SMED30028291

Overview
NameSMED30028291
Smed IDSMED30028291
Length (bp)693
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30028291 (SMED30028291) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028291 (SMED30028291) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30028291

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
testisSMED30028291 SMED30028291smed_20140614PMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028291 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000376:91772..92561 +3412
Homology
[Close]
BLAST of SMED30028291 vs. Ensembl Zebrafish
Match: rnf6 (ring finger protein (C3H2C3 type) 6 [Source:ZFIN;Acc:ZDB-GENE-100209-1])

HSP 1 Score: 47.7506 bits (112), Expect = 4.833e-6
Identity = 17/50 (34.00%), Postives = 28/50 (56.00%), Query Frame = -2 
Query:  477 IKIMNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 626
            + +  E    C++C++   Q N    LPC H+F + CI +W+ EN  CP+
Sbjct:  638 VNLEGEQGRACSVCINEYAQGNKLRRLPCAHEFHIHCIDRWLSENNTCPI 687
[Close]
BLAST of SMED30028291 vs. Ensembl Zebrafish
Match: rnf6 (ring finger protein (C3H2C3 type) 6 [Source:ZFIN;Acc:ZDB-GENE-100209-1])

HSP 1 Score: 47.7506 bits (112), Expect = 4.887e-6
Identity = 17/50 (34.00%), Postives = 28/50 (56.00%), Query Frame = -2 
Query:  477 IKIMNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 626
            + +  E    C++C++   Q N    LPC H+F + CI +W+ EN  CP+
Sbjct:  674 VNLEGEQGRACSVCINEYAQGNKLRRLPCAHEFHIHCIDRWLSENNTCPI 723
[Close]
BLAST of SMED30028291 vs. UniProt/SwissProt
Match: sp|P84445|ICP0_EHV1V (E3 ubiquitin-protein ligase ICP0 OS=Equine herpesvirus 1 (strain V592) OX=310273 GN=ICP0 PE=3 SV=1)

HSP 1 Score: 50.0618 bits (118), Expect = 6.061e-6
Identity = 22/40 (55.00%), Postives = 27/40 (67.50%), Query Frame = -2 
Query:  477 CNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 596
            C ICL  E  +NY++ LPC H FC  CI +WI +NP CPL
Sbjct:    8 CPICL--EDPSNYSMALPCLHAFCYVCITRWIRQNPTCPL 45
[Close]
BLAST of SMED30028291 vs. UniProt/SwissProt
Match: sp|P28990|ICP0_EHV1B (E3 ubiquitin-protein ligase ICP0 OS=Equine herpesvirus 1 (strain Ab4p) OX=31520 GN=63 PE=1 SV=1)

HSP 1 Score: 50.0618 bits (118), Expect = 6.061e-6
Identity = 22/40 (55.00%), Postives = 27/40 (67.50%), Query Frame = -2 
Query:  477 CNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 596
            C ICL  E  +NY++ LPC H FC  CI +WI +NP CPL
Sbjct:    8 CPICL--EDPSNYSMALPCLHAFCYVCITRWIRQNPTCPL 45
[Close]
BLAST of SMED30028291 vs. Ensembl Cavefish
Match: rnf6 (ring finger protein 6 [Source:NCBI gene;Acc:103037065])

HSP 1 Score: 47.7506 bits (112), Expect = 4.956e-6
Identity = 17/45 (37.78%), Postives = 26/45 (57.78%), Query Frame = -2 
Query:  477 EMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 611
            E    C++C++   Q N    LPC H+F + CI +W+ EN  CP+
Sbjct:  637 EQGRACSVCINEYAQGNKLRSLPCAHEFHIHCIDRWLSENNTCPI 681
[Close]
BLAST of SMED30028291 vs. Ensembl Medaka
Match: rnf6 (ring finger protein 6 [Source:NCBI gene;Acc:101173899])

HSP 1 Score: 48.1358 bits (113), Expect = 3.198e-6
Identity = 17/45 (37.78%), Postives = 27/45 (60.00%), Query Frame = -2 
Query:  477 EMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPL 611
            E+   C++C++   Q N    LPC H+F + CI +W+ EN  CP+
Sbjct:  664 EIGRACSVCINEYAQGNKLRRLPCSHEFHIHCIDRWLSENNTCPI 708
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BLAST of SMED30028291 vs. Planmine SMEST
Match: SMESG000043150.1 (SMESG000043150.1)

