SMED30004959

Overview
NameSMED30004959
Smed IDSMED30004959
Length (bp)815
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




SMED30004959

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30004959h1SMcG0006019 dd_Smed_v4_14435_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30004959h1SMcG0006019 dd_Smed_v4_14435_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
SMED30004959 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.021228:6465..7272 -3936
v31.018214:12530..13344 -3882
Homology
BLAST of SMED30004959 vs. TrEMBL
Match: V9XRT9 (X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 7.909e-8
Identity = 38/96 (39.58%), Postives = 55/96 (57.29%), Query Frame = -2
Query:  386 ETSEI-----LIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 658
            E+ EI      I  K H IFG +   CG  +L  DPLLP +  Y +S+  AG+FM ISGI SI+A +   K +LI +   NI+A + +  G +V++
Sbjct:   50 ESKEIRSGSKFINSKSHRIFGYILIACGIFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAI 145          
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046821.1 (SMESG000046821.1)

HSP 1 Score: 206.068 bits (523), Expect = 6.282e-99
Identity = 104/107 (97.20%), Postives = 106/107 (99.07%), Query Frame = -2
Query:  356 KILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSLRNLLNSCMNF 676
            +ILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGY+VSLRN LNSCMNF
Sbjct:   32 QILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYVVSLRN-LNSCMNF 137          

HSP 2 Score: 125.561 bits (314), Expect = 6.282e-99
Identity = 59/60 (98.33%), Postives = 60/60 (100.00%), Query Frame = -3
Query:  175 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRITENFQTENVEFGIRRE 354
            CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISK+SRITENFQTENVEFGIRRE
Sbjct:  138 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKRSRITENFQTENVEFGIRRE 197          

HSP 3 Score: 69.707 bits (169), Expect = 6.282e-99
Identity = 31/32 (96.88%), Postives = 31/32 (96.88%), Query Frame = -1
Query:  675 MDLVPCTNSMESSEPRLSLDHPELTQVQMRYQ 770
            MDLVPCTNSME SEPRLSLDHPELTQVQMRYQ
Sbjct:    1 MDLVPCTNSMEISEPRLSLDHPELTQVQMRYQ 32          
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046821.1 (SMESG000046821.1)

HSP 1 Score: 124.405 bits (311), Expect = 4.691e-36
Identity = 59/60 (98.33%), Postives = 60/60 (100.00%), Query Frame = -3
Query:  175 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRITENFQTENVEFGIRRE 354
            CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISK+SRITENFQTENVEFGIRRE
Sbjct:   37 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKRSRITENFQTENVEFGIRRE 96          
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046812.1 (SMESG000046812.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.186e-20
Identity = 41/103 (39.81%), Postives = 67/103 (65.05%), Query Frame = -2
Query:  356 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSLRNLLNSCMNF 664
            +   + +L Y+++H I+G +  + G + +  DP+LP+IF+Y YS+   G+FM ISG+CSI  +R  +K  LI SL FNI+A +++FT YI+ +  L  S  +F
Sbjct:   66 EESQNSMLRYKRMHLIYGTIYVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILAMIVIFTNYIIGILALNQSGFSF 168          

HSP 2 Score: 33.113 bits (74), Expect = 1.186e-20
Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3
Query:  220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345
            + +G +  A ++ +  + L VL+ WD SLK G++  KK + T
Sbjct:  185 YTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQT 226          
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046815.1 (SMESG000046815.1)

HSP 1 Score: 84.3445 bits (207), Expect = 1.621e-20
Identity = 38/93 (40.86%), Postives = 64/93 (68.82%), Query Frame = -2
Query:  386 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 664
            +   + +L Y+++H I+G ++ + G + +  DP+LP+IF+Y YS+   G+FM ISG+CSI  +R  +K  LI SL FNI+A +++FT YI+ +
Sbjct:   66 EESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGI 158          

HSP 2 Score: 33.113 bits (74), Expect = 1.621e-20
Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3
Query:  220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345
            + +G +  A ++ +  + L VL+ WD SLK G++  KK + T
Sbjct:  185 YTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQT 226          
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046819.1 (SMESG000046819.1)

HSP 1 Score: 84.3445 bits (207), Expect = 2.653e-20
Identity = 38/93 (40.86%), Postives = 64/93 (68.82%), Query Frame = -2
Query:  386 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 664
            +   + +L Y+++H I+G ++ + G + +  DP+LP+IF+Y YS+   G+FM ISG+CSI  +R  +K  LI SL FNI+A +++FT YI+ +
Sbjct:   66 EESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGI 158          

HSP 2 Score: 32.3426 bits (72), Expect = 2.653e-20
Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3
Query:  220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345
            + +G + LA ++ +  + L VL+ WD SLK G++  K  + T
Sbjct:  185 YTEGVKGLAIFNVVFGMILFVLMIWDSSLKCGDVCFKNQKQT 226          
The following BLAST results are available for this feature:
BLAST of SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRT97.909e-839.58X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=... [more]
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BLAST of SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 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 SMED30004959 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046821.16.282e-9997.20SMESG000046821.1[more]
SMESG000046821.14.691e-3698.33SMESG000046821.1[more]
SMESG000046812.11.186e-2039.81SMESG000046812.1[more]
SMESG000046815.11.621e-2040.86SMESG000046815.1[more]
SMESG000046819.12.653e-2040.86SMESG000046819.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004959 ID=SMED30004959|Name=SMED30004959|organism=Schmidtea mediterranea sexual|type=transcript|length=815bp
AAATTTAATAAAAATTTATTTAAACTTTAACACTATTGAATTTCAAGGTC
ACACTAATAAATGTAAAACCACCTGCTGAATATTTGAACTAATTCTAAAT
TAAATATAAAGAATAATATTCCGTACCATTTTTATTGATTTTTAATAAAT
TAACGAGCAATAAATTCCATATCATTCTCTTCTTATACCGAATTCTACGT
TTTCTGTTTGGAAATTTTCAGTAATTCTTGACTTTTTAGAAATGATCTCT
CCAAATTTTAAACTTAAATCCCAATAGATTAAAACTATCAAACCTACCGC
AACTATTGCGTGATAAAAGGCCAAATTTCTTTGTCCTTGTTGAAATTTCG
TGCATAAAATTCATACATGAATTCAGGAGGTTCCGAAGGCTAACGATGTA
CCCTGTAAAAAGTAAAACTCCAGCCATGATATTGAAAGATAATGATATGA
TTAAGAAATGTTTGCTAACAGTCCTAGTGGCTTTAATAGAGCAGATGCCA
CTGATGAACATGAAAATACCAGCAAATACTAACGAGTAGTTGTACCTAAA
TATTGCTGGAAGTAGGGGGTCAAAAACTAACAGTACACATCCACAAATAG
TTGTTACGATTCCAAAGATAAAATGTAATTTTTGATAAATTAATATTTCT
GAAGTTTCACTCTTATTGAGGATTTTGATATCTCATTTGAACCTGAGTTA
GTTCTGGATGGTCCAAGCTCAATCGTGGCTCTGAACTTTCCATACTGTTT
GTACATGGAACTAAATCCATATTTATGTTTTCGGTAATCGTTTCTCTAAT
TAAAGGTTTTTCATG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
Vocabulary: INTERPRO
TermDefinition
IPR007237CD20-like
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane