SMED30005306

Overview
NameSMED30005306
Smed IDSMED30005306
Length (bp)340
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



SMED30005306

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
X1 cellSMED30005306 SmedASXL_061098SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005306 SmedASXL_061098SmedAsxl_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
SMED30005306 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.020937:9863..10202 +1700
v31.005420:14803..15142 +1700
v31.002204:35737..36077 -1436
v31.000076:207078..207418 -1400
v31.001783:68240..68580 -1355
v31.008059:2696..3033 +1283
v31.000833:147944..148288 -1257
Homology
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BLAST of SMED30005306 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 96.2857 bits (238), Expect = 4.037e-25
Identity = 75/90 (83.33%), Postives = 80/90 (88.89%), Query Frame = -1 
Query:   71 QPTSIPAQINITMDNHSFEMPINMQISIASRTTPNRDAXXXXXXXXXXXSVVESTIYRDQRANNLPRAXXXXXXXXXXXKYLPVYIDEED 340
            QP  IPAQINITMDN+S EM INMQISIASRTTP+RDAISSG SSPQIISV+E TI R QR++NLPRA SSSTTRPPKRKYLPV IDEED
Sbjct:  207 QPAPIPAQINITMDNYSAEMLINMQISIASRTTPDRDAISSGRSSPQIISVIEPTINRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEED 296
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BLAST of SMED30005306 vs. Planmine SMEST
Match: SMESG000042773.1 (SMESG000042773.1)

HSP 1 Score: 65.0846 bits (157), Expect = 4.466e-14
Identity = 53/90 (58.89%), Postives = 65/90 (72.22%), Query Frame = -1 
Query:   71 QPTSIPAQINITMDNHSFEMPINMQISIASRTTPNRDAXXXXXXXXXXXSVVESTIYRDQRANNLPRAXXXXXXXXXXXKYLPVYIDEED 340
             P   PAQI IT ++HS E PIN+QIS +SRTTP+++  SSG SSPQIISVVE TI R+QR NN  +   +  +R PKR+YLPV ID ED
Sbjct:  105 HPVPTPAQITITTNSHSAEAPINIQISTSSRTTPDQEFPSSGRSSPQIISVVEPTITRNQRVNNSNQTDPNPISRSPKRRYLPVDIDGED 194
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BLAST of SMED30005306 vs. Planmine SMEST
Match: SMESG000026554.1 (SMESG000026554.1)

HSP 1 Score: 63.929 bits (154), Expect = 6.012e-14
Identity = 43/67 (64.18%), Postives = 53/67 (79.10%), Query Frame = -1 
Query:  140 QPTSIPAQINITMDNHSFEMPINMQISIASRTTPNRDAXXXXXXXXXXXSVVESTIYRDQRANNLPR 340
            QP   PAQI IT  +HS E+PI++QIS +SRTTP+R+A SSG  SPQIISV+E T+ R+QRANNL R
Sbjct:   69 QPVPSPAQITITTGSHSAEIPISIQISTSSRTTPDRNAPSSGRYSPQIISVIEPTVSRNQRANNLHR 135
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BLAST of SMED30005306 vs. Planmine SMEST
Match: SMESG000057066.1 (SMESG000057066.1)

HSP 1 Score: 62.3882 bits (150), Expect = 4.479e-13
Identity = 53/89 (59.55%), Postives = 65/89 (73.03%), Query Frame = -1 
Query:   71 SIP--AQINITMDNHSFEMPINMQISIASRTTPNRDAXXXXXXXXXXXSVVESTIYRDQRANNLPRAXXXXXXXXXXXKYLPVYIDEED 331
            S+P  AQI IT  +HS E+PIN+ IS +SRTTP+RD  SSG   PQIISVVE T+ R+Q A+N  +  S+ TTRP KR+YLPV ID ED
Sbjct:  107 SVPTLAQITITTSSHSAEVPINIHISTSSRTTPDRDVPSSGRFLPQIISVVEPTVSRNQMASNFHQTGSNPTTRPSKRRYLPVDIDGED 195
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BLAST of SMED30005306 vs. Planmine SMEST
Match: SMESG000068296.1 (SMESG000068296.1)

HSP 1 Score: 56.6102 bits (135), Expect = 6.911e-11
Identity = 46/83 (55.42%), Postives = 58/83 (69.88%), Query Frame = -1 
Query:   71 QINITMDNHSFEMPINMQISIASRTTPNRDAXXXXXXXXXXXSVVESTIYRDQRANNLPRAXXXXXXXXXXXKYLPVYIDEED 319
            QI IT  +HS E+PIN+ I  +SR TP+RD  +SG S PQIISVVE T+ R+Q A+N  +   +  TRP KR+YLPV ID ED
Sbjct:  113 QITITTSSHSAEVPINIHIPTSSRKTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRPSKRRYLPVDIDGED 195
The following BLAST results are available for this feature:
BLAST of SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 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 SMED30005306 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046646.14.037e-2583.33SMESG000046646.1[more]
SMESG000042773.14.466e-1458.89SMESG000042773.1[more]
SMESG000026554.16.012e-1464.18SMESG000026554.1[more]
SMESG000057066.14.479e-1359.55SMESG000057066.1[more]
SMESG000068296.16.911e-1155.42SMESG000068296.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005306 ID=SMED30005306|Name=SMED30005306|organism=Schmidtea mediterranea sexual|type=transcript|length=340bp
GAAATATAAATATTAAAAGGTTCGTCACAGAAGAACGCAGTTTTCATTAA
TACATCAGTCGCTTCCATCAATCTTCTTCATCAATATACACCGGTAAATA
TTTTCTTTTGGGTGGCCTTGTCGTGGAGCTCGAAGAGGCTCGTGGAAGAT
TGTTAGCCCTCTGGTCTCGATATATCGTCGACTCAACGACGGAGATGATT
TGTGGCGAAGATCACCCGCTGGATATTGCGTCTCTGTTGGGAGTCGTCCG
AGAAGCGATGGAAATCTGCATATTTATTGGCATTTCAAACGAGTGATTGT
CCATGGTGATGTTGATTTGCGCTGGTATGGAAGTTGGTTG
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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