SMED30021298

Overview
NameSMED30021298
Smed IDSMED30021298
Length (bp)1243
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 SMED30021298 (SMED30021298) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021298 (SMED30021298) 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



SMED30021298

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30021298 dd_Smed_v4_21183_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
SMED30021298 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001063:51945..53020 -4997
v31.004092:21057..22203 -4324
Homology
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BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 229.95 bits (585), Expect = 1.313e-72
Identity = 154/308 (50.00%), Postives = 192/308 (62.34%), Query Frame = 1 
Query:  286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEIIPAPXXXXXXXXXXXXXXXXYQWIFALWRYQQTYKSSFLPGL---------PLRDVVPKISSGRSSPQIISVIEPQVRGNFDRVASNLSRTLSNFGPRRPKKRCLPIDIDEE 1182
            MN+PRI +I+PAPS VA AQYL KLE EN  L+EKY++LK TWCSPE TRE YKKI RLSRARDDL IE+R QRI I Y+ +A RQIFTEKE Q +LP RNM Q LDIIP HHL  N  N  ++ + N  T +   S  N+RH+ N+NRRRRQ+++AE A LQ+NL V EN +L  I+E F  +P+ + +  DL +I APR  + S                       Y +  L  +         P RD    ISSGRSSPQIISVIEP +  N  + + NL R  S+   R PK++ LP+DIDEE
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITM--------DNYSAEMLINMQISIASRTTPDRDA---ISSGRSSPQIISVIEPTI--NRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEE 295
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BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000004294.1 (SMESG000004294.1)

HSP 1 Score: 185.652 bits (470), Expect = 5.515e-57
Identity = 106/197 (53.81%), Postives = 124/197 (62.94%), Query Frame = 1 
Query:  286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEII 876
            MN+PRI +I+P PS VAAAQYL KLE EN  L+EKY+KLK TWCS EATRELYK I RLSRARDDL IE+R QRITI  Q++ LRQIFTEKELQ +LP RNM Q LDII AHHL  N  N  +   PN     P                     RAE   +QANL V EN +L  ++E F  EP  + +  +L +I
Sbjct:    1 MNLPRIPKISPPPSAVAAAQYLEKLERENFALREKYNKLKFTWCSTEATRELYKMITRLSRARDDLIIENRSQRITISDQNATLRQIFTEKELQARLPSRNMVQRLDIILAHHLSKNPENQRDYWPPNCRRCQPEIGV-----------------RAENTLIQANLGVRENASLGSVTELFGLEPTVLNDGENLGVI 180
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BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000062943.1 (SMESG000062943.1)

HSP 1 Score: 176.022 bits (445), Expect = 8.029e-54
Identity = 92/132 (69.70%), Postives = 104/132 (78.79%), Query Frame = 1 
Query:  286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINS-----SNLTNSEDP 666
            MN+ RI RIAPAPS VAAAQY  KL+ EN  L+EKY+KLK TWCSPEAT+EL KKI  LSRARDDL I++RGQRITI  QS+ALRQIFTEKELQ +LP RNM Q LDIIPAHHL  NS     +N TN++ P
Sbjct:    1 MNLRRIPRIAPAPSTVAAAQYAEKLKRENFTLREKYNKLKCTWCSPEATKELIKKITWLSRARDDLIIKNRGQRITISDQSAALRQIFTEKELQARLPSRNMTQRLDIIPAHHLPANSEGSKENNETNTQFP 132
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BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 178.333 bits (451), Expect = 5.537e-53
Identity = 136/297 (45.79%), Postives = 175/297 (58.92%), Query Frame = 1 
Query:  286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPXXXXXXXXXXXXXXXXXAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEIIPAPXXXXXXXXXXXXXXXXYQWIFALWRYQQTYKSSFLPGLPLRDVVPKISSGRSSPQIISVIEPQVRGNFDRVASNLSRTLSNFGPRRPKKRCLPIDID 1176
            MN+P I+RI  AP  VA  Q L  LE EN I++EKY K+KGTWCSP+AT+EL+KKI  LSR RDDL IE+R Q++TI  QS+ALRQIFTEKELQ +LP RN+AQ ++IIPAHHL  N+ N   ++D   ST     S  NRRHK N+NRR+RQ++RAE   L ANLR  E P+++ + ++   E     +  D EII AP               I+  I    R     +                SSGRSSP II V EP      +++A    +  S+   R PK+RCLP+DID
Sbjct:    1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIREKYEKIKGTWCSPDATKELHKKITSLSRDRDDLVIETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQD--NSTPEDGISHANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAI--SGYDKEIIYAP----------LNPSPIHINIATTSRAMLEEEGQ--------------SSGRSSPLIILVTEPTAPQ--EQMAGFPQQPESHPTARCPKRRCLPVDID 267
[Close]
BLAST of SMED30021298 vs. Planmine SMEST
Match: SMESG000021652.1 (SMESG000021652.1)

HSP 1 Score: 167.162 bits (422), Expect = 1.591e-50
Identity = 86/136 (63.24%), Postives = 101/136 (74.26%), Query Frame = 1 
Query:  286 MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATRELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGRNMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNS 693
            M++P+I +I  AP VV AAQ+L  LENE  ILKEKY+K+KG W S EAT ELYKKI R+SRA DDL IE+R QRITI  QS+ALRQ FTEKELQ +LPGRN AQ L+ IPA+HL ++SSN    E  N  TT P S
Sbjct:    1 MHLPKIPKITQAPLVVTAAQHLPNLENEQRILKEKYAKMKGIWLSKEATSELYKKITRISRAHDDLIIENRSQRITIADQSAALRQTFTEKELQARLPGRNTAQPLNSIPAYHLLVDSSNYAEHEVSNIVTTTPTS 136
The following BLAST results are available for this feature:
BLAST of SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 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 SMED30021298 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046646.11.313e-7250.00SMESG000046646.1[more]
SMESG000004294.15.515e-5753.81SMESG000004294.1[more]
SMESG000062943.18.029e-5469.70SMESG000062943.1[more]
SMESG000021151.15.537e-5345.79SMESG000021151.1[more]
SMESG000021652.11.591e-5063.24SMESG000021652.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021298 ID=SMED30021298|Name=SMED30021298|organism=Schmidtea mediterranea sexual|type=transcript|length=1243bp
GAGACAATTATTTTGTAGGCCGATCATTCAAATTGAACAATGATCGCTAT
ATACGCTTCTACACCCATCAATGCAATATAATCGAGCTAAAACTAACTAA
GTATTATTTCTAAAAATCTAACACATCCGCGAAAATTGTATTTCTTTGTT
TTTGTTTTGTGTCTGAGAACTCGAGTCGAATTCAAGAATTTACGGAGTAC
TTACAATAATTTCATTTATTTCTAACAAATATCACTCACTTAAATCTCAT
ATCAATTCTATCACCTTCAGAAAGTCTCAGCAACAATGAACATGCCAAGA
ATTCTGAGAATAGCCCCAGCCCCATCAGTTGTCGCTGCCGCTCAATACCT
GGCGAAGTTAGAAAATGAAAATTGTATTTTAAAGGAAAAATATTCCAAAT
TGAAAGGAACATGGTGCTCCCCAGAGGCCACGAGGGAGCTGTATAAGAAA
ATAATGCGGCTTTCCCGAGCCCGCGATGATCTCAGTATAGAAAGCCGAGG
ACAAAGGATCACAATTTTATATCAGAGTTCCGCATTGAGGCAAATATTTA
CCGAGAAGGAGCTGCAGGTGCAGCTACCGGGTCGGAATATGGCCCAATTA
CTCGATATCATCCCGGCACATCACCTGCAAATCAATTCCTCAAATCTAAC
GAACAGCGAAGACCCTAATGCGTCCACCACAATACCAAATTCGTCGGCCC
CTAATCGTCGACATAAGCTAAATAAGAACCGACGAAGAAGACAAAAGAAG
AGGGCTGAGACTGCCGCATTACAGGCGAATTTGAGAGTCATAGAAAATCC
GAATCTGAGCAGAATATCGGAGACATTTTTGCAAGAACCTGTGTTTATGC
CTAATGATACCGATCTGGAAATAATTCCTGCGCCCAGATTATCGAATTCT
TCCAGTCTGCTCCGACGCCTTCTCATATCAATATATCAATGGATATTCGC
TCTATGGAGATACCAACAAACGTACAAATCTTCATTTCTACCAGGACTAC
CACTGAGAGACGTCGTACCCAAAATCTCCAGTGGTAGATCTTCGCCGCAA
ATTATTTCGGTCATTGAACCACAGGTACGAGGTAATTTCGACCGGGTAGC
CAGCAACCTCTCGCGAACACTTTCGAACTTCGGGCCACGACGGCCTAAGA
AGAGATGTCTGCCAATAGATATCGACGAGGAATATGGGTGAGAAACTTTG
AATGGTTTATAAAACTTATCCTCATTGTGAAAAAACCGTCGCT
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protein sequence of SMED30021298-orf-1

>SMED30021298-orf-1 ID=SMED30021298-orf-1|Name=SMED30021298-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=302bp
MNMPRILRIAPAPSVVAAAQYLAKLENENCILKEKYSKLKGTWCSPEATR
ELYKKIMRLSRARDDLSIESRGQRITILYQSSALRQIFTEKELQVQLPGR
NMAQLLDIIPAHHLQINSSNLTNSEDPNASTTIPNSSAPNRRHKLNKNRR
RRQKKRAETAALQANLRVIENPNLSRISETFLQEPVFMPNDTDLEIIPAP
RLSNSSSLLRRLLISIYQWIFALWRYQQTYKSSFLPGLPLRDVVPKISSG
RSSPQIISVIEPQVRGNFDRVASNLSRTLSNFGPRRPKKRCLPIDIDEEY
G*
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protein sequence of SMED30021298-orf-2

>SMED30021298-orf-2 ID=SMED30021298-orf-2|Name=SMED30021298-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
RRFFHNEDKFYKPFKVSHPYSSSISIGRHLFLGRRGPKFESVRERLLATR
SKLPRTCGSMTEIICGEDLPLEILGTTSLSGSPGRNEDLYVCWYLHRANI
H*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell