SMED30018325

Overview
NameSMED30018325
Smed IDSMED30018325
Length (bp)649
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30018325 (SMED30018325) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018325 (SMED30018325) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30018325

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30018325SMESG000069018.1 SmedASXL_001757SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30018325SMESG000069018.1 dd_Smed_v4_84586_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018325SMESG000069018.1 dd_Smed_v4_84586_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30018325SMESG000069018.1 dd_Smed_v4_84586_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
SMED30018325 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007771:1371..6669 +2999
Homology
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BLAST of SMED30018325 vs. Ensembl Xenopus
Match: ENSXETT00000021660.1 (hepatic lectin-like [Source:NCBI gene;Acc:101735287])

HSP 1 Score: 48.9062 bits (115), Expect = 1.451e-6
Identity = 33/113 (29.20%), Postives = 48/113 (42.48%), Query Frame = 3 
Query:   81 NSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQPL---KLGFNYSRWAKYEPNHAEAKEFCSYAYADGSWADYSC 410
             SC+Y +  E       +W  A  +C   N  L I+ +         L   S  W+GLK+D+   + W+   L     GF    W K EPN++  KE C + + D  W D  C
Sbjct:  120 GSCYYIVTTE------TNWTDAQAICKSMNSDLVIITSEKEQNFLESLTDESEFWIGLKRDKD-RWRWVDGTLHNPSEGF----WMKGEPNNSGGKEDCVHMWRDKKWNDKVC 221
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BLAST of SMED30018325 vs. TrEMBL
Match: A0A1I8HBV4 (C-type lectin domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 4.291e-10
Identity = 46/178 (25.84%), Postives = 76/178 (42.70%), Query Frame = 3 
Query:  126 FVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQP-----------LKLGFNYS-RWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDP---ILIYCHRFSDHKCQFSSPSKITFNEQAWYWPIIFSFITLI----FVLCIPLVLKQI 602
            +++W  A   C  +N TLP++   +     R      R W G  +     + W S             +K G      W+K EP+++   E C+    DG+ ADY C+ +  WDSC +P   +L  CHR     C+++S          +Y  +  +F  LI     VL + L++K +
Sbjct:   45 YLTWAQARDFCALYNATLPMMRTAYGWQRLRIYIENRRFWTGFVRTGSSEWTWQSGSDFDGSLATEDFVKTGNTTGIEWSKSEPSYSYCVENCTMVSYDGNLADYPCENVPPWDSCAEPADVVLTVCHRSDIEVCRYTSNPPAIPTPHDYYIIVGATFAALIGCAGAVLGVRLIVKTL 222
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BLAST of SMED30018325 vs. TrEMBL
Match: A0A1I8HKR3 (C-type lectin domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 9.533e-8
Identity = 42/157 (26.75%), Postives = 67/157 (42.68%), Query Frame = 3 
Query:   72 TSMNSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKK---------------DQQLNYFWISQPLKLGFNYS-------RWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDP---ILIYCHR 467
            +S + C ++L+       F++W  A   C  FN TLP+L   ++    R  A   R W+G+ +               DQ L  ++   P +   + S        W++ EP++A   E C     DG+ ADY+C  +  WD CGD    +   C R
Sbjct:  145 SSEHHCLFQLHARI----FLTWRQAAEFCALFNATLPVLRTQFAWQTLRSYAQNHRFWVGVVRAEGAVREGSQSATAGDQDLWRWYTDGPEEPPLSTSDFSRTGVEWSRSEPSNAHCGEACGVVNYDGNLADYACATVPPWDPCGDESHVVRTVCQR 297
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BLAST of SMED30018325 vs. TrEMBL
Match: A0A267FNQ0 (C-type lectin domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig007782g1 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.672e-7
Identity = 36/129 (27.91%), Postives = 57/129 (44.19%), Query Frame = 3 
Query:  126 FVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQP-----------LKLGFNYS-RWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDP---ILIYCHR 467
            +++W  A   C  +N TLP++   +     R      R W G  +    ++ W S             +K G      W+K EP+++   E C+    DG+ ADY C+ +  WDSC +P   +L  CHR
Sbjct:   78 YLTWAQARDFCALYNATLPMVRTAYGWQQLRIYIENRRFWTGFVRTGSSDWTWQSGSDFDGSLATEDFVKTGNTTGIEWSKSEPSYSYCVENCTMVSYDGNLADYPCENVPPWDSCAEPADVVLTVCHR 206
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BLAST of SMED30018325 vs. TrEMBL
Match: A0A1I8G8U9 (C-type lectin domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.986e-7
Identity = 42/161 (26.09%), Postives = 67/161 (41.61%), Query Frame = 3 
Query:   72 TSMNSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKK---------------DQQLNYFWISQPLKLGFNYS-----------RWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDP---ILIYCHR 467
            +S + C ++L+       F++W  A   C  FN TLP+L   ++    R  A   R W+G+ +               DQ L  ++   P +   + S            W++ EP++A   E C     DG+ ADY+C  +  WD CGD    +   C R
Sbjct:  138 SSEHHCLFQLHARI----FLTWRQAAEFCALFNATLPVLRTQFAWQTLRSYAQNHRIWVGVVRAEGAVREGSQSATAGDQDLWRWYTDGPEEPPLSTSDFSRTDNRTGVEWSRSEPSNAHCGEACGVVNYDGNLADYACATVPPWDPCGDESHVVRTVCQR 294
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BLAST of SMED30018325 vs. Planmine SMEST
Match: SMESG000069018.1 (SMESG000069018.1)

HSP 1 Score: 398.282 bits (1022), Expect = 1.954e-143
Identity = 190/190 (100.00%), Postives = 190/190 (100.00%), Query Frame = 3 
Query:   78 MNSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQPLKLGFNYSRWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDPILIYCHRFSDHKCQFSSPSKITFNEQAWYWPIIFSFITLIFVLCIPLVLKQIGDKYVKMNSKSYLTN 647
            MNSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQPLKLGFNYSRWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDPILIYCHRFSDHKCQFSSPSKITFNEQAWYWPIIFSFITLIFVLCIPLVLKQIGDKYVKMNSKSYLTN
Sbjct:    1 MNSCFYRLYFENGTVPFVSWNTAFGLCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQPLKLGFNYSRWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDPILIYCHRFSDHKCQFSSPSKITFNEQAWYWPIIFSFITLIFVLCIPLVLKQIGDKYVKMNSKSYLTN 190
The following BLAST results are available for this feature:
BLAST of SMED30018325 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 SMED30018325 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 SMED30018325 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 SMED30018325 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 SMED30018325 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSXETT00000021660.11.451e-629.20hepatic lectin-like [Source:NCBI gene;Acc:10173528... [more]
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BLAST of SMED30018325 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 SMED30018325 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 SMED30018325 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A1I8HBV44.291e-1025.84C-type lectin domain-containing protein OS=Macrost... [more]
A0A1I8HKR39.533e-826.75C-type lectin domain-containing protein OS=Macrost... [more]
A0A267FNQ02.672e-727.91C-type lectin domain-containing protein OS=Macrost... [more]
A0A1I8G8U92.986e-726.09C-type lectin domain-containing protein OS=Macrost... [more]
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BLAST of SMED30018325 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 SMED30018325 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 SMED30018325 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 SMED30018325 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 SMED30018325 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 SMED30018325 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000069018.11.954e-143100.00SMESG000069018.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018325 ID=SMED30018325|Name=SMED30018325|organism=Schmidtea mediterranea sexual|type=transcript|length=649bp
CTTCGATAGTAAATGTAATTAATCTCAGTAAAATTTGTTTTCAGTCTCAG
CCGGTTCTGGATATGAAAAAGACCTCAATGAACTCGTGCTTTTATCGTCT
CTATTTTGAGAATGGTACGGTACCATTTGTAAGCTGGAACACTGCATTTG
GACTATGCCACAAGTTCAATGATACATTGCCGATTCTTTTCAATCACTGG
TCAATCTTTGCTTTTAGAGAATTGGCATTAACTTCGAGAAGCTGGCTAGG
TTTGAAGAAAGATCAACAATTAAATTATTTTTGGATTTCTCAACCTTTAA
AGTTGGGATTTAATTATTCTCGATGGGCAAAATATGAACCAAATCATGCT
GAGGCTAAAGAGTTTTGCTCGTACGCTTATGCTGATGGATCCTGGGCGGA
TTATTCGTGCGATGAAATAGCTGATTGGGACAGTTGTGGAGATCCAATTC
TGATATATTGTCATCGGTTTTCGGATCATAAATGTCAATTTTCATCGCCT
TCTAAAATAACATTTAATGAGCAAGCTTGGTATTGGCCTATAATATTCTC
TTTTATTACTTTGATATTTGTTCTTTGTATTCCTTTGGTTTTGAAGCAAA
TTGGTGATAAATATGTGAAAATGAATTCCAAATCATATTTGACAAATCC
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protein sequence of SMED30018325-orf-1

>SMED30018325-orf-1 ID=SMED30018325-orf-1|Name=SMED30018325-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp
SIVNVINLSKICFQSQPVLDMKKTSMNSCFYRLYFENGTVPFVSWNTAFG
LCHKFNDTLPILFNHWSIFAFRELALTSRSWLGLKKDQQLNYFWISQPLK
LGFNYSRWAKYEPNHAEAKEFCSYAYADGSWADYSCDEIADWDSCGDPIL
IYCHRFSDHKCQFSSPSKITFNEQAWYWPIIFSFITLIFVLCIPLVLKQI
GDKYVKMNSKSYLTN
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR016186C-type_lectin-like/link_sf
IPR001304C-type_lectin-like
IPR016187CTDL_fold
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR016186C-type lectin-like/link domain superfamilyGENE3DG3DSA:3.10.100.10coord: 7..143
e-value: 1.6E-12
score: 49.3
IPR001304C-type lectin-likePFAMPF00059Lectin_Ccoord: 44..138
e-value: 6.4E-6
score: 26.9
IPR001304C-type lectin-likePROSITEPS50041C_TYPE_LECTIN_2coord: 44..138
score: 12.442
IPR016187C-type lectin foldSUPERFAMILYSSF56436C-type lectin-likecoord: 43..139
NoneNo IPR availableTMHMMTMhelixcoord: 175..197