SMED30017136

Overview
NameSMED30017136
Smed IDSMED30017136
Length (bp)410
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



SMED30017136

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30017136h1SMcG0022520 Contig44698newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017136h1SMcG0022520 Contig44698uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30017136h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017136h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30017136h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30017136h1SMcG0022520 dd_Smed_v4_15048_0_1dd_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
SMED30017136 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005740:1139..1596 +1999
Homology
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BLAST of SMED30017136 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 251.136 bits (640), Expect = 5.542e-79
Identity = 135/136 (99.26%), Postives = 135/136 (99.26%), Query Frame = 2 
Query:    2 HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSXXXXXXXXXXXXIMNFSN 409
            HEQIPLIGLFNSPGIRGT MSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN
Sbjct:  418 HEQIPLIGLFNSPGIRGTAMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN 553
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BLAST of SMED30017136 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 251.136 bits (640), Expect = 5.714e-79
Identity = 135/136 (99.26%), Postives = 135/136 (99.26%), Query Frame = 2 
Query:    2 HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSXXXXXXXXXXXXIMNFSN 409
            HEQIPLIGLFNSPGIRGT MSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN
Sbjct:  412 HEQIPLIGLFNSPGIRGTAMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN 547
[Close]
BLAST of SMED30017136 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 251.136 bits (640), Expect = 7.102e-79
Identity = 135/136 (99.26%), Postives = 135/136 (99.26%), Query Frame = 2 
Query:    2 HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSXXXXXXXXXXXXIMNFSN 409
            HEQIPLIGLFNSPGIRGT MSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN
Sbjct:  412 HEQIPLIGLFNSPGIRGTAMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN 547
[Close]
BLAST of SMED30017136 vs. Planmine SMEST
Match: SMESG000016303.1 (SMESG000016303.1)

HSP 1 Score: 203.371 bits (516), Expect = 1.280e-61
Identity = 100/136 (73.53%), Postives = 119/136 (87.50%), Query Frame = 2 
Query:    2 HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSXXXXXXXXXXXXIMNFSN 409
            HEQIPLIGLFNSPGIRGT M STGALCQLQIN+NIFNEIG+KK PYH+ N + A+ AYEELM+LNS + SNF+SRTLHR++GLT+YPYWNQGV++G N  R YY NVFDNIGKCQN+SF+ ++ +D F+KIMNFSN
Sbjct:  401 HEQIPLIGLFNSPGIRGTGMHSTGALCQLQINANIFNEIGTKKPPYHIPNAVGASSAYEELMILNSATFSNFWSRTLHRSNGLTLYPYWNQGVVVGSNELRWYYHNVFDNIGKCQNTSFYNSMNEDNFMKIMNFSN 536
[Close]
BLAST of SMED30017136 vs. Planmine SMEST
Match: SMESG000016303.1 (SMESG000016303.1)

HSP 1 Score: 202.986 bits (515), Expect = 1.478e-61
Identity = 100/136 (73.53%), Postives = 119/136 (87.50%), Query Frame = 2 
Query:    2 HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTNILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVHRKYYKNVFDNIGKCQNSSXXXXXXXXXXXXIMNFSN 409
            HEQIPLIGLFNSPGIRGT M STGALCQLQIN+NIFNEIG+KK PYH+ N + A+ AYEELM+LNS + SNF+SRTLHR++GLT+YPYWNQGV++G N  R YY NVFDNIGKCQN+SF+ ++ +D F+KIMNFSN
Sbjct:  394 HEQIPLIGLFNSPGIRGTGMHSTGALCQLQINANIFNEIGTKKPPYHIPNAVGASSAYEELMILNSATFSNFWSRTLHRSNGLTLYPYWNQGVVVGSNELRWYYHNVFDNIGKCQNTSFYNSMNEDNFMKIMNFSN 529
The following BLAST results are available for this feature:
BLAST of SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 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 SMED30017136 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016292.15.542e-7999.26SMESG000016292.1[more]
SMESG000016292.15.714e-7999.26SMESG000016292.1[more]
SMESG000016292.17.102e-7999.26SMESG000016292.1[more]
SMESG000016303.11.280e-6173.53SMESG000016303.1[more]
SMESG000016303.11.478e-6173.53SMESG000016303.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017136 ID=SMED30017136|Name=SMED30017136|organism=Schmidtea mediterranea sexual|type=transcript|length=410bp
CCATGAACAAATTCCTCTGATAGGTTTATTCAATAGTCCTGGAATTAGAG
GAACCGTTATGTCCTCAACAGGGGCTCTTTGTCAATTGCAAATCAATTCA
AATATATTCAATGAAATTGGATCAAAGAAAAAGCCTTATCATCTGACTAA
TATATTGAAGGCGAATGACGCATATGAAGAGCTTATGTTATTGAACTCTG
TGAGCGTTTCAAATTTTTACAGTAGAACTCTCCATAGGACCAGCGGACTG
ACAATTTACCCGTATTGGAATCAAGGCGTCCTAATCGGAGATAACGTACA
CCGAAAATATTACAAAAATGTTTTCGATAATATCGGAAAATGTCAAAATT
CCTCTTTCTTTAAAACTCTTACCAAGGATAAATTTCTGAAAATTATGAAC
TTTAGCAACA
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protein sequence of SMED30017136-orf-1

>SMED30017136-orf-1 ID=SMED30017136-orf-1|Name=SMED30017136-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
HEQIPLIGLFNSPGIRGTVMSSTGALCQLQINSNIFNEIGSKKKPYHLTN
ILKANDAYEELMLLNSVSVSNFYSRTLHRTSGLTIYPYWNQGVLIGDNVH
RKYYKNVFDNIGKCQNSSFFKTLTKDKFLKIMNFSN
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