SMED30030072

Overview
NameSMED30030072
Smed IDSMED30030072
Length (bp)2235
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 SMED30030072 (SMED30030072) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030072 (SMED30030072) 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 SMED30030072 (SMED30030072) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030072 (SMED30030072) 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



SMED30030072

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
X1 cellSMED30030072SMESG000031871.1 SmedASXL_005540SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30030072SMESG000031871.1 dd_Smed_v4_34984_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30030072SMESG000031871.1 dd_Smed_v4_34984_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30030072SMESG000031871.1 Contig30998newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30030072SMESG000031871.1 Contig30998uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
zeta neoblastSMED30030072SMESG000031871.1 dd_Smed_v4_34984_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
SMED30030072 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015687:6461..8823 -10890
v31.025998:710..3061 -10719
Homology
[Close]
BLAST of SMED30030072 vs. Planmine SMEST
Match: SMESG000031871.1 (SMESG000031871.1)

HSP 1 Score: 272.707 bits (696), Expect = 1.377e-90
Identity = 130/130 (100.00%), Postives = 130/130 (100.00%), Query Frame = 1 
Query:  136 MDKLSLVNAIDTDYVCKENSCKCAFLPFFISKNLNYSNGKSLALNLLKKIVSLSPAITGYLYFAKRIVIEGAISYNVIIYFTDPIDPRHLKIDNCFWIDKENLKVFHNIYGYYNMGNELENILPLKDPSE 525
            MDKLSLVNAIDTDYVCKENSCKCAFLPFFISKNLNYSNGKSLALNLLKKIVSLSPAITGYLYFAKRIVIEGAISYNVIIYFTDPIDPRHLKIDNCFWIDKENLKVFHNIYGYYNMGNELENILPLKDPSE
Sbjct:   42 MDKLSLVNAIDTDYVCKENSCKCAFLPFFISKNLNYSNGKSLALNLLKKIVSLSPAITGYLYFAKRIVIEGAISYNVIIYFTDPIDPRHLKIDNCFWIDKENLKVFHNIYGYYNMGNELENILPLKDPSE 171

HSP 2 Score: 81.2629 bits (199), Expect = 1.377e-90
Identity = 40/41 (97.56%), Postives = 40/41 (97.56%), Query Frame = 2 
Query:   14 MNDICAIIIPKISNPSEILLVDIYDIVDLTTPTSAPSQISL 136
            MNDICAIIIPKISNPSEILLVDIYDIVDLTTPTSAPSQIS 
Sbjct:    1 MNDICAIIIPKISNPSEILLVDIYDIVDLTTPTSAPSQISF 41
[Close]
BLAST of SMED30030072 vs. Planmine SMEST
Match: SMESG000063572.1 (SMESG000063572.1)

HSP 1 Score: 50.447 bits (119), Expect = 1.438e-18
Identity = 22/29 (75.86%), Postives = 25/29 (86.21%), Query Frame = -3 
Query: 1682 DYQCRSISKTDINKVPINDESIFGQYECH 1768
            D Q R+ISKTD  +VPINDES+FGQYECH
Sbjct:  241 DSQGRTISKTDTIQVPINDESVFGQYECH 269

HSP 2 Score: 41.9726 bits (97), Expect = 1.438e-18
Identity = 30/48 (62.50%), Postives = 38/48 (79.17%), Query Frame = -1 
Query: 1540 YRTHKSGKTLITSVNIIAQ-XXXXXXXXXXXXXTPYIR*FRLNEEFSI 1680
            YR HKSGKT I +VNIIA+ + +  S SYS+TITPY + FRLNE+FS+
Sbjct:  270 YRAHKSGKTFIATVNIIAESASSTISTSYSITITPYPQKFRLNEKFSM 317

HSP 3 Score: 39.6614 bits (91), Expect = 1.438e-18
Identity = 24/44 (54.55%), Postives = 28/44 (63.64%), Query Frame = -2 
Query: 1764 QDFILKISTSAVKIQIGAS----------KKCVRFKLAQSTERL 1865
            +D ILKIS  AV+IQI AS          +KCV FKLA+STER 
Sbjct:  192 KDVILKISQPAVQIQILASEKLIINGLIHRKCVGFKLAESTERF 235
[Close]
BLAST of SMED30030072 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 49.2914 bits (116), Expect = 5.334e-17
Identity = 21/29 (72.41%), Postives = 25/29 (86.21%), Query Frame = -3 
Query: 1682 DYQCRSISKTDINKVPINDESIFGQYECH 1768
            D Q R+ISKTD  +VPINDES+FG+YECH
Sbjct:  967 DSQGRTISKTDTIQVPINDESVFGRYECH 995

