SMED30008334

Overview
NameSMED30008334
Smed IDSMED30008334
Length (bp)652
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 SMED30008334 (SMED30008334) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008334 (SMED30008334) 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



SMED30008334

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



PAGE Curations: 21

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30008334SMESG000017098.1 Contig702GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30008334SMESG000068935.1 Contig702GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30008334SMESG000068935.1 SmedASXL_012945SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30008334SMESG000068935.1 dd_Smed_v4_357_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30008334SMESG000068935.1 dd_Smed_v4_357_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30008334SMESG000068935.1 dd_Smed_v4_357_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig22580newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig22580uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig43594newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig9917newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig9917uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig27150newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008334SMESG000068935.1 Contig27150uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30008334SMESG000068935.1 dd_357dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
head regionSMED30008334SMESG000068935.1 dd_Smed_v6_357_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30008334SMESG000068935.1 OX_Smed_1.0.08964ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
head regionSMED30008334SMESG000068935.1 OX_Smed_1.0.18450ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30008334SMESG000068935.1 dd_Smed_v6_357_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30008334SMESG000068935.1 dd_Smed_v4_357_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30008334SMESG000068935.1 dd_Smed_v4_357_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30008334SMESG000068935.1 dd_Smed_v4_357_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
Homology
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BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1)

HSP 1 Score: 211.846 bits (538), Expect = 1.817e-63
Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 
Query:   27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521
            +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y  DY  PTSA+YI+FK R   KW+AAL  KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A    A+   QSW+A A L
Sbjct:  677 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 841
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BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1)

HSP 1 Score: 211.846 bits (538), Expect = 1.929e-63
Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 
Query:   27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521
            +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y  DY  PTSA+YI+FK R   KW+AAL  KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A    A+   QSW+A A L
Sbjct:  689 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 853
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BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068971.1 (SMESG000068971.1)

HSP 1 Score: 211.46 bits (537), Expect = 2.045e-63
Identity = 124/165 (75.15%), Postives = 140/165 (84.85%), Query Frame = 3 
Query:   27 STILKSPTLVAANQXXXXXXXXXXXXXXXXXXXXEDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQTSAAPKTQSWLATAFL 521
            +TILKSPTLVAANQTTTVS TATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDE Y  DY  PTSA+YI+FK R   KW+AAL  KL+RLIEIIINSL+SGSVKADM +N+AS S++ST D+QNTVTQAAQAAYG+SLQ+ SI+A    A+   QSW+A A L
Sbjct:  665 ATILKSPTLVAANQTTTVSLTATTSLPITTLSIIEDPPRKNERSYKIIIKCSFTDETYYDDYKTPTSARYINFKARHHAKWKAALIFKLLRLIEIIINSLSSGSVKADMEMNIASNSSISTADLQNTVTQAAQAAYGSSLQVFSITATSLDASSTDQSWIAAAVL 829
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BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000068935.1 (SMESG000068935.1)

HSP 1 Score: 85.1149 bits (209), Expect = 2.077e-19
Identity = 81/218 (37.16%), Postives = 118/218 (54.13%), Query Frame = 3 
Query:    3 MTAVIITNSTILKSPTLVAANQXXXXXXXXXXXXXXXX----XXXXEDPPR----------KNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSL--TSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQI------------------LSISAKQTSAAPKTQSWLATAFLXXXXXXXXGLD 554
            MTAV+I+NSTILK PTLV AN TTT  P ++ +   T+    L      P+            E S  + ++  F++  Y   ++N TS++ + F    +    ++L +  IR++  ++NS+   +GSVKA  ++ VA   A++   + N    A  +AY + + I                  ++ISAKQTSAAPKTQSWLATA LVPVVVVIVGLD
Sbjct:  132 MTAVVISNSTILKEPTLVGANLTTTALPASSATSVATSQITTLLTTTIIPKVPIVIGMAAQPGEYSASLYLQILFSNRTYIQAFSNVTSSESVSFFNEYYRNINSSLMSNKIRVVSAVVNSMRFVNGSVKAVYTIEVAMNGAMTDESLSNNFINATNSAYSSVVIITNSTVLQTSTLVTSTTAPITISAKQTSAAPKTQSWLATAVLVPVVVVIVGLD 349
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BLAST of SMED30008334 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.645e-12
Identity = 42/115 (36.52%), Postives = 62/115 (53.91%), Query Frame = 3 
Query:  129 EDPPRKNERSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRLIEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQILSISAKQ 473
            E P    E   ++ + CS+T E Y ++Y N  S  Y  F  + F   + +L  KL+RLIEII +SL  GSV A+M+  +AS S L  +++   V  AA  A  NS+ +  I+  Q
Sbjct:  843 EKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSLDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNSIVVNKITVIQ 957
The following BLAST results are available for this feature:
BLAST of SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 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 SMED30008334 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068971.11.817e-6375.15SMESG000068971.1[more]
SMESG000068971.11.929e-6375.15SMESG000068971.1[more]
SMESG000068971.12.045e-6375.15SMESG000068971.1[more]
SMESG000068935.12.077e-1937.16SMESG000068935.1[more]
SMESG000067876.11.645e-1236.52SMESG000067876.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008334 ID=SMED30008334|Name=SMED30008334|organism=Schmidtea mediterranea sexual|type=transcript|length=652bp
TTATGACTGCGGTAATTATCACTAATTCTACGATCTTGAAAAGTCCCACA
TTAGTGGCAGCGAATCAAACAACAACAGTTTCTCCAACAGCAACAACGAG
CCTACCAATAACAACTTTATCAATTATAGAAGATCCTCCTAGAAAGAATG
AACGTTCCTACAAAATTATTATTAAATGTTCATTTACAGATGAAGTATAT
ACTACTGACTATAACAATCCGACCTCCGCAAAATATATTGATTTTAAAGG
GAGGCAATTTGTGAAATGGCAAGCGGCCCTTAATGCGAAATTAATAAGAT
TGATAGAAATTATTATCAACTCTCTAACTTCAGGAAGTGTAAAAGCCGAC
ATGTCATTGAATGTTGCATCCACTTCAGCTCTTTCAACTACTGATATACA
AAATACAGTAACGCAGGCAGCTCAAGCTGCCTATGGTAACAGTCTCCAAA
TACTTTCAATATCGGCTAAACAAACGAGTGCTGCACCAAAAACTCAATCG
TGGTTAGCCACTGCTTTCCTTGTTCCGGTTGTCGTGGTCATCGTTGGATT
AGATTAACACTTATTTATTTCATTTTAGTCAGGATTTTTACAACATTATG
ATTACATTTGTCTTAGTATTTCAATAAAACTTTTGAGTGTGATTAAAAAA
AA
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protein sequence of SMED30008334-orf-1

>SMED30008334-orf-1 ID=SMED30008334-orf-1|Name=SMED30008334-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=185bp
MTAVIITNSTILKSPTLVAANQTTTVSPTATTSLPITTLSIIEDPPRKNE
RSYKIIIKCSFTDEVYTTDYNNPTSAKYIDFKGRQFVKWQAALNAKLIRL
IEIIINSLTSGSVKADMSLNVASTSALSTTDIQNTVTQAAQAAYGNSLQI
LSISAKQTSAAPKTQSWLATAFLVPVVVVIVGLD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR000651Ras-like_Gua-exchang_fac_N
IPR000082SEA_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000082SEA domainPFAMPF01390SEAcoord: 58..149
e-value: 1.2E-5
score: 25.4
NoneNo IPR availableTMHMMTMhelixcoord: 164..183