SMED30013279

Overview
NameSMED30013279
Smed IDSMED30013279
Length (bp)708
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



SMED30013279

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30013279 dd_Smed_v4_51110_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013279 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000266:71530..72385 -3534
v31.000548:89279..90148 +2432
Homology
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BLAST of SMED30013279 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 95.1301 bits (235), Expect = 1.527e-29
Identity = 54/87 (62.07%), Postives = 62/87 (71.26%), Query Frame = -2 
Query:  333 ELTPQLSTNERQSISRRLAPEQQRQIIQFSSTAAAQ*RQIL*DYGY*VSTPGDTK*RARLGLIKDIDLRGIIIKKRPDGTQPERLAR 593
            ELTPQLSTN RQS  RR  P  +R+IIQFSSTA+AQ R IL DY Y VSTPGD+   AR GLI+D+D+ GI IK+ P G  P R  R
Sbjct:    4 ELTPQLSTNGRQSTVRRHVPGPEREIIQFSSTASAQCRHILWDYEYSVSTPGDSTLPARPGLIEDLDIPGIAIKREP-GRNPARETR 89

HSP 2 Score: 52.7582 bits (125), Expect = 1.527e-29
Identity = 37/52 (71.15%), Postives = 42/52 (80.77%), Query Frame = -3 
Query:  179 EDIEFYXXXXXXXXXXXXXXXRMAQMELDKINHDIAAGRIPCSDVYGPHYNA 334
            + +EFYLL L EE+RRLQH RRM Q+ELDKIN DIAAGRI C+ VY P YNA
Sbjct:   90 QKVEFYLLLLVEEERRLQHRRRMPQVELDKINRDIAAGRILCTGVYAPDYNA 141
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BLAST of SMED30013279 vs. Planmine SMEST
Match: SMESG000049568.1 (SMESG000049568.1)

HSP 1 Score: 97.8265 bits (242), Expect = 2.282e-26
Identity = 48/70 (68.57%), Postives = 57/70 (81.43%), Query Frame = -3 
Query:   59 MAQMELDKINHDIAAGRIPCSDVYGPHYNASYEFDDPALKILTAPTLVAIPN*LIHLVMLERLELLH*EG 268
            M Q+EL++INH+IAAGRIP SD+Y P +NASYE +DPALK L APT VAIP+ LIH +MLERLEL   EG
Sbjct:    1 MVQVELNQINHEIAAGRIPYSDIYAPVHNASYELNDPALKALMAPTRVAIPDALIHPIMLERLELQRQEG 70
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BLAST of SMED30013279 vs. Planmine SMEST
Match: SMESG000008996.1 (SMESG000008996.1)

HSP 1 Score: 91.2781 bits (225), Expect = 1.064e-23
Identity = 49/70 (70.00%), Postives = 51/70 (72.86%), Query Frame = -3 
Query:   59 MAQMELDKINHDIAAGRIPCSDVYGPHYNASYEFDDPALKILTAPTLVAIPN*LIHLVMLERLELLH*EG 268
            MAQME D+IN  IAAG IPC D Y P YNASYE DD ALK L A T VAIP+ LIH VMLE LELL  EG
Sbjct:    1 MAQMEQDQINRKIAAGTIPCLDAYAPDYNASYELDDLALKTLMALTRVAIPSKLIHPVMLECLELLRQEG 70
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BLAST of SMED30013279 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 61.6178 bits (148), Expect = 9.223e-16
Identity = 27/63 (42.86%), Postives = 39/63 (61.90%), Query Frame = -3 
Query:   80 MAQMELDKINHDIAAGRIPCSDVYGPHYNASYEFDDPALKILTAPTLVAIPN*LIHLVMLERL 268
            +A+  L ++N DIA+G IP +D + P Y  S+E DDP L  +TAPT + IP  L+   +  RL
Sbjct: 1227 LARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRL 1289

HSP 2 Score: 39.6614 bits (91), Expect = 9.223e-16
Identity = 27/68 (39.71%), Postives = 38/68 (55.88%), Query Frame = -2 
Query:  333 EQQRQIIQFSSTAAAQ*RQIL*DYGY*VSTPGDTK*RARLGL-IKDIDLRGIIIKKRPDGTQPERLAR 533
            +  R  +Q  S +AA+ RQ+L D GY +ST GD+    R     ++I+L  I IK+ P G  P R AR
Sbjct: 1138 DNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREP-GHNPAREAR 1204
[Close]
BLAST of SMED30013279 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.593e-15
Identity = 27/63 (42.86%), Postives = 39/63 (61.90%), Query Frame = -3 
Query:   80 MAQMELDKINHDIAAGRIPCSDVYGPHYNASYEFDDPALKILTAPTLVAIPN*LIHLVMLERL 268
            +A+  L ++N DIA+G IP +D + P Y  S+E DDP L  +TAPT + IP  L+   +  RL
Sbjct:  865 LARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRL 927

HSP 2 Score: 38.891 bits (89), Expect = 1.593e-15
Identity = 27/68 (39.71%), Postives = 38/68 (55.88%), Query Frame = -2 
Query:  333 EQQRQIIQFSSTAAAQ*RQIL*DYGY*VSTPGDTK*RARLGL-IKDIDLRGIIIKKRPDGTQPERLAR 533
            +  R  +Q  S +AA+ RQ+L D GY +ST GD+    R     ++I+L  I IK+ P G  P R AR
Sbjct:  776 DNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREP-GHNPAREAR 842
The following BLAST results are available for this feature:
BLAST of SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 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 SMED30013279 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004514.11.527e-2962.07SMESG000004514.1[more]
SMESG000049568.12.282e-2668.57SMESG000049568.1[more]
SMESG000008996.11.064e-2370.00SMESG000008996.1[more]
SMESG000044971.19.223e-1642.86SMESG000044971.1[more]
SMESG000031842.11.593e-1542.86SMESG000031842.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013279 ID=SMED30013279|Name=SMED30013279|organism=Schmidtea mediterranea sexual|type=transcript|length=708bp
GGATTAGTTCCTTCATTATACTACTGGATTTCGAATCAGGATCTCGCCAC
ATGAGGTCTCCTTCTTAATGAAGCAGCTCCAGGCGTTCCAGCATGACCAG
GTGGATTAATTAGTTTGGAATTGCCACTAGAGTCGGGGCTGTCAGAATTT
TCAGAGCTGGATCGTCGAACTCATATGAAGCATTGTAGTGCGGGCCATAA
ACATCCGAGCATGGAATTCTACCTGCTGCTATGTCGTGATTGATTTTGTC
TAGTTCCATCTGGGCCATCCGTCGTCAGTGTTGCAGTCGTCTATCTTCCT
CGTCCAAGCGGAGTAAATAAAATTCTATATCCTCTGGCAAGCCTCTCTGG
CTGGGTTCCATCAGGGCGTTTTTTGATTATGATACCGCGGAGGTCTATGT
CTTTTATCAGCCCCAGTCGGGCCCGTCACTTGGTATCTCCTGGCGTGGAG
ACCTAATATCCATAATCTCACAAGATTTGGCGTCATTGGGCGGCCGCGGT
TGAACTGAATTGAATGATCTGCCTTTGTTGCTCTGGCGCCAGTCTTCTTG
AGATGGATTGCCTTTCATTTGTTGACAGTTGTGGCGTTAGCTCGAATTTC
ACTGCGTGCGAATTTGAGCCGCGCACGTTTTCTCTATAGGCTTCTCACAT
TTTCCGTTCTCGTACTCTGTTTTCCGGCCTTCGATTTGAGTTTTGGGTGT
TTGATTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR019774Aromatic-AA_hydroxylase_C
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process
Vocabulary: molecular function
TermDefinition
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..53
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..27