HSP 2 Score: 41.5874 bits (96), Expect = 5.334e-17
Identity = 32/47 (68.09%), Postives = 37/47 (78.72%), Query Frame = -1 
Query: 1540 YRTHKSGKTLITSVNIIAQXXXXXXXXXXXXXTPYIR*FRLNEEFSI 1680
            Y  HKSGKT I SVNIIAQS +   ASYS+TITPY + FRLNE+FS+
Sbjct:  996 YTAHKSGKTFIASVNIIAQSSSSALASYSITITPYPQKFRLNEKFSM 1042

HSP 3 Score: 36.1946 bits (82), Expect = 5.334e-17
Identity = 22/42 (52.38%), Postives = 26/42 (61.90%), Query Frame = -2 
Query: 1770 QDFILKISTSAVKIQIGAS----------KKCVRFKLAQSTE 1865
            +D ILKIST  V+IQI +S          +KCV FKLA STE
Sbjct:  918 KDVILKISTPPVQIQILSSEKLKINGLIHRKCVGFKLAHSTE 959
[Close]
BLAST of SMED30030072 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 48.9062 bits (115), Expect = 6.357e-17
Identity = 21/29 (72.41%), Postives = 25/29 (86.21%), Query Frame = -3 
Query: 1682 DYQCRSISKTDINKVPINDESIFGQYECH 1768
            D Q R+ISKTD  +VPINDES+FG+YECH
Sbjct:  449 DSQGRTISKTDTIQVPINDESVFGRYECH 477

HSP 2 Score: 41.5874 bits (96), Expect = 6.357e-17
Identity = 32/47 (68.09%), Postives = 37/47 (78.72%), Query Frame = -1 
Query: 1540 YRTHKSGKTLITSVNIIAQXXXXXXXXXXXXXTPYIR*FRLNEEFSI 1680
            Y  HKSGKT I SVNIIAQS +   ASYS+TITPY + FRLNE+FS+
Sbjct:  478 YTAHKSGKTFIASVNIIAQSSSSALASYSITITPYPQKFRLNEKFSM 524

HSP 3 Score: 36.1946 bits (82), Expect = 6.357e-17
Identity = 22/42 (52.38%), Postives = 26/42 (61.90%), Query Frame = -2 
Query: 1770 QDFILKISTSAVKIQIGAS----------KKCVRFKLAQSTE 1865
            +D ILKIST  V+IQI +S          +KCV FKLA STE
Sbjct:  400 KDVILKISTPPVQIQILSSEKLKINGLIHRKCVGFKLAHSTE 441
[Close]
BLAST of SMED30030072 vs. Planmine SMEST
Match: SMESG000069362.1 (SMESG000069362.1)

HSP 1 Score: 47.7506 bits (112), Expect = 6.288e-10
Identity = 24/37 (64.86%), Postives = 28/37 (75.68%), Query Frame = -3 
Query: 1682 LNRL---KDYQCRSISKTDINKVPINDESIFGQYECH 1783
            +NRL   K YQ ++I KTD  +VPINDESIFG YECH
Sbjct:  500 INRLIHRKYYQVQAILKTDTIQVPINDESIFGIYECH 536

HSP 2 Score: 35.8094 bits (81), Expect = 6.288e-10
Identity = 36/76 (47.37%), Postives = 45/76 (59.21%), Query Frame = -1 
Query: 1474 YRTHKSGKTLITSVNIIAQXXXXXXXXXXXXXTPYIR*FRLNEEFS-------ISN*LKFT*TYYKYILNTIVLFL 1680
            Y THK     I  +NII QS T  SASYS+TIT Y + FRL+E+FS        SN  K     ++YILN +V+FL
Sbjct:  537 YTTHKPVNAFIAEINIIVQSMTAISASYSITITSYPQKFRLHEKFSTLCQVDHASNQPKCAGFCFEYILNVVVVFL 612
The following BLAST results are available for this feature:
BLAST of SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 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 SMED30030072 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031871.11.377e-90100.00SMESG000031871.1[more]
SMESG000063572.11.438e-1875.86SMESG000063572.1[more]
SMESG000026481.15.334e-1772.41SMESG000026481.1[more]
SMESG000026481.16.357e-1772.41SMESG000026481.1[more]
SMESG000069362.16.288e-1064.86SMESG000069362.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030072 ID=SMED30030072|Name=SMED30030072|organism=Schmidtea mediterranea sexual|type=transcript|length=2235bp
CTTCCGATCTCAAATGAATGACATTTGTGCTATTATTATACCTAAAATTA
GCAATCCATCAGAAATTCTACTTGTGGACATTTACGACATAGTGGATTTA
ACAACTCCAACTAGTGCACCGTCTCAAATTTCATTATGGATAAATTATCA
TTAGTCAATGCAATAGATACTGATTACGTATGTAAAGAAAACAGTTGCAA
ATGTGCTTTTCTACCATTTTTCATTTCAAAAAATTTAAATTATAGCAATG
GGAAAAGTCTTGCATTAAATTTATTGAAAAAAATTGTCTCACTGTCACCA
GCAATAACTGGCTATTTATATTTTGCAAAACGAATTGTGATCGAAGGAGC
TATTTCATATAATGTTATTATTTATTTTACTGACCCAATTGATCCGCGAC
ATTTGAAAATTGATAATTGTTTTTGGATTGACAAAGAAAATCTTAAAGTG
TTTCATAATATTTACGGTTACTATAACATGGGCAATGAATTAGAAAACAT
TCTCCCATTGAAAGACCCGAGTGAATGTGGGATCTATTAATTTTTATCTA
AAATTGAACAATTATATAATTTAATGATATTTTAATATTAACTAAGTATA
AATTTTAATTTTGCGGTCATTATTTATATTTTTTAACAAAAATTGAGTTT
TGTAGCTGTATTGTTGGTCCCGTTGAACCTACCAAGCCATCGATTAAAAG
TTAATGCTATAAACAATATTTACAGTAAATGGATTCATGCGAGAATCAAT
TTTTGTGCTTATTATTTTGAAAGTTTTCTTTATACAAACCTACTGTAAAT
ACCTTACAATTGTTATTTAATAAATATCATTTACAACTGCATCACTGAGG
TGCTTGAGCCTGTCACAATTATTGGAAATTCGAAATTTAGCCGTAACAGT
AGTGCACCAGAACGATTGGAACGAAAATTTAGTTTAATTGAGATCTTCAA
TTAACTCCATCTTTATTTTTACCTGAGCTGTAAAAACCAATGAAGAAAAA
TCTTTAAATCGATAATAATGGAGTTTGAGGGGAGAAGGATTGTGAAATTG
GTAATATTGGTATTGTTAGATGGATAATACGTCTATCACAATTATCAGAC
TCCAAATTTACAATTACAACTGCTTGTAAATAAACTAAGAACTCTTTTAT
TGATTATAAGGTTTATTGAAATAAAATTTACACTTTATAAATAATAAATA
TGAGTTACACACAGCGGCGTTGTACTTAAGAGGCTTGGCGTGCCCAAGCT
CTCTAAACTTTTGCTACTGGATGGTTTAATAGCCTTTGCATAGAACTGAT
AAACGTATTTTATATTTTTTTATTGTAAAATACTTCGAATTCATGAGATT
AAGTTTGTTTCAGTATTTGAATTTGGATATTACTAAATTTTAAAAATTAA
TTTTCCTATTTACTAAGTAATTAATAGATGATAACGATATAACACATTCA
TTCATTTTATATTAAATATGCTGTAGGAACAAAACAATAGTATTTAAAAT
ATATTTGTAATAAGTTCAAGTAAATTTGAGTTAATTCGATATTGAGAATT
CCTCATTCAATCGGAACTATCGAATGTAAGGAGTAATTGTGACGGAATAT
GAGGCTGATGTGACTGTTTAGGATTGAGCGATAATGTTGACGGATGTGAT
TAATGTCTTGCCTGATTTGTGAGTTCTGTAAATGACATTCGTATTGCCCG
AATATCGATTCATCATTTATTGGAACTTTATTTATGTCAGTTTTCGAGAT
TGATCTGCATTGGTAATCTTTCAGTCGATTGAGCCAATTTGAATCTGACA
CATTTCTTAGAAGCTCCAATCTGAATTTTAACAGCTGAAGTAGAAATCTT
TAGAATGAAATCTTGGTATCCTTCAACACAGAGATGACTGTGCTGAAACT
GTCATGAAACAACGCAATATTTAAAAGTTGTTGGTAAATTTTGAAAATAA
AAAAATTCATGTTAAAAGATGAAGGTATTTAAACAAAACTAAATATTTGT
TATTTTTAATAACGCATTTGTAATTTAATTTAAATTTAGTAAAATCAATT
GAAAATTAAATTGATTAAAAGAATTACGCAACATTGGCTTTTAATTAAAT
AAAAAACATCAATCCAACATATATATTCTACTACAGTATATTTCGATAGA
ATCATTGTCTTAGTCTGGTAGATTTGAACCTAAACTGTATTGATTTAAAA
TCCTTTATTCAAACAAATAAAAATATCGGACTCTG
back to top

protein sequence of SMED30030072-orf-1

>SMED30030072-orf-1 ID=SMED30030072-orf-1|Name=SMED30030072-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MDKLSLVNAIDTDYVCKENSCKCAFLPFFISKNLNYSNGKSLALNLLKKI
VSLSPAITGYLYFAKRIVIEGAISYNVIIYFTDPIDPRHLKIDNCFWIDK
ENLKVFHNIYGYYNMGNELENILPLKDPSECGIY*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell