SMED30009213

Overview
NameSMED30009213
Smed IDSMED30009213
Length (bp)1412
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 SMED30009213 (SMED30009213) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009213 (SMED30009213) 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 SMED30009213 (SMED30009213) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009213 (SMED30009213) 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




SMED30009213

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
headSMED30009213SMESG000036688.1 SmedASXL_015375SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30009213SMESG000036688.1 dd_Smed_v4_13309_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30009213SMESG000036688.1 dd_Smed_v6_13309_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009213 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005568:11159..20850 -6822
Homology
BLAST of SMED30009213 vs. TrEMBL
Match: A0A4C1ZQR1 (Zinc finger MYM-type protein 1 OS=Eumeta variegata OX=151549 GN=ZMYM1 PE=4 SV=1)

HSP 1 Score: 88.5817 bits (218), Expect = 8.490e-15
Identity = 68/219 (31.05%), Postives = 94/219 (42.92%), Query Frame = 1
Query:  784 MPRPASFFQGNLKSTLSQNTDNNAGHSVSAAGTDSGTADVIKITGPS-------KVNESKSTELTVNKSVNVSEDYYKLATTCSLVTSLKSSSNCNRDNDPGTWQKFDSDYAAYWIDKESSD*QHHCGLFHNSVRAFPNERKKKRICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLI---RFAAQGFDDWKNPVVIEQHGKSPVH 1410
            +P+  SFF  N    L    DNN      +  +     D    TG S       ++N    T + V    + SE +       S +  L    N N++ D G W +F  +   YWID    + QHH G FH S R + +  K  R C+  +F+    + ET  REWLL S +   LY FV K    +       +FAA GF DW+N + IE H  S  H
Sbjct:  133 LPKMTSFFPTN---QLESGKDNNVCQESQSLSSVRKQIDKNSTTGTSDDHFDDDEINSEIKTPVPVP---DKSEPFIVAIPEVSKIELL----NSNKNIDAGLWTEFSEEDICYWIDHGPENCQHHQGPFHESRRTYASG-KSVRFCTPRLFFGKKANGETYKREWLLYSKTKGSLYCFVCKLFGNKSIATAPSQFAADGFSDWRNVIAIEHHENSSAH 340          
BLAST of SMED30009213 vs. TrEMBL
Match: A0A4C1VLS1 (Zinc finger MYM-type protein 1 OS=Eumeta variegata OX=151549 GN=ZMYM1 PE=4 SV=1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.823e-13
Identity = 47/126 (37.30%), Postives = 62/126 (49.21%), Query Frame = 1
Query: 1042 NCNRDNDPGTWQKFDSDYAAYWIDKESSD*QHHCGLFHNSVRAFPNERKKKRICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLI---RFAAQGFDDWKNPVVIEQHGKSPVH 1410
            N N+  D G W +F  +   YWID    + Q H G FH S R + +  K  R C+  +F+    + ET  REWLL S +   LY FV K    +       +FAA GF DW+N + IE H  S  H
Sbjct:  205 NSNKKTDAGLWTEFSEEDICYWIDHGPENCQLHQGPFHESRRTYASG-KSVRFCTPRLFFGKKANGETYKREWLLYSKTKGSLYCFVCKLFGNKSIATAPSQFAADGFSDWRNVIAIEHHENSSAH 329          
BLAST of SMED30009213 vs. TrEMBL
Match: A0A4C1V5P8 (TTF-type domain-containing protein OS=Eumeta variegata OX=151549 GN=EVAR_30704_1 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 7.384e-11
Identity = 43/118 (36.44%), Postives = 57/118 (48.31%), Query Frame = 1
Query: 1066 GTWQKFDSDYAAYWIDKESSD*QHHCGLFHNSVRAFPNERKKKRICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLI---RFAAQGFDDWKNPVVIEQHGKSPVH 1410
            G W +F  +   YWID    + QHH G FH S   + +  K    C+  +F+    + ET  REWLL S +   LY FV K    +       +FAA GF DW+N + IE H  S  H
Sbjct:  266 GLWTEFSEEDICYWIDHGPENCQHHQGPFHESRHTYASG-KSVCFCTPRLFFGKKANGETYKREWLLYSKTKGSLYCFVCKLFGNKSIATAPSQFAADGFSDWRNVIAIEHHENSSAH 382          
BLAST of SMED30009213 vs. TrEMBL
Match: K7IYW1 (Uncharacterized protein OS=Nasonia vitripennis OX=7425 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 9.499e-8
Identity = 56/183 (30.60%), Postives = 87/183 (47.54%), Query Frame = 1
Query:  880 TDSGTADVIK--ITGPS-KVNESKSTELTVNKSVNVSEDYYKLATTCSLVTSLKSSSNCNRD--NDPGTWQKFDSDYAAYWIDKESSD*QHHCGLFHNSVRAF-PNERKKKRICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLIRFAAQGFDDWKNPVVIEQHGKSPVH 1410
            T  GTAD+ +  I   S  +N S+ +EL+V   V ++    + A       +L+S+S  N     D   W + +     YW+ K      +    F  S R +   +++K R  +KS+F   + +NE   REWL  SPST  +Y FV +  S      +F   GF+DWK+P  I +H +S  H
Sbjct:   44 TPKGTADLQENVIQNESVDLNPSEQSELSVATQVLINHRTEEEA-------ALRSTSEKNESYSTDIALWGEINEKLRLYWLQKNPGLCSNKDKDFSKSARIYQEGDKQKVRTLNKSLFQLKLQNNEIVEREWLSYSPSTGRIYCFVCRLFSSEKD--QFTFYGFNDWKHPERITEHEQSKAH 217          
BLAST of SMED30009213 vs. TrEMBL
Match: G3TY18 (TTF-type domain-containing protein OS=Loxodonta africana OX=9785 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 2.416e-7
Identity = 31/72 (43.06%), Postives = 40/72 (55.56%), Query Frame = 1
Query: 1195 RICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLIRFAAQGFDDWKNPVVIEQHGKSPVH 1410
            R CS+++F     + E   REWLL SPS   +Y FV K  SP+    RFA  GF DW N  +I +H  S +H
Sbjct:    1 RFCSQNIFLGCKANGENYKREWLLYSPSVGSVYCFVCKLFSPKSFNSRFATDGFSDWSNSNMIHKHENSSIH 72          
BLAST of SMED30009213 vs. Planmine SMEST
Match: SMESG000032685.1 (SMESG000032685.1)

