SMED30020808

Overview
NameSMED30020808
Smed IDSMED30020808
Length (bp)901
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30020808

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
nervous systemSMED30020808h1SMcG0008817 dd_Smed_v4_28244_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020808h1SMcG0008817 dd_Smed_v4_28244_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30020808h1SMcG0008817 dd_Smed_v4_28244_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
SMED30020808 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001132:8416..9315 -4491
Homology
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BLAST of SMED30020808 vs. Planmine SMEST
Match: SMESG000076257.1 (SMESG000076257.1)

HSP 1 Score: 542.732 bits (1397), Expect = 0.000e+0
Identity = 261/261 (100.00%), Postives = 261/261 (100.00%), Query Frame = 2 
Query:  119 MAVEKYLIFLLISGLPADPLSRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVFLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFPTRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYNDS 901
            MAVEKYLIFLLISGLPADPLSRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVFLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFPTRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYNDS
Sbjct:    1 MAVEKYLIFLLISGLPADPLSRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVFLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFPTRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYNDS 261
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BLAST of SMED30020808 vs. Planmine SMEST
Match: SMESG000032522.1 (SMESG000032522.1)

HSP 1 Score: 236.884 bits (603), Expect = 3.706e-77
Identity = 118/264 (44.70%), Postives = 165/264 (62.50%), Query Frame = 2 
Query:  140 IFLLISGLPADPL----SRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPV---FLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFP----TRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYND 898
            IF+L   + A PL      M C  T Y  KL+YF+I   IC  PQ +  Q    + Q  +E++P  + VFR+VT SGVS+L   + +N  T  G     ++ D+K+NYS+N RS ILD+WN IKP  MNVTI+D ND TVAWLFF V ++D+L+SWF ++NLL S  W++  +  + Y +FNI+    P     R FFIN     CP ++GV C+FD+ D C +G++T GYPLI+Y + NG G NW  ++  AKS+EI ATY++
Sbjct:    5 IFMLSVFMLAGPLVGLLGAMQCPITNYNKKLSYFVIPKPICNPPQEVASQSFQMNLQIRFESLPKPMTVFRLVTGSGVSSLKFFSEKNGGTQAGQSETKYVIDKKRNYSQNFRSLILDEWNSIKPINMNVTIKDSNDFTVAWLFFKVDKTDTLISWFKKENLLSSHPWNIKMLLGNLYNYFNISGHAPPDQPVIRLFFINLSYGGCPNDVGVFCVFDRADPCPFGKSTCGYPLIKYAIHNGNGANWNHYSTAAKSMEIVATYDE 268
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BLAST of SMED30020808 vs. Planmine SMEST
Match: SMESG000076260.1 (SMESG000076260.1)

HSP 1 Score: 233.417 bits (594), Expect = 6.880e-76
Identity = 121/251 (48.21%), Postives = 165/251 (65.74%), Query Frame = 2 
Query:  164 PADPLSRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRST--DYGPVF-LFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFP--TRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYNDS 901
            PA P  ++ CA TA   KL YFI+ NQ C++PQ  +        QF ++ +PN+L V R+V+ SGV+    L GQN S+  D   +F + D+  NYS N RS +LD+W+ +KP FMNVTI+D +  T AWLFF V  +DSL SWF + NLLKSF W+V+ + R+ Y +F+IT        R FFIN     CPG++GVLC+F   D C YGQT SGYPLI+YV++NG G NW  +++TA+++EITA Y+DS
Sbjct:   20 PA-PAKQIECAMTALNKKLIYFIMLNQTCFNPQSTSSLSFQIKLQFMFQKLPNQLVVLRIVSGSGVNPPYFLIGQNISSQIDTSDIFSVVDKMSNYSNNFRSILLDEWSNVKPMFMNVTIKDSSAITKAWLFFKVDPNDSLSSWFRKTNLLKSFPWNVEILLRNNYNYFDITGHTTDQLKRNFFINIYYNYCPGDVGVLCVFGIADGCSYGQTNSGYPLIKYVIKNGNGGNWTSYSVTAQAMEITAIYDDS 269
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BLAST of SMED30020808 vs. Planmine SMEST
Match: SMESG000034452.1 (SMESG000034452.1)

HSP 1 Score: 231.876 bits (590), Expect = 1.381e-75
Identity = 120/242 (49.59%), Postives = 161/242 (66.53%), Query Frame = 2 
Query:  176 LSRMNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVFLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNE--KFPTRYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYN 895
            ++ +NCA  A+  KL+Y +IAN+ CYHPQ +T Q   T++QF Y  +PN L VFR++T S V+ +   T Q    D   +F+ D+++    N RSPILD+WN IKP FMNVTI+D ND  V WLFF V Q+DSLLSWF++ NLL SF WD+DK+  + Y FF++  +      R FFI+ L Y CP + G+LCIF   D C Y Q+T+GYPLI+YV+ NG G  W   ++ AKSLEI ATY+
Sbjct:    1 MNVVNCAIDAFNKKLSYLVIANETCYHPQNMTSQPFQTNSQF-YVRIPNLLTVFRILTGSEVNPVTFFTMQMVLNDI--MFVEDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLNSFPWDIDKLLSNNYRFFSVIGDINLNKQRNFFISILYYGCPNDTGILCIFGLSDPCSYSQSTAGYPLIKYVINNGNGGLWNTSSL-AKSLEIIATYD 238
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BLAST of SMED30020808 vs. Planmine SMEST
Match: SMESG000034404.1 (SMESG000034404.1)

HSP 1 Score: 231.106 bits (588), Expect = 4.600e-75
Identity = 125/257 (48.64%), Postives = 164/257 (63.81%), Query Frame = 2 
Query:  137 LIFLLISGLPADPLSR--MNCAATAYLNKLNYFIIANQICYHPQRLTPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVFLFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQSDSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFPT--RYFFINSLNYQCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAKSLEITATYN 895
            +I LL+    A P S   +NC+  A+  KL+Y +IAN+ CYHPQ +T Q   T++Q  Y  +PN L VFR++T SGV+ +   T Q   +D   +F  D+++    N RSPILD+WN IKP FMNVTI+D ND  V WLFF V Q+DSLLSWF++ NLLKSF WD+DK+  S Y  F++  +  P   R FFI+ L   C  + G+LCIF   D C YGQ+T+GYPLIRY +  G G  W    + AKSLEI ATY+
Sbjct:    5 IILLLVLSPLAVPQSMDIINCSIVAFNKKLSYMVIANETCYHPQNMTSQPFQTNSQI-YARIPNLLTVFRILTGSGVNPVTFFTKQMVLSDV--MFAEDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLKSFPWDIDKLLSSYYPVFSVIGDTQPNVQRNFFISILYNGCSYDSGILCIFGLSDPCSYGQSTAGYPLIRYAINYGNGGPWTTSNL-AKSLEIIATYD 257
The following BLAST results are available for this feature:
BLAST of SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 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 SMED30020808 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000076257.10.000e+0100.00SMESG000076257.1[more]
SMESG000032522.13.706e-7744.70SMESG000032522.1[more]
SMESG000076260.16.880e-7648.21SMESG000076260.1[more]
SMESG000034452.11.381e-7549.59SMESG000034452.1[more]
SMESG000034404.14.600e-7548.64SMESG000034404.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020808 ID=SMED30020808|Name=SMED30020808|organism=Schmidtea mediterranea sexual|type=transcript|length=901bp
GTAAATGAAAACAATTCATTTTTAGTATTAATATAAGTGAAATATGTGAA
ATATTAATTATTTATTATTTATTTGATTAGTTTCTGATTTTCTGCTGTGC
TTGCAGACTCGAGCCGTGATGGCTGTTGAGAAATATTTGATATTCCTTCT
CATATCCGGGCTGCCGGCCGATCCGCTCAGTCGGATGAACTGTGCTGCTA
CTGCGTATCTCAATAAATTGAACTATTTTATAATTGCTAATCAGATTTGC
TACCATCCACAACGTTTGACCCCCCAATTGCTCCATACCGACACTCAATT
CACATATGAAAATGTCCCGAATGAACTGGCCGTGTTTCGGGTTGTCACGG
CAAGTGGAGTGAGCACTCTGGACTTGCTTACTGGCCAGAACCGTTCGACA
GACTATGGGCCAGTTTTCCTGTTCGATAGAAAGAAAAATTACTCGGAAAA
CATTCGAAGTCCCATTCTCGATGATTGGAACATCATCAAGCCAACATTTA
TGAATGTCACGATCCAGGATTACAATGATTCCACAGTTGCGTGGCTGTTT
TTCACGGTTAAACAATCGGATTCTTTGCTTTCCTGGTTCAGCAGAGATAA
TCTCTTGAAATCCTTCTACTGGGACGTTGATAAAATAGCAAGAAGTGCTT
ACATTTTCTTTAATATCACTAATGAAAAATTCCCAACTCGCTATTTCTTC
ATAAATTCCTTGAATTATCAATGTCCTGGAAACATGGGTGTTCTTTGTAT
TTTTGATAAATGGGATGAATGCGAATACGGACAAACGACTTCCGGATATC
CGCTAATAAGATACGTGATGCGTAACGGTGAAGGGTACAACTGGAAGGTA
TTTGCAATCACCGCAAAATCGCTGGAAATAACAGCGACCTATAATGACTC
C
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protein sequence of SMED30020808-orf-1

>SMED30020808-orf-1 ID=SMED30020808-orf-1|Name=SMED30020808-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=261bp
MAVEKYLIFLLISGLPADPLSRMNCAATAYLNKLNYFIIANQICYHPQRL
TPQLLHTDTQFTYENVPNELAVFRVVTASGVSTLDLLTGQNRSTDYGPVF
LFDRKKNYSENIRSPILDDWNIIKPTFMNVTIQDYNDSTVAWLFFTVKQS
DSLLSWFSRDNLLKSFYWDVDKIARSAYIFFNITNEKFPTRYFFINSLNY
QCPGNMGVLCIFDKWDECEYGQTTSGYPLIRYVMRNGEGYNWKVFAITAK
SLEITATYNDS
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..17
score: 0.471