SMED30035843

Overview
NameSMED30035843
Smed IDSMED30035843
Length (bp)612
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 SMED30035843 (SMED30035843) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035843 (SMED30035843) 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




SMED30035843

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
parenchymal cellSMED30035843SMESG000014680.1 dd_Smed_v4_21954_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035843 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006902:5955..6566 +2979
v31.001355:3972..4581 -2846
v31.015300:11544..12159 +2373
v31.010585:8982..9545 -2174
v31.018146:4719..5353 +1322
Homology
BLAST of SMED30035843 vs. Planmine SMEST
Match: SMESG000014680.1 (SMESG000014680.1)

HSP 1 Score: 197.978 bits (502), Expect = 1.511e-69
Identity = 105/128 (82.03%), Postives = 106/128 (82.81%), Query Frame = 2
Query:   20 YNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKHNELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKRQLHDIQWCQREVHELRDLLSQSEKLIKRTWNPST 403
            YN ENPINESYNI NKVNDVNEINEWQREIKHGRYKPRDI+ KHNELKQVLKSNERNPSSNVKDKDQSRQYE              ELLDKFKRQLHDIQWCQREVHELRDLLSQSEKLIK    P T
Sbjct:  109 YNIENPINESYNISNKVNDVNEINEWQREIKHGRYKPRDIMPKHNELKQVLKSNERNPSSNVKDKDQSRQYE--------------ELLDKFKRQLHDIQWCQREVHELRDLLSQSEKLIK---EPGT 219          

HSP 2 Score: 83.5741 bits (205), Expect = 1.511e-69
Identity = 42/51 (82.35%), Postives = 46/51 (90.20%), Query Frame = 3
Query:  381 KEPGTHQQSLVDESILRRLEGEKDQYLNDLQKITTEREKARLCQSSEDLEN 533
            KEPGTHQQSL D+S+LRRL+ E+DQYLN LQK TTEREKARL QSSEDLEN
Sbjct:  215 KEPGTHQQSLGDQSMLRRLKWERDQYLNYLQKTTTEREKARLFQSSEDLEN 265          
BLAST of SMED30035843 vs. Planmine SMEST
Match: SMESG000070566.1 (SMESG000070566.1)

HSP 1 Score: 161.384 bits (407), Expect = 1.156e-53
Identity = 91/142 (64.08%), Postives = 106/142 (74.65%), Query Frame = 2
Query:    2 IESDQDYNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKHNELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKRQLHDI------------------QWCQREVHELRDLLSQSEK 373
            IESDQDYNN   IN+S NI NKVND+NEI+E Q+E+KH R+K +DI+ ++NELKQVL+SNERN S  VKDKD SRQYEV LKK++ME DSLQELLDKF+RQLHDI                  Q CQREVHELR+ L QSEK
Sbjct:  432 IESDQDYNNRKSINDSDNISNKVNDINEIDELQKELKHCRHKLKDIMRENNELKQVLESNERNSSPPVKDKDHSRQYEVELKKVRMERDSLQELLDKFERQLHDIQGNIRVLTQERDMINDCYQGCQREVHELRESLIQSEK 573          

HSP 2 Score: 67.0106 bits (162), Expect = 1.156e-53
Identity = 41/74 (55.41%), Postives = 48/74 (64.86%), Query Frame = 3
Query:  381 KEPGTHQQSLVDESILRRLEGEKDQYLNDLQKITTER----------------EKARLCQSSEDLEN*ISKLLE 554
            K+ GT+Q SL  +S+LRRLE E+DQ LNDL K+TTER                EKARLCQ  EDLEN IS+LLE
Sbjct:  576 KDSGTNQPSLAVQSMLRRLEVERDQSLNDLHKMTTERDSLRERLKTVTDSAISEKARLCQRLEDLENQISRLLE 649          
BLAST of SMED30035843 vs. Planmine SMEST
Match: SMESG000070566.1 (SMESG000070566.1)

HSP 1 Score: 160.999 bits (406), Expect = 1.517e-53
Identity = 91/142 (64.08%), Postives = 106/142 (74.65%), Query Frame = 2
Query:    2 IESDQDYNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKHNELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKRQLHDI------------------QWCQREVHELRDLLSQSEK 373
            IESDQDYNN   IN+S NI NKVND+NEI+E Q+E+KH R+K +DI+ ++NELKQVL+SNERN S  VKDKD SRQYEV LKK++ME DSLQELLDKF+RQLHDI                  Q CQREVHELR+ L QSEK
Sbjct:  432 IESDQDYNNRKSINDSDNISNKVNDINEIDELQKELKHCRHKLKDIMRENNELKQVLESNERNSSPPVKDKDHSRQYEVELKKVRMERDSLQELLDKFERQLHDIQGNIRVLTQERDMINDCYQGCQREVHELRESLIQSEK 573          

HSP 2 Score: 67.0106 bits (162), Expect = 1.517e-53
Identity = 41/74 (55.41%), Postives = 48/74 (64.86%), Query Frame = 3
Query:  381 KEPGTHQQSLVDESILRRLEGEKDQYLNDLQKITTER----------------EKARLCQSSEDLEN*ISKLLE 554
            K+ GT+Q SL  +S+LRRLE E+DQ LNDL K+TTER                EKARLCQ  EDLEN IS+LLE
Sbjct:  576 KDSGTNQPSLAVQSMLRRLEVERDQSLNDLHKMTTERDSLRERLKTVTDSAISEKARLCQRLEDLENQISRLLE 649          
BLAST of SMED30035843 vs. Planmine SMEST
Match: SMESG000070566.1 (SMESG000070566.1)

HSP 1 Score: 160.614 bits (405), Expect = 1.607e-53
Identity = 91/142 (64.08%), Postives = 106/142 (74.65%), Query Frame = 2
Query:    2 IESDQDYNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKHNELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKRQLHDI------------------QWCQREVHELRDLLSQSEK 373
            IESDQDYNN   IN+S NI NKVND+NEI+E Q+E+KH R+K +DI+ ++NELKQVL+SNERN S  VKDKD SRQYEV LKK++ME DSLQELLDKF+RQLHDI                  Q CQREVHELR+ L QSEK
Sbjct:  432 IESDQDYNNRKSINDSDNISNKVNDINEIDELQKELKHCRHKLKDIMRENNELKQVLESNERNSSPPVKDKDHSRQYEVELKKVRMERDSLQELLDKFERQLHDIQGNIRVLTQERDMINDCYQGCQREVHELRESLIQSEK 573          

HSP 2 Score: 67.0106 bits (162), Expect = 1.607e-53
Identity = 41/74 (55.41%), Postives = 48/74 (64.86%), Query Frame = 3
Query:  381 KEPGTHQQSLVDESILRRLEGEKDQYLNDLQKITTER----------------EKARLCQSSEDLEN*ISKLLE 554
            K+ GT+Q SL  +S+LRRLE E+DQ LNDL K+TTER                EKARLCQ  EDLEN IS+LLE
Sbjct:  576 KDSGTNQPSLAVQSMLRRLEVERDQSLNDLHKMTTERDSLRERLKTVTDSAISEKARLCQRLEDLENQISRLLE 649          
BLAST of SMED30035843 vs. Planmine SMEST
Match: SMESG000070566.1 (SMESG000070566.1)

HSP 1 Score: 160.614 bits (405), Expect = 1.866e-53
Identity = 91/142 (64.08%), Postives = 106/142 (74.65%), Query Frame = 2
Query:    2 IESDQDYNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKHNELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKRQLHDI------------------QWCQREVHELRDLLSQSEK 373
            IESDQDYNN   IN+S NI NKVND+NEI+E Q+E+KH R+K +DI+ ++NELKQVL+SNERN S  VKDKD SRQYEV LKK++ME DSLQELLDKF+RQLHDI                  Q CQREVHELR+ L QSEK
Sbjct:  432 IESDQDYNNRKSINDSDNISNKVNDINEIDELQKELKHCRHKLKDIMRENNELKQVLESNERNSSPPVKDKDHSRQYEVELKKVRMERDSLQELLDKFERQLHDIQGNIRVLTQERDMINDCYQGCQREVHELRESLIQSEK 573          

HSP 2 Score: 67.0106 bits (162), Expect = 1.866e-53
Identity = 41/74 (55.41%), Postives = 48/74 (64.86%), Query Frame = 3
Query:  381 KEPGTHQQSLVDESILRRLEGEKDQYLNDLQKITTER----------------EKARLCQSSEDLEN*ISKLLE 554
            K+ GT+Q SL  +S+LRRLE E+DQ LNDL K+TTER                EKARLCQ  EDLEN IS+LLE
Sbjct:  576 KDSGTNQPSLAVQSMLRRLEVERDQSLNDLHKMTTERDSLRERLKTVTDSAISEKARLCQRLEDLENQISRLLE 649          
The following BLAST results are available for this feature:
BLAST of SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 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 SMED30035843 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014680.11.511e-6982.03SMESG000014680.1[more]
SMESG000070566.11.156e-5364.08SMESG000070566.1[more]
SMESG000070566.11.517e-5364.08SMESG000070566.1[more]
SMESG000070566.11.607e-5364.08SMESG000070566.1[more]
SMESG000070566.11.866e-5364.08SMESG000070566.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035843 ID=SMED30035843|Name=SMED30035843|organism=Schmidtea mediterranea sexual|type=transcript|length=612bp
TATTGAAAGCGATCAAGATTACAATAATGAAAACCCCATAAACGAATCCT
ACAATATCATCAATAAAGTCAATGATGTTAATGAAATTAATGAGTGGCAA
AGAGAAATCAAACATGGCCGGTATAAACCTAGAGATATAATACTTAAACA
TAATGAGTTGAAACAAGTGTTAAAGTCTAATGAAAGAAATCCATCTTCAA
ATGTTAAAGATAAAGATCAATCACGACAATATGAAGTTTATTTGAAAAAG
CTACAGATGGAATGCGATTCGTTACAGGAGTTATTAGATAAATTTAAAAG
GCAATTGCACGATATCCAGTGGTGTCAAAGAGAGGTTCACGAATTAAGAG
ACTTATTGAGTCAATCTGAAAAATTAATAAAAAGAACCTGGAACCCATCA
ACAATCTTTAGTTGATGAGTCGATACTACGAAGACTTGAAGGGGAAAAAG
ATCAGTATTTGAATGATTTACAAAAAATAACTACAGAAAGAGAAAAGGCA
CGACTTTGTCAAAGCTCGGAAGATTTAGAAAATTAGATTTCGAAACTTTT
AGAAGATATTCAAAGTAGAAGAGGAGAAAATGGAAGAGTGATTTAAATCA
GGTTCATTTAAA
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protein sequence of SMED30035843-orf-1

>SMED30035843-orf-1 ID=SMED30035843-orf-1|Name=SMED30035843-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
IESDQDYNNENPINESYNIINKVNDVNEINEWQREIKHGRYKPRDIILKH
NELKQVLKSNERNPSSNVKDKDQSRQYEVYLKKLQMECDSLQELLDKFKR
QLHDIQWCQREVHELRDLLSQSEKLIKRTWNPSTIFS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell