SMED30009786

Overview
NameSMED30009786
Smed IDSMED30009786
Length (bp)1179
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




SMED30009786

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
headSMED30009786SMESG000013744.1 SmedASXL_007847SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
headSMED30009786SMESG000013744.1 dd_Smed_v6_17991_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009786 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002617:56391..57534 -4767
Homology
BLAST of SMED30009786 vs. Planmine SMEST
Match: SMESG000013744.1 (SMESG000013744.1)

HSP 1 Score: 251.906 bits (642), Expect = 1.108e-83
Identity = 124/139 (89.21%), Postives = 131/139 (94.24%), Query Frame = 1
Query:  634 MKNCLLLLAFVITVTCSDRTEIIPSRSWPEIIEYIHSIVTDHYANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCSIIPMQ 1050
            M+  +L+++  I++ CS  TEIIPSRSWPEIIEYIHSIVTDH ANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCSIIPMQ
Sbjct:    6 MELYVLVISLFISIVCSRGTEIIPSRSWPEIIEYIHSIVTDHNANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCSIIPMQ 144          
BLAST of SMED30009786 vs. Planmine SMEST
Match: SMESG000081054.1 (SMESG000081054.1)

HSP 1 Score: 87.4261 bits (215), Expect = 8.381e-21
Identity = 38/116 (32.76%), Postives = 70/116 (60.34%), Query Frame = 1
Query:  688 RTEIIPSRSWPEIIEYIHSIVTDHYANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCS 1035
            R   +  RSWPEI E++   + +H A+ ++   I + N  Q ++L  ++PTKC E Y++ I P+ +PP  I++ENC  C    + + FK ++I K+  ++YL++ E  ++++ QC 
Sbjct:    8 RDHYVQKRSWPEIFEFVDLQLKNHSAHPKLLDFISIKNFKQILKLQITIPTKCKESYYLEIEPYLEPPVKIFVENC-KCTNIYKTETFKKYKIIKWPEDEYLLIEEFQEKYVSQCK 122          
BLAST of SMED30009786 vs. Planmine SMEST
Match: SMESG000013745.1 (SMESG000013745.1)

HSP 1 Score: 67.781 bits (164), Expect = 1.279e-13
Identity = 35/130 (26.92%), Postives = 67/130 (51.54%), Query Frame = 1
Query:  646 LLLLAFVITVTCSDRTEIIPSRSWPEIIEYIHSIVTDHYANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQEIQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCS 1035
            +++L     + C    E +   +WP++++ I+ IV  +   +  P  I + N  Q I+L+T++ ++C E Y++ I PH +PP++I +ENC  C     K  F+ + +      +YL V +     +V C 
Sbjct:    5 IMILMMAAMINC----EYLVFTTWPKVMKNINEIVNTYDQRLSSPEFIPIVNCPQKIELATTISSECGETYYLEIDPHQNPPSIITVENC-KCQPINNKIKFRKYNLFSKGHTKYLFVEDDLKDLVVNCK 129          
BLAST of SMED30009786 vs. Planmine SMEST
Match: SMESG000023071.1 (SMESG000023071.1)

HSP 1 Score: 55.0694 bits (131), Expect = 5.303e-9
Identity = 34/108 (31.48%), Postives = 52/108 (48.15%), Query Frame = 1
Query:  646 LLLLAFVITVTCSDRTEIIPSRSWPEIIEYIHSIVTDHYANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENC-FNCHQEIQKKVFKIFQI 966
            LLL   V  +      E +P R W +++ YI  ++  H +    P  I++    QTI+L    P  C   Y+++I+P  DPPA I   NC + C +  +   FK  QI
Sbjct:   17 LLLYLTVTPLDAQGNREYLPPRLWSDVMSYIDDMLRSHPSQPIFPDYIRMFEKDQTIELIVKNPNICVGCYYLKINPLQDPPAYIIASNCKYECIEVNKVYGFKKLQI 124          
BLAST of SMED30009786 vs. Planmine SMEST
Match: SMESG000023071.1 (SMESG000023071.1)

HSP 1 Score: 54.6842 bits (130), Expect = 7.082e-9
Identity = 34/108 (31.48%), Postives = 52/108 (48.15%), Query Frame = 1
Query:  646 LLLLAFVITVTCSDRTEIIPSRSWPEIIEYIHSIVTDHYANIEIPANIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENC-FNCHQEIQKKVFKIFQI 966
            LLL   V  +      E +P R W +++ YI  ++  H +    P  I++    QTI+L    P  C   Y+++I+P  DPPA I   NC + C +  +   FK  QI
Sbjct:   24 LLLYLTVTPLDAQGNREYLPPRLWSDVMSYIDDMLRSHPSQPIFPDYIRMFEKDQTIELIVKNPNICVGCYYLKINPLQDPPAYIIASNCKYECIEVNKVYGFKKLQI 131          
The following BLAST results are available for this feature:
BLAST of SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 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 SMED30009786 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013744.11.108e-8389.21SMESG000013744.1[more]
SMESG000081054.18.381e-2132.76SMESG000081054.1[more]
SMESG000013745.11.279e-1326.92SMESG000013745.1[more]
SMESG000023071.15.303e-931.48SMESG000023071.1[more]
SMESG000023071.17.082e-931.48SMESG000023071.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009786 ID=SMED30009786|Name=SMED30009786|organism=Schmidtea mediterranea sexual|type=transcript|length=1179bp
AAGTCTTTAGAATTCAATTTGTCATCGGTTATCACTCCACCAAAAAATAC
TGATTTTCACTTTATTTGAATTTTTAATTAGCTCTTAATTAATTTCTTAT
AATAATAAATTTTTAAATTTCACATTTTCGTTTTTGTATAACCTCAACAG
ATCATATGGACCGCATTTCATACAATAAGGAATAATATAATAAATTTACA
TTTTATTATTTGGCTTAAACTTTTAAATAAATGAAAACCAATAAAATTGA
ATAAATTATCGCGTCATATAGAAATATTATTATGATATTGTCGAATAATT
TTTATATTGGTTTCAAACAATTATCTCAAAAATCACGTTTTTATTAATTT
TTGATATAAAGTACTTCCACCATGATGGTACTATATAGAATTTTTAATAG
ATAAGCATCAGCAGAAAATTACTAAGTGTAATAAAAAAAGAAACAATTTA
ATAATAACATATTTAAAATTTCTGACAGAAAGTTTTAGATAATTAATTTG
TCCGTATGTAAACGTTGCGTTACAATAACAATTAAAGAACAAAACTGTTT
CAAAATTAGCACATTTAATTAATTTTAGAAATTTTTATTTGTATAAAAGA
TTCGTAGAGCATGATTGAAAAATATTTTCAGAAATGAAAAATTGTTTATT
GTTACTAGCTTTCGTGATAACAGTTACTTGCTCTGATAGAACTGAGATCA
TTCCAAGCAGGTCATGGCCAGAAATAATAGAATATATCCATTCAATTGTA
ACAGATCATTATGCAAATATCGAGATTCCGGCAAATATTCAAGTGACAAA
TGTAACCCAAACTATTCAATTGTCCACAAGTTTGCCCACAAAATGTCACG
AGAAGTACTTTATTAGAATTTCTCCACATTTTGATCCTCCAGCTGTCATT
TATATTGAGAATTGTTTTAATTGCCATCAAGAAATTCAAAAAAAAGTGTT
TAAGATCTTTCAAATTGAAAAATACGCTTCAAACCAATATTTAGTTGTCA
ATGAAATATCTGATCAATTCATCGTCCAGTGCTCAATAATACCAATGCAA
TAATGTGATTTGTTTGTTTTAATTGGCACACTAATGTAATGTATATATTA
AATTTTAATTGTTGTTTGATTAATTAAAGATTTCCTCTTTTGTAATGCCT
ATTATTTAACACCTATTTTTATGAAATTT
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protein sequence of SMED30009786-orf-1

>SMED30009786-orf-1 ID=SMED30009786-orf-1|Name=SMED30009786-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
MKNCLLLLAFVITVTCSDRTEIIPSRSWPEIIEYIHSIVTDHYANIEIPA
NIQVTNVTQTIQLSTSLPTKCHEKYFIRISPHFDPPAVIYIENCFNCHQE
IQKKVFKIFQIEKYASNQYLVVNEISDQFIVQCSIIPMQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.732