SMED30029969

Overview
NameSMED30029969
Smed IDSMED30029969
Length (bp)524
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



SMED30029969

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cement glandSMED30029969SMESG000057760.1 GDAG01078994.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
vitelline glandSMED30029969SMESG000057760.1 GDAG01078994.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029969 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003035:17090..17613 +2593
Homology
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BLAST of SMED30029969 vs. Planmine SMEST
Match: SMESG000057760.1 (SMESG000057760.1)

HSP 1 Score: 223.016 bits (567), Expect = 8.093e-76
Identity = 130/130 (100.00%), Postives = 130/130 (100.00%), Query Frame = -1 
Query:   36 MQTFYKYEKKFLINSIMKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPHMNXXXXXXXXXXXXXXXKTYVNQLKTLSKK 425
            MQTFYKYEKKFLINSIMKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPHMNKFFAVAVDKDVKKSVKTYVNQLKTLSKK
Sbjct:    1 MQTFYKYEKKFLINSIMKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPHMNKFFAVAVDKDVKKSVKTYVNQLKTLSKK 130
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BLAST of SMED30029969 vs. Planmine SMEST
Match: SMESG000048474.1 (SMESG000048474.1)

HSP 1 Score: 136.346 bits (342), Expect = 1.347e-41
Identity = 66/100 (66.00%), Postives = 80/100 (80.00%), Query Frame = -1 
Query:  126 MQTFYKYEKKFLINSIMKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPH 425
            MQT YKYE KFL+N IMKQ VIFLLV IS FSPL A P NLC ++F+DN+IPFL+ KDVK AL K  K++++ EF+ LLCDLN++K KK EY+ ELNSPH
Sbjct:    1 MQTIYKYENKFLVNLIMKQFVIFLLVAISVFSPLFAKPSNLCNDKFADNEIPFLSEKDVKVALIKTMKQMTKTEFNTLLCDLNEIKEKKPEYMAELNSPH 100
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BLAST of SMED30029969 vs. Planmine SMEST
Match: SMESG000005261.1 (SMESG000005261.1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.136e-14
Identity = 35/87 (40.23%), Postives = 53/87 (60.92%), Query Frame = -1 
Query:  126 MKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYL---PELNSPH 377
            MK  + FL VVI+ F  LL      C ++F D DIPF   KD  +A+  +KK + + ++D+L+CD+N++K  KA+Y+     LNS H
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDH 87
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BLAST of SMED30029969 vs. Planmine SMEST
Match: SMESG000005262.1 (SMESG000005262.1)

HSP 1 Score: 64.3142 bits (155), Expect = 9.907e-14
Identity = 34/88 (38.64%), Postives = 54/88 (61.36%), Query Frame = -1 
Query:  123 MKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEY---LPELNSPHM 377
            MK  + FL VVI+ F  LL      C ++F D DIPF   KD  +A+  +KK + + ++D+L+CD+N++K  KA+Y   +  L+S H+
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHV 88
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BLAST of SMED30029969 vs. Planmine SMEST
Match: SMESG000048005.1 (SMESG000048005.1)

HSP 1 Score: 63.1586 bits (152), Expect = 2.891e-13
Identity = 33/83 (39.76%), Postives = 50/83 (60.24%), Query Frame = -1 
Query:  129 MKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSP 377
            M Q ++FL VV++ F  +L +    C   F D++I   T K +K  L KAKK IS+ EF++++CDLNKVK    +++    SP
Sbjct:    1 MNQRLLFLYVVVTIFLLILTESSTGCSENFKDDEIIGYTTKQIKVGLDKAKKVISKKEFNEIVCDLNKVKSMSRQFVNGKLSP 83
The following BLAST results are available for this feature:
BLAST of SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 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 SMED30029969 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057760.18.093e-76100.00SMESG000057760.1[more]
SMESG000048474.11.347e-4166.00SMESG000048474.1[more]
SMESG000005261.11.136e-1440.23SMESG000005261.1[more]
SMESG000005262.19.907e-1438.64SMESG000005262.1[more]
SMESG000048005.12.891e-1339.76SMESG000048005.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029969 ID=SMED30029969|Name=SMED30029969|organism=Schmidtea mediterranea sexual|type=transcript|length=524bp
CTAACAATTTTTTTAATTATATTCATTCTCAGTTACTTTTTAGAAAGGGT
CTTAAGCTGATTTACATATGTTTTCACCGATTTTTTAACATCTTTGTCAA
CAGCCACAGCGAAAAACTTATTCATATGCGGTGAATTGAGCTCTGGCAAG
TATTCGGCTTTCTTTCCTTTGACTTTGTTCAAGTCACACAGCAGTTGATC
GAATTCGGGTTCGCTTATTTCTTTCTTTGCTTTCCTCAAAGCATCTTTGA
CATCTTTCGCCGTAAGAAATGGAATATCATTGTCACTGAATTCATTTTTG
CATAAATTGTCAGGGTCAGCAAGAAGAGGCGAGAATTCGGAAATGACAAC
TAAAAGAAATATGACCAGTTGTTTCATAATTGAATTAATAAGAAATTTCT
TTTCGTATTTATAGAAAGTTTGCATAAGAACAACAAATTGAGCTCCTTTC
AGTATAATCTACTTTTGTTTATGGCATAATTTTGTATAATAGACTATTTA
TTTGTGAAATTTATGGAATGTCTG
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protein sequence of SMED30029969-orf-1

>SMED30029969-orf-1 ID=SMED30029969-orf-1|Name=SMED30029969-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MQTFYKYEKKFLINSIMKQLVIFLLVVISEFSPLLADPDNLCKNEFSDND
IPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPH
MNKFFAVAVDKDVKKSVKTYVNQLKTLSKK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000224cement gland
PLANA:0000231vitelline gland