1-Jun

Overview
Name1-Jun (AFJ24819.1)
Smed IDSMED30001802
Length (bp)902
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of 1-Jun (SMED30001802) t-SNE clustered cells

Violin plots show distribution of expression levels for 1-Jun (SMED30001802) in cells (dots) of each of the 12 neoblast clusters.

 

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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 1-Jun (SMED30001802) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for 1-Jun (SMED30001802) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30001802

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30001802SMESG000062649.1 SmedASXL_005346SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30001802SMESG000062649.1 dd_Smed_v4_5749_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30001802SMESG000062649.1 dd_Smed_v4_5749_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001802SMESG000062649.1 dd_Smed_v4_5749_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001802SMESG000062649.1 dd_Smed_v4_5749_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001802SMESG000062649.1 dd_Smed_v4_5749_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30001802SMESG000062649.1 dd_Smed_v4_5749_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
Homology
[Close]
BLAST of 1-Jun vs. TrEMBL
Match: I1ZIG5 (1-Jun OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 397.897 bits (1021), Expect = 7.870e-138
Identity = 213/213 (100.00%), Postives = 213/213 (100.00%), Query Frame = 1 
Query:   85 MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYXXXXXXXXXXXXXXXXXXPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE 723
            MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYSSDVQSCSSNNDSNSSNQPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE
Sbjct:    1 MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYSSDVQSCSSNNDSNSSNQPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE 213
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BLAST of 1-Jun vs. TrEMBL
Match: T1DFA5 (1-Jun OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1)

HSP 1 Score: 147.902 bits (372), Expect = 1.454e-39
Identity = 111/222 (50.00%), Postives = 141/222 (63.51%), Query Frame = 1 
Query:   97 KHKPNSLNFKD--YNNTTG-QFTPSTPTVISLLQDMTPTNCGYNF-DISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYXXXXXXXXXXXXXXXXX---------XPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE 723
            K KP++L   +     T G Q TPSTPTVIS LQD+TPTN  Y+  D  DKD+V + FS HYKSIED +++ E   +Y  NNN+ FT+DLL+ DD   D+N          + RP  + S  SSDV S SS++ +  S+          P ++    +AKKRERNRLAAEKCRLKKQ KI +LENEK+ R+QENN LLE V KRTE ++ L+IFY KL  GE
Sbjct:    7 KTKPSTLQLNEGWRGPTRGLQLTPSTPTVISSLQDVTPTNFKYSLLDTPDKDDVARAFSRHYKSIEDQYQRYESYKSYDNNNNY-FTLDLLNCDD---DMN------GIGEIERPQQATSTCSSDVHSSSSSSGNKLSSSSYNDSSSGVPDVLKL--TAKKRERNRLAAEKCRLKKQRKIKDLENEKRLRVQENNKLLEIVTKRTEKIRNLQIFYNKLINGE 216
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BLAST of 1-Jun vs. Planmine SMEST
Match: SMESG000062649.1 (SMESG000062649.1)

HSP 1 Score: 397.897 bits (1021), Expect = 2.189e-141
Identity = 213/213 (100.00%), Postives = 213/213 (100.00%), Query Frame = 1 
Query:   85 MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYXXXXXXXXXXXXXXXXXXPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE 723
            MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYSSDVQSCSSNNDSNSSNQPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE
Sbjct:    1 MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISDKDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDVNVNNYSTDYENVNRPLPSESAYSSDVQSCSSNNDSNSSNQPQLVGHVQSAKKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLKKLKIFYKKLQMGE 213
The following BLAST results are available for this feature:
BLAST of 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
I1ZIG57.870e-138100.001-Jun OS=Schmidtea mediterranea OX=79327 PE=2 SV=1[more]
T1DFA51.454e-3950.001-Jun OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1[more]
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BLAST of 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun 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 1-Jun vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000062649.12.189e-141100.00SMESG000062649.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30001802
GenBankAFJ24819.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001802 ID=SMED30001802|Name=1-Jun|organism=Schmidtea mediterranea sexual|type=transcript|length=902bp
TCAAGTCTTATTTTTAGTAACCTCGCTGGGGTATTTATTATGAGTCACTG
CTAGAGAAACTAATTCGTCATTTCATTTTATTTAATGCTGTCTTCTAAGC
ATAAACCAAATTCTTTAAATTTTAAAGACTACAATAACACCACAGGTCAA
TTTACTCCTAGTACTCCAACAGTAATAAGTTTACTTCAAGATATGACTCC
TACAAATTGTGGATATAATTTTGACATTTCTGACAAAGATGAAGTTGTAA
AGCAATTTTCAATGCATTATAAATCGATTGAAGATTCTCATAGACAAAAT
GAATTGCAATTCAATTATGCAATAAATAACAATCACAACTTTACAATGGA
TTTATTAAGCAATGACGATTTTCAAATAGATGTTAATGTAAATAACTATT
CGACTGATTATGAAAATGTGAATCGACCTCTTCCATCCGAATCTGCTTAT
AGTTCTGACGTTCAATCATGTTCGAGTAATAATGACTCGAATTCCAGTAA
CCAGCCACAACTTGTTGGTCATGTTCAATCTGCGAAAAAACGTGAACGAA
ATAGATTAGCAGCAGAAAAATGCCGATTAAAGAAGCAAGGTAAAATTACT
GAGCTTGAAAATGAAAAAAAGCGACGCATACAAGAAAACAACGCGCTTTT
AGAAAAGGTTAAAAAACGAACAGAAACCCTCAAAAAACTCAAAATTTTCT
ACAAAAAACTGCAAATGGGTGAATTTCAATCGCAGCAATTTTATTAATTG
GGTTTACTTTTCTTTTTTAGATGCATTTGTACATAATTTATAAGCTTTTT
ATTGATTTTGAGTATTTTTTTATGTTTATATTAATGAATTGTTTGCTTAT
TCTGTAAATACGACTGTCATTCATGAAGCAGACTCGAGTTTTTAGTTGAA
CC
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protein sequence of SMED30001802-orf-1

>SMED30001802-orf-1 ID=SMED30001802-orf-1|Name=SMED30001802-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=221bp
MLSSKHKPNSLNFKDYNNTTGQFTPSTPTVISLLQDMTPTNCGYNFDISD
KDEVVKQFSMHYKSIEDSHRQNELQFNYAINNNHNFTMDLLSNDDFQIDV
NVNNYSTDYENVNRPLPSESAYSSDVQSCSSNNDSNSSNQPQLVGHVQSA
KKRERNRLAAEKCRLKKQGKITELENEKKRRIQENNALLEKVKKRTETLK
KLKIFYKKLQMGEFQSQQFY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR004827bZIP
Vocabulary: molecular function
TermDefinition
GO:0003700transcription factor activity, sequence-specific DNA binding
GO:0043565sequence-specific DNA binding
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 171..191
NoneNo IPR availableGENE3DG3DSA:1.20.5.170coord: 148..205
e-value: 1.5E-7
score: 33.5
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 119..146
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 119..155
NoneNo IPR availableSUPERFAMILYSSF57959Leucine zipper domaincoord: 150..203
IPR004827Basic-leucine zipper domainPFAMPF00170bZIP_1coord: 148..203
e-value: 3.9E-7
score: 30.0
IPR004827Basic-leucine zipper domainPROSITEPS00036BZIP_BASICcoord: 151..166
IPR004827Basic-leucine zipper domainPROSITEPS50217BZIPcoord: 146..209
score: 9.887