (SMESG000032556.1)

HSP 1 Score: 88.1965 bits (217), Expect = 7.040e-20
Identity = 44/48 (91.67%), Postives = 44/48 (91.67%), Query Frame = 1 
Query: 1330 ISTAEIFLAIR*MGKTAPGPDCIKYTKLKDNILSMAILFNTCLLTSFL 1473
            I TAEIFLAIR MGKTAPGPD IKYTKLKDNILS AILFNTCLLTSFL
Sbjct:   17 IITAEIFLAIRAMGKTAPGPDGIKYTKLKDNILSTAILFNTCLLTSFL 64
The following BLAST results are available for this feature:
BLAST of SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 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 SMED30005383 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000040682.11.220e-7187.10SMESG000040682.1[more]
SMESG000030694.16.619e-6653.88SMESG000030694.1[more]
SMESG000040671.13.954e-5685.45SMESG000040671.1[more]
SMESG000032594.18.404e-2692.73SMESG000032594.1[more]
SMESG000032556.17.040e-2091.67SMESG000032556.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005383 ID=SMED30005383|Name=SMED30005383|organism=Schmidtea mediterranea sexual|type=transcript|length=1476bp
TTTCTTGTAAGGTAAAGGGTATGGAAATCCAGAGAATATCCTGTGGGCGA
TATCCACGGAAAAAGCACCTCGGCTCTGAAGGACTAACTATCCTAAAGCG
CTTAAATCTATGAACTGGTTACAACCAAAAAAACTACTAAAGAGTCAGGT
GCCACTGCGCCTGCACCAGTTCCCCTAGAAACTGCAGATGAGGTACTCCT
GTAACGGAATATTCCTGAAACCAATCTACCGCCGAATCGAATGGACGAAA
GACAGTCAACATCACCACAACACCGATGCGAAAACTGCGAAAGAAAATTC
AGTACCAAAGTAGGCCTTAAACAACATAGAAAAAAGGCCCACACCAACGA
GTTTATGAAGGATAAGAAAAAGCAGCACCATTAAGAAAACTTCGATGGAC
ATAAAAAGAAATTATCATTGGAGCGGAAATCAGAATCTTAAAAGAGGGAT
CAATAAAGGAACAACAAGAAATGAATAAAATACTCGCCACGAAAATAACT
GGAAGGACACAAGATGGAATAGCAAAGATTCGCCAGAAACAAGAACACAG
GGCAGAAATCCAGAGATGACTTAATAGAACCATAGCCACCAGTGAAACTA
TTGAAAGAGTCGAAACCGAGAGAGCTACCAACCAACAAAACCTGGAAGGA
GGAAGAAATAAAGAAATTACTTGAAGAGGAAGTCAAATTAAAACTGAATA
ACGAGAAAGACATTAACAAGTTGTCAGAAAAATTCACAAACAGAACTATG
GGATCCATAAAGAGCAAACGAACGAAGGATAAAATCTACCATGAGATGGT
ACGGATAGATCTACTTACATCAAAAGAAAATCAATCCAATGAAGAGAACA
GAAACATAAAAGGAAACGACAATACTGATGAATCCAAGAAAGAGGTCCTT
AACTACCTCGAAATATTACTAGCAACCAACAAAGAGGAATAGTGGTTAAC
ACCAACACTGAAGGAAGCAGCTAAACTAGCAGTGCGGGGTATGAAAGAAG
AAGCATCTAAAAAACTAAATGAATATGCCAGCAAAACTCTATTCCCAGGG
CTTAAAACACCAAGTCAGAAAAGAAAAAGAAAATCAAAAAGTCCACCTAA
ACGGGAAGCCAGAAGTCAAGAGTACGCCGAGATGCAGAAGCTGTACAAAA
AGAACATCTCAAGTGCAACTGAGAAAGTAATAGATGGGAAATGGTTTCTA
AGAAATGAAGATCAAGTGCATTCAAATAAAGATCTCATTGAAGCATGGAG
ACCGATACTGGAAGCCCCTCCATTCAGCGACTGTAGACCTATTGAAGACC
AACGAAATATGGACTACGCTTGAACGGAGATAAGCACAGCAGAGATATTC
CTCGCGATAAGATGAATGGGGAAGACTGCTCCAGGACCAGATTGCATAAA
ATATACGAAGCTAAAAGACAATATTCTGTCAATGGCAATTCTATTCAACA
CATGCCTACTGACAAGCTTCCTGCCA
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protein sequence of SMED30005383-orf-1

>SMED30005383-orf-1 ID=SMED30005383-orf-1|Name=SMED30005383-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MKEEASKKLNEYASKTLFPGLKTPSQKRKRKSKSPPKREARSQEYAEMQK
LYKKNISSATEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRP
IEDQRNMDYA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR013087Znf_C2H2_type
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0046872metal ion binding