SMED30014578

Overview
NameSMED30014578
Smed IDSMED30014578
Length (bp)1129
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30014578 (SMED30014578) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014578 (SMED30014578) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30014578 (SMED30014578) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014578 (SMED30014578) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30014578

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
Category 4 cellSMED30014578SMESG000056168.1 dd_Smed_v4_31605_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014578 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016222:2009..3128 +5408
v31.008560:14865..15962 -4386
v31.000953:59139..60253 +4019
v31.009013:20142..21267 -3977
Homology
[Close]
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 161.77 bits (408), Expect = 3.325e-66
Identity = 106/160 (66.25%), Postives = 117/160 (73.12%), Query Frame = 1 
Query:  457 VVLSN*VQRDVTNAVTIMPALPISNQKHKPXXXXXXXXXXXXXXXLLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936
            V LSN V+ D TN  T+ P   I N+KHKPNKNRR++EKRR ENALL+ NL  +EN N I I E TSYES  MPANSDLEII  P L+DF Q AP P QFNI++ENL TDN  + QI I  RSSPIREE HE SS RST QIISV E PQVR SINSTAG
Sbjct:   78 VNLSNCVEWDATNVFTLAPVPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAG 237

HSP 2 Score: 109.768 bits (273), Expect = 3.325e-66
Identity = 52/73 (71.23%), Postives = 61/73 (83.56%), Query Frame = 3 
Query:  237 WCSPEATRELYKKIT*ISQTRDDLIVENKIQRITIADQSAALR*IFTEKKLQALLPDRSIAQLLDIIPAHHQP 455
            WCSPEAT++LYKKIT +S+ RDDLIV+N+ QRITIADQ A LR IFTEK+LQA LPDRSI Q L++IP  H P
Sbjct:    5 WCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQARLPDRSITQQLNMIPVQHLP 77
[Close]
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1)

HSP 1 Score: 200.29 bits (508), Expect = 1.634e-58
Identity = 103/115 (89.57%), Postives = 106/115 (92.17%), Query Frame = 1 
Query:  592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936
            LLKENLSA+ENANPIGIS+ATSYESTSMPANSDLEIIYGP LVDFSQLAPT SQFNIAIENLITDNPASVQITIFTRSSPIREE HEISSRRSTLQIISVIESPQ R  I+   G
Sbjct:   41 LLKENLSAIENANPIGISKATSYESTSMPANSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIG 155
[Close]
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1)

HSP 1 Score: 200.675 bits (509), Expect = 2.708e-57
Identity = 103/115 (89.57%), Postives = 106/115 (92.17%), Query Frame = 1 
Query:  592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAG 936
            LLKENLSA+ENANPIGIS+ATSYESTSMPANSDLEIIYGP LVDFSQLAPT SQFNIAIENLITDNPASVQITIFTRSSPIREE HEISSRRSTLQIISVIESPQ R  I+   G
Sbjct:   41 LLKENLSAIENANPIGISKATSYESTSMPANSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIG 155
[Close]
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000068983.1 (SMESG000068983.1)

HSP 1 Score: 174.096 bits (440), Expect = 1.411e-52
Identity = 103/143 (72.03%), Postives = 118/143 (82.52%), Query Frame = 1 
Query:  592 LLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQITIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAGXXXXXXXXXXXXXXXKRYLPIDMDTEDE 1020
            LL+ NLSA+ENAN IGISE T Y+  SMP +SDLEIIY P LV FSQL P  SQFNI++ENL T NPA+V ITI TRSSP+REEGHEI+S RST QIISVIE PQVRTS+NST  NISR+ PNPS R PRKRYLP+D+D+ED+
Sbjct:   66 LLQANLSAIENANSIGISETTPYKPISMPTDSDLEIIYAPRLVAFSQLDPVRSQFNISMENLTTGNPANVPITISTRSSPVREEGHEITSGRSTPQIISVIEPPQVRTSVNSTVENISRQYPNPSPRRPRKRYLPVDIDSEDD 208
[Close]
BLAST of SMED30014578 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 115.931 bits (289), Expect = 2.939e-45
Identity = 72/118 (61.02%), Postives = 82/118 (69.49%), Query Frame = 3 
Query:  111 MPLPKIPKISSAPAVIAAAQHLAXXXXXXXXXXXXXXXXXXXWCSPEATRELYKKIT*ISQTRDDLIVENKIQRITIADQSAALR*IFTEKKLQALLPDRSIAQLLDIIPAHHQPSSS 464
            MPLPKIP IS A +V      LA L    +    K EK+KG WCSPEAT+ELYK IT IS+ RDDLIVEN+ QRITI D+S ALR +FTEK+LQA LP RS AQ L+II  HH P  S
Sbjct:    1 MPLPKIPNISPALSV------LAPLNTWQIWRIVKYEKMKGTWCSPEATKELYKNITRISRARDDLIVENRTQRITIVDKSPALRQLFTEKELQARLPGRSTAQQLNIISVHHLPVYS 112

HSP 2 Score: 85.5001 bits (210), Expect = 2.939e-45
Identity = 57/85 (67.06%), Postives = 66/85 (77.65%), Query Frame = 1 
Query:  457 VVLSN*VQRDVTNAVTIMPALPISNQKHKPXXXXXXXXXXXXXXXLLKENLSAVENANPIGISEATSYESTSMPANSDLEIIYGP 711
            V  SN ++RDVTNAV   P LPI N+KHKPNKN+R+REKRR ENALL+ NL+A+EN   IGISE T YE  SMPA+SDL IIY P
Sbjct:  110 VYSSNRIERDVTNAVMTRPVLPICNRKHKPNKNQRRREKRRTENALLQANLNAIENVISIGISETTPYEPISMPADSDLAIIYAP 194
The following BLAST results are available for this feature:
BLAST of SMED30014578 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014578 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033974.13.325e-6666.25SMESG000033974.1[more]
SMESG000056168.11.634e-5889.57SMESG000056168.1[more]
SMESG000056168.12.708e-5789.57SMESG000056168.1[more]
SMESG000068983.11.411e-5272.03SMESG000068983.1[more]
SMESG000032225.12.939e-4561.02SMESG000032225.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014578 ID=SMED30014578|Name=SMED30014578|organism=Schmidtea mediterranea sexual|type=transcript|length=1129bp
TTTTACATATTAAATTCAGATCGATATATACAAATTGTTTTTATCATCTA
CCAACCAAATAATTCATCTAAGCCACCATTCTTCAGAAAATCGAATCGCA
CCTACAAATTATGCCTCTACCAAAAATTCCAAAGATTTCGTCAGCTCCAG
CAGTCATTGCCGCTGCTCAACATCTAGCAAATTTGGAGAATAATCACCTC
ATCCTCAAGGAAAAATAAGAAAAAATTAAAGGGATATGGTGTTCCCCAGA
AGCTACAAGGGAGCTGTATAAGAAGATCACTTGAATATCTCAAACCCGCG
ACGATTTGATAGTCGAAAATAAAATTCAACGGATAACCATCGCGGATCAA
AGTGCCGCACTTAGGTAGATTTTCACAGAAAAAAAACTACAAGCGCTGTT
GCCGGATCGCAGTATAGCCCAACTACTCGACATCATTCCGGCTCATCATC
AGCCGAGTAGTTCTGTCAAATTGAGTCCAACGTGATGTAACTAATGCAGT
CACAATAATGCCAGCTCTACCAATCTCCAACCAAAAGCACAAACCCAACA
AAAACCGCCGGAAAAGAGAAAAAAGAAGGGCCGAAAATGCCTTATTGAAG
GAGAATTTGAGTGCTGTAGAAAATGCTAATCCGATTGGGATATCTGAAGC
GACATCTTACGAATCTACCTCAATGCCGGCCAACTCCGATCTGGAGATAA
TCTATGGTCCCCCACTTGTGGATTTTTCCCAGTTGGCCCCGACGCCATCT
CAATTTAACATCGCCATAGAAAATCTCATCACTGATAATCCAGCCAGTGT
GCAAATAACTATATTTACAAGATCATCTCCCATTAGAGAGGAAGGACACG
AAATTTCTAGCAGAAGATCCACCCTGCAGATTATTTCGGTTATTGAATCA
CCACAAGTCCGTACTAGCATCAACTCGACGGCTGGAAATATTTCTCGGCG
GAATCCAAATCCAAGTTCGCGAATACCTAGAAAAAGATATCTTCCGATAG
ACATGGACACCGAAGATGAGTAAAGCTAACGCTCGATTCAAATCTGACAA
AATTCTCATACTGTTATGATTAAAATTGTGGTTTAAATTTTCCTTGACTT
AATAAAATTGTTGCTTAGTTGAAAAAAAA
back to top

protein sequence of SMED30014578-orf-1

>SMED30014578-orf-1 ID=SMED30014578-orf-1|Name=SMED30014578-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp
MPALPISNQKHKPNKNRRKREKRRAENALLKENLSAVENANPIGISEATS
YESTSMPANSDLEIIYGPPLVDFSQLAPTPSQFNIAIENLITDNPASVQI
TIFTRSSPIREEGHEISSRRSTLQIISVIESPQVRTSINSTAGNISRRNP
NPSSRIPRKRYLPIDMDTEDE*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..116