HSP 1 Score: 114.005 bits (284), Expect = 6.467e-30
Identity = 65/132 (49.24%), Postives = 92/132 (69.70%), Query Frame = -2 
Query:  222 MNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLXXXXXXXXXXXXXXXXXXDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIFEIAFKKYISIVEDLKQFWIVFAKNNFQKVLFS 617
            M++   IC+ICLDY   N YAIVLPCQH+FC+ CI+ W+ ENP CPLDRSDI ++ ++++    V  ++V +ILV+ +  NKQ L+ ++LP IIN  + FEI   + ISI++ LK+F   F   NFQK+LFS
Sbjct:    1 MDKSFAICSICLDYNSDNEYAIVLPCQHRFCLSCIRSWVTENPCCPLDRSDITNILIHNNSFDHVQSVTVSDILVDQISKNKQILLENHLPLIINLFKEFEINSGQLISIIQLLKEFKDKFRDCNFQKILFS 132
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BLAST of SMED30028291 vs. Planmine SMEST
Match: SMESG000013345.1 (SMESG000013345.1)

HSP 1 Score: 102.449 bits (254), Expect = 5.723e-26
Identity = 56/114 (49.12%), Postives = 80/114 (70.18%), Query Frame = -2 
Query:  276 MNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLXXXXXXXXXXXXXXXXXXDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIFEIAFKKYISIVEDL 617
            MNE D +CNICLD ++ N ++++ PC HKFC  CIKKWI ENP CP+DR DI  +S+N    ++V  +SV +IL++H++  K+QLI D+L KI +FL+ FEI  +K I   + L
Sbjct:    1 MNETDKVCNICLDDDLNNEFSVLSPCGHKFCFSCIKKWITENPCCPMDRRDISKISINFHAFRTVKTVSVTDILIDHLILVKKQLIKDHLSKIKSFLENFEIYSEKVILFSQSL 114
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BLAST of SMED30028291 vs. Planmine SMEST
Match: SMESG000065437.1 (SMESG000065437.1)

HSP 1 Score: 101.293 bits (251), Expect = 1.298e-25
Identity = 60/126 (47.62%), Postives = 84/126 (66.67%), Query Frame = -2 
Query:  222 ICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLXXXXXXXXXXXXXXXXXXDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIFEIAFKKYISIVEDLKQFWIVFAKNNFQKVLFS 599
            +C+IC+D  ++N  A VLPC+HKFCV CIKKWI ENP CPLDR DI  + +NS+  +S+ ++SV +IL+ H   +++ LIL   PKII+ L+ FE  F    SI+  LK     F KN +Q +L+S
Sbjct:    3 VCSICIDNNLENECATVLPCRHKFCVKCIKKWISENPNCPLDRYDISEILINSNQSESITNLSVTDILIGHFSESRKLLILKNFPKIIDLLEFFENKFDNLNSIIFSLKVLKNEFMKNFYQNILYS 128

HSP 2 Score: 33.113 bits (74), Expect = 1.298e-25
Identity = 23/72 (31.94%), Postives = 34/72 (47.22%), Query Frame = -1 
Query:   31 FNFHNIIDNIKNQTDALRNLSN--------------DRSELQEYFKLVKSFLYFYESIEALSNVFNCNAILF 204
            ++  NI D I+N    L N+                DR EL+EY+ L+ SF+Y YE    L+  F+  A +F
Sbjct:  154 YHSRNINDQIRNHIQVLNNILEALEVKYKQYEQYLVDRLELREYYSLINSFIYCYEIFLYLNKAFDFKARVF 225
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BLAST of SMED30028291 vs. Planmine SMEST
Match: SMESG000016408.1 (SMESG000016408.1)

HSP 1 Score: 103.99 bits (258), Expect = 2.185e-25
Identity = 56/130 (43.08%), Postives = 90/130 (69.23%), Query Frame = -2 
Query:  228 MNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLXXXXXXXXXXXXXXXXXXDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIFEIAFKKYISIVEDLKQFWIVFAKNNFQKVL 617
            MNE+  +C+IC D +++N +AIVLPCQHKFCVPCIK W+ ENP CP+DRS+++ + ++ + +  +  + V +IL +++  NKQ LI  +LP +++ L +F     K +S++  LK F + F +NNFQ +L
Sbjct:    1 MNEITEVCSICYDDQLENEFAIVLPCQHKFCVPCIKTWLIENPSCPIDRSEVIKILIHCNCIHDIQIMFVSDILNDYIKKNKQILITKHLPILVDLLSMFTKYSDKLVSVILSLKDFIMEFTENNFQSIL 130
[Close]
BLAST of SMED30028291 vs. Planmine SMEST
Match: SMESG000023870.1 (SMESG000023870.1)