HSP 1 Score: 53.1434 bits (126), Expect = 3.288e-7
Identity = 43/135 (31.85%), Postives = 59/135 (43.70%), Query Frame = 1
Query: 1012 SLVTSL-KSSSNCNRDNDPGTWQKFDSDYAAYWIDKESSD*QHHCGLFHNSVRAFPNERKKKRICSKSMFYRMMPDNETTIREWLLESPSTEFLYNFV*KFLSPRPRLIRFAAQGFDDWKNP-VVIEQHGKSPVH 1410
            +LV SL +SS N NR+ND G W +  S+   YWI+K     QH    FH+S                    + + ++ T  RE L+ SP    ++ FV K L+        A  G  DWKN    I+ H  S  H
Sbjct:   91 NLVESLIESSPNANRENDVGLWGELSSEDTLYWIEKGPESCQHSTENFHSS--------------------KQLYNDNTYTRESLVYSPKIGNVFCFVCKLLTASN--FNLATNGLRDWKNAGSSIKSHQNSSEH 203          
The following BLAST results are available for this feature:
BLAST of SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4C1ZQR18.490e-1531.05Zinc finger MYM-type protein 1 OS=Eumeta variegata... [more]
A0A4C1VLS11.823e-1337.30Zinc finger MYM-type protein 1 OS=Eumeta variegata... [more]
A0A4C1V5P87.384e-1136.44TTF-type domain-containing protein OS=Eumeta varie... [more]
K7IYW19.499e-830.60Uncharacterized protein OS=Nasonia vitripennis OX=... [more]
G3TY182.416e-743.06TTF-type domain-containing protein OS=Loxodonta af... [more]
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BLAST of SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 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 SMED30009213 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032685.13.288e-731.85SMESG000032685.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009213 ID=SMED30009213|Name=SMED30009213|organism=Schmidtea mediterranea sexual|type=transcript|length=1412bp
AACAAAATGCTTAACCAACTTCAACAGTAAATTGATAGAAAAAATAAGAA
AATCTGAGTCAATCTTCCAACATGCCACCGAGTAAAACGAACAATTTCTG
CTAGTATGCTCTTCAATATACATTTCTGTCGCATAGCCATTCTTGTTGCA
GCGCTTGATTCTAATGTGGAAACATATAGGTAAATGCTGCTGTTAATACA
GACATGTAACAAGCTCAGTGGAAAACTGGTCATTTAGAGGGGGAGGATGG
TGAGAAGTTATTCTTATTTTCGAATTAGATGAACAGTATTATTAATTGAT
CTGTTAGAGAAGAGAATATTTTTTCCCCAGAAATTCACAGAAATGCCTCA
TTATTAATTGCAAGATGGGATTATCAAAGTAAATGCAGCCTTGTACATGA
ACAATCGAATCAGCATGTTTTGTATTTGGTCATGTACGCAGGTGCACACA
CAACATTGCAGTATGCGCACACACATGTGCATACACACAGAGCTCCAAGT
ACAACTGTGACTCCATGAATACACACGACAATAGCCACATCAATAAATTC
TCAAATCTCATTCGTTGAACAGCAACAGAAGATGTATTTGTACATCGTTG
TATTTCATCGTCATTGTCATTATGAATCCTCTTCATTTTCAAGATTATCG
AATTACTCGTGGGTGATTTATTCTTCCGGACTCTACCGTAAATAAAACTA
GTCCAGACAGATAAAAAAAATGAAGCGTGAACAATTAAGTGGGGCGCAGA
AATGAAACATAAGGCTGAAGCTATTGTGCAAAAATGCCAAGACCGGCTTC
ATTCTTTCAAGGAAATTTGAAATCAACATTGTCGCAAAATACGGACAATA
ATGCTGGACATTCTGTATCAGCAGCAGGCACTGACTCTGGTACTGCTGAT
GTAATAAAAATAACAGGTCCAAGTAAAGTTAATGAATCAAAGTCTACAGA
ACTCACTGTGAATAAGTCTGTGAATGTGTCAGAAGATTATTACAAGCTGG
CGACTACTTGCTCATTAGTGACTTCACTGAAATCCAGTAGTAATTGCAAT
AGAGATAATGATCCTGGTACCTGGCAGAAATTCGACAGCGATTATGCAGC
ATACTGGATAGACAAAGAATCATCAGACTGACAGCATCATTGTGGACTAT
TTCATAACTCAGTTCGTGCATTCCCTAATGAACGTAAGAAGAAAAGAATT
TGCTCAAAATCTATGTTTTATCGCATGATGCCTGATAATGAGACAACCAT
TCGTGAATGGCTTCTTGAATCTCCGTCAACAGAATTTCTGTACAATTTTG
TATGAAAATTTCTTTCACCAAGACCACGCTTAATTCGATTTGCTGCACAG
GGGTTCGATGACTGGAAAAATCCTGTTGTCATAGAACAACATGGGAAAAG
TCCTGTTCATGG
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protein sequence of SMED30009213-orf-1

>SMED30009213-orf-1 ID=SMED30009213-orf-1|Name=SMED30009213-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=116bp
MPRPASFFQGNLKSTLSQNTDNNAGHSVSAAGTDSGTADVIKITGPSKVN
ESKSTELTVNKSVNVSEDYYKLATTCSLVTSLKSSSNCNRDNDPGTWQKF
DSDYAAYWIDKESSD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..37
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 8..34