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.

 

back to top


 

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

 

back to top
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
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          
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          
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          
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          
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
back to top
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
back to top
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
back to top
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
back to top
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
back to top
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
back to top
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
back to top
BLAST of SMED30021298 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
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
back to top
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
back to top
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
back to top
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
back to top
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
back to top
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]
back to top
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
back to top

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*
back to top

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*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell