SMED30031867

Overview
NameSMED30031867
Smed IDSMED30031867
Length (bp)449
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



SMED30031867

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
X2 cellSMED30031867 SmedASXL_078402SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031867 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000988:29877..30324 +1785
v31.002124:64087..64533 +1771
v31.000535:15551..16013 -1737
v31.000067:154446..154908 -1733
v31.000205:135254..135709 +1675
v31.024112:4374..4834 +1667
v31.000476:70025..70479 +1416
v31.000476:43320..43774 +1407
Homology
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BLAST of SMED30031867 vs. Planmine SMEST
Match: SMESG000054981.1 (SMESG000054981.1)

HSP 1 Score: 166.777 bits (421), Expect = 6.598e-54
Identity = 81/99 (81.82%), Postives = 91/99 (91.92%), Query Frame = 3 
Query:  153 MPENEPSTSSTRIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAPPEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR 449
            M  NE +++STRIPRLPPSIVALRHKYEDLKIQHRDLQ KHDR++GTWAPPE +R LRQKI RL++A DELIAESRAQRLLIREQSVALH+AYSD+ELR
Sbjct:    1 MTGNEATSTSTRIPRLPPSIVALRHKYEDLKIQHRDLQTKHDRVRGTWAPPEVLRELRQKISRLSRALDELIAESRAQRLLIREQSVALHQAYSDSELR 99
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BLAST of SMED30031867 vs. Planmine SMEST
Match: SMESG000068757.1 (SMESG000068757.1)

HSP 1 Score: 149.058 bits (375), Expect = 1.418e-42
Identity = 73/99 (73.74%), Postives = 86/99 (86.87%), Query Frame = 3 
Query:  153 MPENEPSTSSTRIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAPPEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR 449
            M  N+ ST+ +RIPRL PSIVA+RHKYEDLK+QH DLQAK++RIKGTWAPPE VR LRQKI+RLT+ARDELI ESR+QRLLI EQS AL +A++D ELR
Sbjct:    1 MKNNDESTNPSRIPRLHPSIVAIRHKYEDLKLQHGDLQAKYERIKGTWAPPETVRELRQKILRLTRARDELIVESRSQRLLIHEQSKALRQAFTDVELR 99
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BLAST of SMED30031867 vs. Planmine SMEST
Match: SMESG000064895.1 (SMESG000064895.1)

HSP 1 Score: 143.665 bits (361), Expect = 2.052e-42
Identity = 70/99 (70.71%), Postives = 84/99 (84.85%), Query Frame = 3 
Query:  153 MPENEPSTSSTRIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAPPEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR 449
            M  +  S + +RIPRLPPSIVA+RHKYEDLK QH DL+AK++R+KGTWAPPE VR LRQKI R TQARDELI ESR+Q+LLIREQS+AL +A++D ELR
Sbjct:    1 MENHNESNNLSRIPRLPPSIVAVRHKYEDLKQQHNDLKAKYERMKGTWAPPETVRELRQKIFRFTQARDELIIESRSQQLLIREQSMALRQAFTDVELR 99
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BLAST of SMED30031867 vs. Planmine SMEST
Match: SMESG000011446.1 (SMESG000011446.1)

HSP 1 Score: 133.265 bits (334), Expect = 2.050e-40
Identity = 63/88 (71.59%), Postives = 76/88 (86.36%), Query Frame = 3 
Query:  186 RIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAPPEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR 449
            RIPRL PS+VA+RHKYE LK +H +L+ K++R+KGTWAPPE VR LRQKI R+TQARDELIAESR+QRLLIREQ+ AL RA++D E R
Sbjct:   14 RIPRLSPSVVAVRHKYEKLKREHEELRTKYERVKGTWAPPETVRELRQKIARITQARDELIAESRSQRLLIREQATALRRAFTDVEFR 101
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BLAST of SMED30031867 vs. Planmine SMEST
Match: SMESG000015007.1 (SMESG000015007.1)

HSP 1 Score: 133.265 bits (334), Expect = 9.207e-39
Identity = 66/100 (66.00%), Postives = 84/100 (84.00%), Query Frame = 3 
Query:  162 NEPSTSST----RIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAPPEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR 449
            N PS SST    RIPRL PS+VA+R KYE+LK+QH  L+AK++R+KGTWAPPE VRGL Q+I RLT+AR+ELIAESR+QRLLI+EQ+ AL +A++D EL+
Sbjct:    2 NSPSNSSTNDLPRIPRLSPSVVAMRQKYEELKLQHAALRAKYERVKGTWAPPETVRGLLQEIARLTEAREELIAESRSQRLLIKEQATALRQAFTDVELQ 101
The following BLAST results are available for this feature:
BLAST of SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 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 SMED30031867 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054981.16.598e-5481.82SMESG000054981.1[more]
SMESG000068757.11.418e-4273.74SMESG000068757.1[more]
SMESG000064895.12.052e-4270.71SMESG000064895.1[more]
SMESG000011446.12.050e-4071.59SMESG000011446.1[more]
SMESG000015007.19.207e-3966.00SMESG000015007.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031867 ID=SMED30031867|Name=SMED30031867|organism=Schmidtea mediterranea sexual|type=transcript|length=449bp
TTGAATATCCAAATGAAATGGATCGAATGTCCCCGGGTACCACCGATACT
CCAGTTCGTCAGCCTTGTTTTTAATCTTTCCCTATCAGTTTTTTTTGTAT
TCCCTTCTGTACTATCTATCCATTTTGAACAAAATTTTCTTATTTCAATA
GCATGCCAGAAAACGAACCATCAACCTCTTCGACAAGAATCCCTCGGTTA
CCTCCGTCAATTGTGGCTCTCCGCCACAAATATGAAGACCTCAAGATCCA
ACACCGGGATCTTCAGGCGAAGCACGACAGAATCAAGGGAACCTGGGCCC
CACCGGAAGCCGTCCGGGGGCTCCGACAAAAAATCATTCGCCTAACGCAG
GCCCGCGATGAACTGATCGCCGAGTCGCGCGCCCAGCGTCTTCTGATTAG
AGAGCAGTCCGTGGCACTGCACCGGGCATATTCGGATGCGGAACTCCGA
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protein sequence of SMED30031867-orf-1

>SMED30031867-orf-1 ID=SMED30031867-orf-1|Name=SMED30031867-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=99bp
MPENEPSTSSTRIPRLPPSIVALRHKYEDLKIQHRDLQAKHDRIKGTWAP
PEAVRGLRQKIIRLTQARDELIAESRAQRLLIREQSVALHRAYSDAELR
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protein sequence of SMED30031867-orf-2

>SMED30031867-orf-2 ID=SMED30031867-orf-2|Name=SMED30031867-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
LNIQMKWIECPRVPPILQFVSLVFNLSLSVFFVFPSVLSIHFEQNFLISI
ACQKTNHQPLRQESLGYLRQLWLSATNMKTSRSNTGIFRRSTTESREPGP
HRKPSGGSDKKSFA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..24