SMED30032534

Overview
NameSMED30032534
Smed IDSMED30032534
Length (bp)930
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30032534 (SMED30032534) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032534 (SMED30032534) 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.
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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



SMED30032534

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30032534SMESG000039061.1 SmedASXL_011323SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30032534SMESG000039061.1 dd_Smed_v4_29413_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30032534SMESG000039061.1 dd_Smed_v4_29413_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30032534SMESG000039061.1 dd_Smed_v4_29413_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30032534SMESG000039061.1 dd_29413dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30032534 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002519:52306..54619 -4493
Homology
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BLAST of SMED30032534 vs. Planmine SMEST
Match: SMESG000039061.1 (SMESG000039061.1)

HSP 1 Score: 526.939 bits (1356), Expect = 0.000e+0
Identity = 261/264 (98.86%), Postives = 262/264 (99.24%), Query Frame = 1 
Query:  118 MVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM 909
            MVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYS+SKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYS FENISL YQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM
Sbjct:    1 MVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSNSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSSFENISLIYQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM 264
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BLAST of SMED30032534 vs. Planmine SMEST
Match: SMESG000067818.1 (SMESG000067818.1)

HSP 1 Score: 379.793 bits (974), Expect = 9.759e-132
Identity = 182/291 (62.54%), Postives = 220/291 (75.60%), Query Frame = 1 
Query:   37 KKIRRLEIIAFLFCIANCQCQVLFFGKMVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM 909
            K  +  EI + LFCIA CQCQ  F GKMVCVFT +  +N +DLY+C   C IINC+VF YNNQTSLC FY +KETCQSRN C FVQAF+N+ FID LTN  +GRY++LKG++FSYGSG V  Y NL L+QNE +IIGPA GLHSA+G+Y +SK+L WSFESL+ DMN+R   AN++GNNIVSYLT+G C WYYNCYY I+QYQQYIGI NLVFGVISSS FDY   +NIS  Y+WH IVA NP   +IS  I ++L  YG C+ +  G T G ++DNIC P++AA   TCM
Sbjct:   87 KMFQLKEIGSLLFCIAFCQCQTEFSGKMVCVFTSIRNVNANDLYQCAWLCTIINCEVFQYNNQTSLCYFYFIKETCQSRNYCTFVQAFYNNNFIDTLTNPTSGRYRILKGVDFSYGSGAVVTYSNLNLNQNEALIIGPAKGLHSAVGRYYNSKILTWSFESLIKDMNNRSSKANVIGNNIVSYLTDGFCIWYYNCYYDIEQYQQYIGITNLVFGVISSSSFDYLNIKNISQIYRWHFIVAINPIFENISTHISDMLLTYGLCLWDLSGQTSGKVSDNICQPVIAAEHNTCM 377
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BLAST of SMED30032534 vs. Planmine SMEST
Match: SMESG000067818.1 (SMESG000067818.1)

HSP 1 Score: 379.793 bits (974), Expect = 1.335e-131
Identity = 182/291 (62.54%), Postives = 220/291 (75.60%), Query Frame = 1 
Query:   37 KKIRRLEIIAFLFCIANCQCQVLFFGKMVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM 909
            K  +  EI + LFCIA CQCQ  F GKMVCVFT +  +N +DLY+C   C IINC+VF YNNQTSLC FY +KETCQSRN C FVQAF+N+ FID LTN  +GRY++LKG++FSYGSG V  Y NL L+QNE +IIGPA GLHSA+G+Y +SK+L WSFESL+ DMN+R   AN++GNNIVSYLT+G C WYYNCYY I+QYQQYIGI NLVFGVISSS FDY   +NIS  Y+WH IVA NP   +IS  I ++L  YG C+ +  G T G ++DNIC P++AA   TCM
Sbjct:   96 KMFQLKEIGSLLFCIAFCQCQTEFSGKMVCVFTSIRNVNANDLYQCAWLCTIINCEVFQYNNQTSLCYFYFIKETCQSRNYCTFVQAFYNNNFIDTLTNPTSGRYRILKGVDFSYGSGAVVTYSNLNLNQNEALIIGPAKGLHSAVGRYYNSKILTWSFESLIKDMNNRSSKANVIGNNIVSYLTDGFCIWYYNCYYDIEQYQQYIGITNLVFGVISSSSFDYLNIKNISQIYRWHFIVAINPIFENISTHISDMLLTYGLCLWDLSGQTSGKVSDNICQPVIAAEHNTCM 386
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BLAST of SMED30032534 vs. Planmine SMEST
Match: SMESG000062836.1 (SMESG000062836.1)

HSP 1 Score: 234.572 bits (597), Expect = 3.268e-75
Identity = 113/239 (47.28%), Postives = 159/239 (66.53%), Query Frame = 1 
Query:  106 FFGKMVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSISIPIKNLLAAYGFC 822
            F GK VCVF        S +YEC VQC   NCQVF Y++Q  +CSFYL+ ETCQS+N CNFV+AF+N+ F DN T  NT RY++LKG+NF++G+G  + +      Q E ++IG  GG+ +A GQ  ++K++IW  E L+  MN++     L+ NNIVS LT+ +C WY NCY+SI+ Y +YIG  NLVFG + SS F +++F N    Y WHV++A + + G   I +KNLL+ +G+C
Sbjct:    6 FIGKSVCVFQSEFSFTSSSIYECSVQCCKQNCQVFSYDDQARICSFYLITETCQSQNSCNFVKAFYNTNFYDNFTAPNTVRYRLLKGINFTFGTGNPSLFQMTNPLQTEALLIGIQGGIQAAFGQIRNNKMIIWPSEDLIGKMNNKVEGIELIANNIVSILTSDQCIWYMNCYHSIEMYNKYIGTRNLVFGAVYSSVFSFNEFYNNLSFYNWHVVIAISSSTGMPGIDLKNLLSIFGYC 244
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BLAST of SMED30032534 vs. Planmine SMEST
Match: SMESG000016333.1 (SMESG000016333.1)

HSP 1 Score: 178.333 bits (451), Expect = 8.283e-54
Identity = 104/301 (34.55%), Postives = 159/301 (52.82%), Query Frame = 1 
Query:   34 MKKIRRLEIIAFLFCIANCQCQVLFFGKMVCVFTPVNIINVSDLYECGVQCAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFN---------------SKFIDNL--TNSNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQYSDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSIDQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSISIPIKNLLAAYGFCISNFGGSTGGWITDNICTPLV 885
            M K+ RL  +AFL  +   +    F  +  CVF P       +++ C + C   NC VF +N +T  CS Y  +ETC+S+N C +++++FN               SK++  +     +T RY +LK L+F +G G  + Y  +     EV+++G    + +A+G  S SKL+ W  + L+ +M+ R      L NN+ S+LT+ KCN Y+ CY+ +D Y+  +G+ N +FGV SSS FD   F    + Y+W+VIV  N  I   S  I NLL  +G C+S+  GS    I DNIC  L 
Sbjct:    1 MWKLFRLVALAFLVPV---ELFSYFSLRGACVFNPYKTSLTKNIFMCALFCEADNCDVFTFNRRTFSCSLYQSEETCESKNNCIYLKSYFNRNCSEKVYFYSMKYFSKYLLKIQCKAPSTARYNILKDLDFKFGEGLSSQYGIVDPRITEVIVVGKLKEVLAAVGSRSRSKLIAWPNDVLIKEMDQRLLKVQFLANNLASFLTDRKCNDYFRCYHEVDNYKALVGMENHIFGVQSSSSFDVYDFYKKVIKYEWNVIVGGNFGIIPPSDSIINLLDFFGICLSSHNGSFNWMIDDNICRELT 298
The following BLAST results are available for this feature:
BLAST of SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 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 SMED30032534 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039061.10.000e+098.86SMESG000039061.1[more]
SMESG000067818.19.759e-13262.54SMESG000067818.1[more]
SMESG000067818.11.335e-13162.54SMESG000067818.1[more]
SMESG000062836.13.268e-7547.28SMESG000062836.1[more]
SMESG000016333.18.283e-5434.55SMESG000016333.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032534 ID=SMED30032534|Name=SMED30032534|organism=Schmidtea mediterranea sexual|type=transcript|length=930bp
TAAAAAATTGATTATGATTTCCTTTGGATTCTGATGAAAAAAATCCGTAG
GTTGGAAATAATTGCATTTCTTTTCTGCATTGCCAATTGTCAATGTCAGG
TTTTATTTTTCGGAAAGATGGTCTGCGTATTCACGCCGGTCAACATAATA
AATGTCTCTGACTTGTATGAATGTGGCGTCCAATGTGCTATAATAAATTG
TCAAGTATTCCTATACAATAACCAAACATCCCTCTGTTCTTTCTATTTGT
TAAAAGAAACTTGTCAATCACGTAACCGCTGTAACTTTGTTCAGGCCTTT
TTCAACAGCAAATTCATTGATAACCTTACAAATTCAAATACTGGACGATA
CAAAGTATTGAAAGGGTTGAATTTTAGCTACGGTTCAGGGGGTGTGACGG
CTTATGTCAATTTAAGGTTAGATCAAAATGAAGTTGTGATAATAGGTCCA
GCGGGAGGTCTGCATTCCGCGATTGGGCAGTACAGTGATAGTAAACTATT
GATATGGTCCTTTGAAAGTCTACTAAATGACATGAATAGTAGGAAGCCAA
ATGCCAATCTCCTTGGAAATAATATCGTTTCATATCTCACAAATGGTAAA
TGTAATTGGTATTACAATTGCTATTATTCCATTGACCAATACCAACAATA
TATTGGGATAAATAATTTGGTATTTGGAGTGATCTCCTCTTCGTATTTCG
ATTATTCAAAGTTTGAAAATATCTCTTTGACGTATCAATGGCACGTAATT
GTTGCGACAAATCCTGCAATTGGAAGCATTAGCATTCCAATAAAGAATTT
ACTGGCGGCTTATGGATTTTGTATTTCGAATTTTGGGGGGTCAACTGGTG
GATGGATAACTGATAATATTTGCACTCCGTTAGTAGCAGCTACAGCAGTC
ACATGCATGTGATTAAGAACTTTATCATTA
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protein sequence of SMED30032534-orf-1

>SMED30032534-orf-1 ID=SMED30032534-orf-1|Name=SMED30032534-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=293bp
MKKIRRLEIIAFLFCIANCQCQVLFFGKMVCVFTPVNIINVSDLYECGVQ
CAIINCQVFLYNNQTSLCSFYLLKETCQSRNRCNFVQAFFNSKFIDNLTN
SNTGRYKVLKGLNFSYGSGGVTAYVNLRLDQNEVVIIGPAGGLHSAIGQY
SDSKLLIWSFESLLNDMNSRKPNANLLGNNIVSYLTNGKCNWYYNCYYSI
DQYQQYIGINNLVFGVISSSYFDYSKFENISLTYQWHVIVATNPAIGSIS
IPIKNLLAAYGFCISNFGGSTGGWITDNICTPLVAATAVTCM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000421tail