HSP 1 Score: 100.908 bits (250), Expect = 4.720e-25
Identity = 57/132 (43.18%), Postives = 79/132 (59.85%), Query Frame = -2 
Query:  222 MNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLXXXXXXXXXXXXXXXXXXDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIFEIAFKKYISIVEDLKQFWIVFAKNNFQKVLFS 617
            MNE D +C+IC D    N YAI+ PCQHKFCV CIK WI ENP+CPL                   +++V +I+ + +   +Q +I ++LP II+ L   EI  K +IS+VE LK +   F++ NFQK+LFS
Sbjct:    1 MNEFDDLCSICYDCYKVNEYAIISPCQHKFCVSCIKIWIIENPICPL-----------------DRNLNVGDIISDQLSHEEQLIIAEHLPIIIDLLHNLEIYSKMFISLVESLKLYKTNFSEINFQKILFS 115
The following BLAST results are available for this feature:
BLAST of SMED30028291 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 SMED30028291 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 SMED30028291 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 SMED30028291 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
rnf64.833e-634.00ring finger protein (C3H2C3 type) 6 [Source:ZFIN;A... [more]
rnf64.887e-634.00ring finger protein (C3H2C3 type) 6 [Source:ZFIN;A... [more]
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BLAST of SMED30028291 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 SMED30028291 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 SMED30028291 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 2
Match NameE-valueIdentityDescription
sp|P84445|ICP0_EHV1V6.061e-655.00E3 ubiquitin-protein ligase ICP0 OS=Equine herpesv... [more]
sp|P28990|ICP0_EHV1B6.061e-655.00E3 ubiquitin-protein ligase ICP0 OS=Equine herpesv... [more]
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BLAST of SMED30028291 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 SMED30028291 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rnf64.956e-637.78ring finger protein 6 [Source:NCBI gene;Acc:103037... [more]
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BLAST of SMED30028291 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 SMED30028291 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 SMED30028291 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 SMED30028291 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rnf63.198e-637.78ring finger protein 6 [Source:NCBI gene;Acc:101173... [more]
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BLAST of SMED30028291 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043150.16.467e-3049.24SMESG000043150.1[more]
SMESG000013345.15.723e-2649.12SMESG000013345.1[more]
SMESG000065437.11.298e-2547.62SMESG000065437.1[more]
SMESG000016408.12.185e-2543.08SMESG000016408.1[more]
SMESG000023870.14.720e-2543.18SMESG000023870.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028291 ID=SMED30028291|Name=SMED30028291|organism=Schmidtea mediterranea sexual|type=transcript|length=693bp
CGTTTTTTTAATTGTATTTTTTATAGTTGTGAATAATATGGCGTTGCAAT
TAAACACATTACTTAAAGCTTCAATTGATTCATAGAAATAAAGAAAGGAT
TTGACCAATTTGAAGTATTCTTGGAGTTCTGATCTATCATTTGATAGGTT
TCTCAAAGCATCGGTTTGATTTTTTATGTTGTCAATAATGTTGTGAAAGT
TAAAAATGCATTTTTTTATCGGGAAAATAAAACCTTTTGAAAATTATTTT
TCGCAAACACAATCCAGAACTGTTTCAAGTCTTCGACAATGGAAATATAT
TTTTTGAATGCAATTTCAAAAATTTGAAGAAAATTTATTATTTTTGGTAA
GTAATCTAAAATTAGTTGCTGTTTGTTTGTCAGCATATGCTCAACGAGAA
TTTCAACAACAGATATATGGTCTACAGATTGGACAACGTCCGAATTAACT
GATACACTGACGATGTCGGAACGATCTAATGGGCAGACTGGATTTTCGGG
AATCCATTTTTTAATGCATGGTACACAGAATTTGTGTTGACACGGTAAAA
CAATTGCATAATTATTCTGAATTTCGTAATCTAAGCAAATGTTGCAAATG
TAATCCATTTCGTTCATTATTTTTATTAGAATTTTACCTTCTATTTAAAT
AAAGGAGATTCATTTCATTTTTCAATATTTTTGTAAAACTGTT
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protein sequence of SMED30028291-orf-1

>SMED30028291-orf-1 ID=SMED30028291-orf-1|Name=SMED30028291-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MNEMDYICNICLDYEIQNNYAIVLPCQHKFCVPCIKKWIPENPVCPLDRS
DIVSVSVNSDVVQSVDHISVVEILVEHMLTNKQQLILDYLPKIINFLQIF
EIAFKKYISIVEDLKQFWIVFAKNNFQKVLFSR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding