SMED30001770

Overview
NameSMED30001770
Smed IDSMED30001770
Length (bp)392
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



SMED30001770

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30001770 Contig46054uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30001770 Contig46054newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30001770 Contig46054uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30001770 Contig46054newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001770 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014158:9417..9808 +1537
Homology
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BLAST of SMED30001770 vs. Planmine SMEST
Match: SMESG000020958.1 (SMESG000020958.1)

HSP 1 Score: 127.102 bits (318), Expect = 8.970e-35
Identity = 94/123 (76.42%), Postives = 98/123 (79.67%), Query Frame = 1 
Query:    1 DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPVTXXXXXXXXXMNPISEAPVLPVESVVPQPPIGVVESVVIXXXXXXXXXXXXXXXXXXXXEEVLIGLEPAE 369
            DELITESRAQRLLIKEQSTALRRAFTD EL+A VPGSIRASQLDIIPA+HLP  +VSSS S S NPI E P LPVE +V QP IG  ES  I R RRRPNRNRRRR RRRR EE L GLE  E
Sbjct:  967 DELITESRAQRLLIKEQSTALRRAFTDTELQACVPGSIRASQLDIIPAYHLPTANVSSSPSVSRNPIPETPSLPVEPIVSQPSIGNAESAAITRTRRRPNRNRRRRERRRRVEEDLTGLELTE 1089
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BLAST of SMED30001770 vs. Planmine SMEST
Match: SMESG000063980.1 (SMESG000063980.1)

HSP 1 Score: 109.768 bits (273), Expect = 1.007e-28
Identity = 63/92 (68.48%), Postives = 69/92 (75.00%), Query Frame = 1 
Query:    1 DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPVTXXXXXXXXXMNPIS-EAPVLPVESVVPQPPIGVVESVV 273
            DELI+ESRAQRLLIKEQS ALRRAFTDVEL+AHVPGSIRASQL IIPAHHLPVT V      + NPI+ E   LP    +PQ P  V E+ V
Sbjct:   71 DELISESRAQRLLIKEQSIALRRAFTDVELQAHVPGSIRASQLGIIPAHHLPVTDVLPFTPVT-NPIAPEIRTLPELLTLPQQPTEVRETSV 161
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BLAST of SMED30001770 vs. Planmine SMEST
Match: SMESG000011446.1 (SMESG000011446.1)

HSP 1 Score: 96.6709 bits (239), Expect = 2.003e-26
Identity = 44/53 (83.02%), Postives = 50/53 (94.34%), Query Frame = 1 
Query:    1 DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPV 159
            DELI ESR+QRLLI+EQ+TALRRAFTDVE R HVPGS+RASQL++IPAHHLPV
Sbjct:   71 DELIAESRSQRLLIREQATALRRAFTDVEFRTHVPGSVRASQLNLIPAHHLPV 123
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BLAST of SMED30001770 vs. Planmine SMEST
Match: SMESG000009535.1 (SMESG000009535.1)

HSP 1 Score: 101.293 bits (251), Expect = 6.570e-26
Identity = 80/130 (61.54%), Postives = 93/130 (71.54%), Query Frame = 1 
Query:    1 DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPVTXXXXXXXXXMNPISEAPVLPVESVVPQPPIGVVESVVIXXXXXXXXXXXXXXXXXXXXEEVLIGLEPAETSCPFSD 390
            DEL+TESR QRLLI+EQSTALRRAFTD+ELR  VPG++RASQL+IIPAHH+PV  +  SL  S    SEA       VV QPP G VE+  I+  RRRPNRNRRRR RRRR EE+  G+E +E S    D
Sbjct:  103 DELVTESRIQRLLIREQSTALRRAFTDIELRTLVPGNVRASQLEIIPAHHIPVMGILPSLPVSNPSTSEARAPAATPVVSQPPTGAVETPTISTTRRRPNRNRRRRDRRRREEELSQGVETSELSRQTGD 232
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BLAST of SMED30001770 vs. Planmine SMEST
Match: SMESG000028821.1 (SMESG000028821.1)

HSP 1 Score: 99.7525 bits (247), Expect = 8.509e-26
Identity = 48/54 (88.89%), Postives = 52/54 (96.30%), Query Frame = 1 
Query:    1 DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPVT 162
            DELITESRAQRLLIKEQSTALRRAFTD ELRAHVPGS+RAS L+IIPAHHLP++
Sbjct:   57 DELITESRAQRLLIKEQSTALRRAFTDGELRAHVPGSVRASHLEIIPAHHLPIS 110

HSP 2 Score: 66.6254 bits (161), Expect = 1.103e-13
Identity = 35/71 (49.30%), Postives = 47/71 (66.20%), Query Frame = 1 
Query:   13 TESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHHLPVTXXXXXXXXXMNPISEAPVLPV 225
            T+SR+QR+LIKE ST LR+ FTD ELRA +PGS+ A  L+IIP  +LP+       S    P++E P + V
Sbjct:  151 TQSRSQRVLIKEHSTTLRQIFTDAELRARIPGSVWARSLNIIPEQYLPLEVARPIPSTPAPPVAEPPQISV 221
The following BLAST results are available for this feature:
BLAST of SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 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 SMED30001770 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020958.18.970e-3576.42SMESG000020958.1[more]
SMESG000063980.11.007e-2868.48SMESG000063980.1[more]
SMESG000011446.12.003e-2683.02SMESG000011446.1[more]
SMESG000009535.16.570e-2661.54SMESG000009535.1[more]
SMESG000028821.18.509e-2688.89SMESG000028821.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001770 ID=SMED30001770|Name=SMED30001770|organism=Schmidtea mediterranea sexual|type=transcript|length=392bp
GATGAGCTGATCACGGAATCTCGCGCTCAGCGACTGCTTATCAAAGAGCA
GTCAACCGCACTCCGACGTGCGTTTACGGACGTCGAGCTTCGGGCTCACG
TCCCGGGAAGCATCAGGGCCAGTCAACTAGATATAATACCAGCCCATCAT
CTGCCCGTTACCAGTGTCTCTTCTTCCCTCTCCGCCTCCATGAATCCGAT
TTCTGAAGCTCCCGTCCTACCCGTCGAGTCAGTTGTTCCTCAACCGCCCA
TCGGAGTTGTAGAAAGTGTTGTTATCAACCGGGCGCGGCGGCGACCGAAT
CGGAATCGACGACGTCGCGCACGACGCCGTCGAGCGGAAGAAGTACTCAT
AGGATTGGAGCCCGCTGAGACCTCCTGCCCGTTCAGTGACCC
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protein sequence of SMED30001770-orf-1

>SMED30001770-orf-1 ID=SMED30001770-orf-1|Name=SMED30001770-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
DELITESRAQRLLIKEQSTALRRAFTDVELRAHVPGSIRASQLDIIPAHH
LPVTSVSSSLSASMNPISEAPVLPVESVVPQPPIGVVESVVINRARRRPN
RNRRRRARRRRAEEVLIGLEPAETSCPFSD
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland