SMED30031701

Overview
NameSMED30031701
Smed IDSMED30031701
Length (bp)1025
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 SMED30031701 (SMED30031701) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031701 (SMED30031701) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30031701 (SMED30031701) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031701 (SMED30031701) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30031701

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30031701SMESG000072330.1 SmedASXL_005608SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30031701SMESG000072330.1 SmedASXL_005608SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
zeta neoblastSMED30031701SMESG000072330.1 dd_Smed_v4_21473_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
SMED30031701 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001496:13107..14131 +5080
Homology
[Close]
BLAST of SMED30031701 vs. TrEMBL
Match: I1ZID3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 3.498e-9
Identity = 82/341 (24.05%), Postives = 144/341 (42.23%), Query Frame = 3 
Query:   18 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLS-PTKFLISPGLRNRLLKAVDILVSYFE------------------------------------MNSLNNSIHKSFC-------MENMLYQKLSETDSGNNTNNNLMFSANI-------------------LDISENDSRISAPKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVLKRE-LDFNLVPKENFDLEFHFNSDSISNSYGNYICYYC-----NKKKLKFKFTAMLKVVYGNIKSHLKKH 833
            M+ ++ N I  L     V NWLELC FE ++D    N N +  +E YI   CS M  + R+ Y++ +     P +F  +P L++RLL   D +   F                                      +S++NSI +SF        +E  LYQ  S+ D  + T N   F+ +I                   L I      +    H +  + S ++  +S +     +  EI L   S+ + + + K++ +    + ++  +++ +D +LV   +F++    + DS   + G ++CY C     N+ K+KF FT+   VV+ NI +HL+ H
Sbjct:    1 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSICSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQ--SDKDEKHETKNGF-FACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRIL----SSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIH 334
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BLAST of SMED30031701 vs. Planmine SMEST
Match: SMESG000072330.1 (SMESG000072330.1)

HSP 1 Score: 552.747 bits (1423), Expect = 0.000e+0
Identity = 274/276 (99.28%), Postives = 275/276 (99.64%), Query Frame = 3 
Query:   18 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEMNSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVLKRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKHPLNS 845
            MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFE+NSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKH ESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVLKRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKHPLNS
Sbjct:    1 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEINSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHYESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVLKRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKHPLNS 276
[Close]
BLAST of SMED30031701 vs. Planmine SMEST
Match: SMESG000072336.1 (SMESG000072336.1)

HSP 1 Score: 143.28 bits (360), Expect = 1.973e-37
Identity = 91/274 (33.21%), Postives = 157/274 (57.30%), Query Frame = 3 
Query:   36 NAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEMNSLNNSI---HKS----FCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVEVL-KRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKH 833
            + I+ L   PK+   L+LCKF  + DF+NFN+ ++D +++Y++I CS+M +  R++YL+E D+ +P  + I+PG+RNRLLKAV ++++   +N + ++    HK+    F +EN         D  N  +N L FS +    S    +       +S  S + +GYE  L   ++N    C+ + ++D  + EF+        + +    + +++    PK +FDLEFH  +D+   S+G +IC+ CNKKKLKF F++ + + +G+IKSHLK H
Sbjct:   11 DVISILTGRPKLVQCLKLCKFRSILDFINFNDKSIDNVQEYVRIICSIMSVEERKMYLDEDDIPNPQDYFITPGIRNRLLKAVTVILASIGINKVKSNDLFNHKTPPKRFELEN--------NDFPN--SNALEFSPSKKPSSSPQVKYRKRLISKSIESKE-IGYEHRLSKASSN----CVESTTED-PIDEFRGFFKHVRNNLLGFYNEHKMESKHKPKIHFDLEFHIENDT-KKSFGYFICFNCNKKKLKFSFSSKMVISFGSIKSHLKTH 267
[Close]
BLAST of SMED30031701 vs. Planmine SMEST
Match: SMESG000072339.1 (SMESG000072339.1)

HSP 1 Score: 118.242 bits (295), Expect = 1.051e-30
Identity = 92/290 (31.72%), Postives = 146/290 (50.34%), Query Frame = 3 
Query:   18 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEMNSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHDESTNSSQTLGYESTLEVINN--------NDSEICLANQSKDLQVGEFKINIDQYF-----EDFVEVLKRELDFN-----LVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKLKFKFTAMLKVVYGNIKSHLKKH 833
            M+I+I +A+ YL    K +   +LC F  + D L+FN+ ++DK+E+YIQ+QCSLM +  R +YL+  D+ +P  F+ISPGLRNR+ KAV  +V+   MN  + S+ +     N +       D G    +N++   NI  +S  D+     K   STN  QT    ++   + N        N  +I  ++   D  +   K  +DQ       E+F   +  +   N     L+PK++FD++ + N  +  NS   Y+C  CN K +KF     LK +   IKSH + H
Sbjct:    1 MDINIFDALNYLTGSSKTSARFKLCDFNTITDLLSFNDTSIDKMEEYIQLQCSLMDLAERSIYLDGDDIQNPKCFMISPGLRNRICKAVSTIVN--SMNGASLSLSQKLLNHNFI-------DYG--FKDNIVSVKNIKPLSITDNMFMNQKSFNSTN-IQTKALATSKNNLANISKLYTPINSKKIVKSSNKLDNPIARGK-KVDQKLIELVTENFYHTIANDQPLNFDNCHLIPKKDFDIKINLNYKNFQNSKFYYVCNLCNGKLVKFNLNKDLKPIQTGIKSHNRTH 277
[Close]
BLAST of SMED30031701 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 94.7449 bits (234), Expect = 3.919e-22
Identity = 84/285 (29.47%), Postives = 138/285 (48.42%), Query Frame = 3 
Query:   18 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAV-----DILVSYFEMNSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVE-VLKRELDFNLVPKENFDLEFHFN--SDSISNSYGNYICYYCNKK-----KLKFKFTAMLKVVYGNIKSHLKKH 833
            MN  +   IA + E P V + LE+ +    DDF+NF++  VD +E YI+ + S+M IN R  YL+   +  P KF+ +PG+RNRLLKA      D+  + FE N        S C  N +           ++NNN     N L           P+++ S  +S  +  +  L  +N++     +  Q  D+       N+++Y+ D V+   K  ++ +L+P    D++FH +   +  ++  G Y C+ C  +     K+KF+F+    V+Y NI SHLK H
Sbjct:    1 MNSRVRETIANVVESPLVLSCLEIAELLEPDDFINFSHTNVDILENYIRCRTSVMEINDRIPYLSGEFIHFPEKFMFTPGMRNRLLKAAKLISKDVYAAVFESN------QTSDCESNEM---------SCDSNNNSTTPMNKL----------QPQNNISIENS-LIENQFLLSPLNSS-----IIKQELDMNRSRHLQNMEKYYNDIVKNAAKNFIECSLIP----DVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTH 250
[Close]
BLAST of SMED30031701 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 94.7449 bits (234), Expect = 4.912e-22
Identity = 84/285 (29.47%), Postives = 138/285 (48.42%), Query Frame = 3 
Query:   18 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAV-----DILVSYFEMNSLNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISAPKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQYFEDFVE-VLKRELDFNLVPKENFDLEFHFN--SDSISNSYGNYICYYCNKK-----KLKFKFTAMLKVVYGNIKSHLKKH 833
            MN  +   IA + E P V + LE+ +    DDF+NF++  VD +E YI+ + S+M IN R  YL+   +  P KF+ +PG+RNRLLKA      D+  + FE N        S C  N +           ++NNN     N L           P+++ S  +S  +  +  L  +N++     +  Q  D+       N+++Y+ D V+   K  ++ +L+P    D++FH +   +  ++  G Y C+ C  +     K+KF+F+    V+Y NI SHLK H
Sbjct:   13 MNSRVRETIANVVESPLVLSCLEIAELLEPDDFINFSHTNVDILENYIRCRTSVMEINDRIPYLSGEFIHFPEKFMFTPGMRNRLLKAAKLISKDVYAAVFESN------QTSDCESNEM---------SCDSNNNSTTPMNKL----------QPQNNISIENS-LIENQFLLSPLNSS-----IIKQELDMNRSRHLQNMEKYYNDIVKNAAKNFIECSLIP----DVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTH 262
The following BLAST results are available for this feature:
BLAST of SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZID33.498e-924.05Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 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 SMED30031701 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072330.10.000e+099.28SMESG000072330.1[more]
SMESG000072336.11.973e-3733.21SMESG000072336.1[more]
SMESG000072339.11.051e-3031.72SMESG000072339.1[more]
SMESG000047524.13.919e-2229.47SMESG000047524.1[more]
SMESG000047524.14.912e-2229.47SMESG000047524.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031701 ID=SMED30031701|Name=SMED30031701|organism=Schmidtea mediterranea sexual|type=transcript|length=1025bp
ATAAATTTTTGTAGGTTATGAATATTGATATTCCTAATGCTATTGCATAT
TTATGTGAATTTCCAAAAGTGGCAAATTGGTTAGAATTATGTAAATTTGA
ATTAATGGATGATTTCCTAAATTTTAATAACAACACAGTTGATAAAATAG
AAAAATATATTCAAATTCAATGTTCTTTAATGCCCATTAATGTAAGACAA
CTTTACTTGAATGAATCTGATCTATTAAGTCCTACAAAATTTTTAATTTC
TCCTGGATTACGAAACCGATTATTAAAAGCTGTTGACATTCTAGTGTCGT
ATTTTGAAATGAATTCATTAAACAATTCAATTCATAAATCTTTCTGTATG
GAAAATATGTTGTATCAAAAATTATCAGAAACTGACTCAGGGAATAATAC
AAATAATAATCTAATGTTTTCTGCTAATATACTTGATATATCAGAAAATG
ATTCTAGAATATCAGCTCCAAAACATGATGAATCGACAAATAGTTCACAA
ACTTTGGGATATGAATCTACTTTGGAAGTTATCAACAATAATGACTCTGA
GATTTGTTTGGCAAACCAATCAAAAGATTTGCAAGTTGGCGAATTTAAAA
TAAACATTGATCAATATTTTGAAGACTTTGTTGAAGTGTTGAAAAGAGAG
TTAGATTTCAATTTAGTTCCAAAGGAAAATTTTGATTTGGAATTTCATTT
TAACTCTGATTCAATTAGTAACTCGTACGGCAATTATATTTGCTATTACT
GCAACAAAAAGAAGTTGAAATTTAAATTCACCGCGATGTTGAAAGTTGTT
TATGGAAATATTAAATCACACTTGAAAAAGCATCCACTCAATAGCTAACC
AAATTTATTGACAAACATTTAACAACAGAGCTAACGATAAATTTCTATGA
ATATATTTTATGTTGAACTTTTGCTTATTGTTTAAATGCTTAATTATAAT
TTTGATTTTATTGGATTTTAAAAAATTAATTCTTTGTGGTGTGATCGGTC
CATTTTCCTCCAGTTATAATGCTGC
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protein sequence of SMED30031701-orf-1

>SMED30031701-orf-1 ID=SMED30031701-orf-1|Name=SMED30031701-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=277bp
MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQI
QCSLMPINVRQLYLNESDLLSPTKFLISPGLRNRLLKAVDILVSYFEMNS
LNNSIHKSFCMENMLYQKLSETDSGNNTNNNLMFSANILDISENDSRISA
PKHDESTNSSQTLGYESTLEVINNNDSEICLANQSKDLQVGEFKINIDQY
FEDFVEVLKRELDFNLVPKENFDLEFHFNSDSISNSYGNYICYYCNKKKL
KFKFTAMLKVVYGNIKSHLKKHPLNS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell