SMED30035076

Overview
NameSMED30035076
Smed IDSMED30035076
Length (bp)1490
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 SMED30035076 (SMED30035076) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035076 (SMED30035076) 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.
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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



SMED30035076

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
X1 cellSMED30035076 SmedASXL_069664SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30035076 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 752.666 bits (1942), Expect = 0.000e+0
Identity = 387/501 (77.25%), Postives = 408/501 (81.44%), Query Frame = 3 
Query:    3 INRYVMETAKEFKEIEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQKSIIGISRDYKFQKFIPFMARKNXXXXXXXXXXXXXXXXQNRLPIVIITPMEEPKSEHRRPEKRGASNDTIVLSDEEFPLLKRRILPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIKCKKCGKVWENVRNGLNHLRQKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS*LSQAAIEVYLRNILKMKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCESKSSFILDSDSQMTLHQKCNIKAKFDKFFEGTFEEKTVLENLEIEYNQLTNNFDTSIAVYM*YQ*FIKIYQ*L-YKRPKKMRI---------------------PN---TGF*KKFRLL*INVNEVFHWFTTEYQKSLPKM 1430
            INRYVMETA EFKE EFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQ+SIIGISRDYKFQK IPFMARK    ETTST+ TT PTE+NRLP+VIITP+EEPK EHRRPEKRGASNDTIVLSDEEFPLLKRR LPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQI+CK+CGKVWENVRNG+NHLRQKHDFPNRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNE                    +NQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANC+SK+S ILDSD+QMTL Q+CNIKAKFDKF EGTFEEK VL  LE    Q  NNFD  + V      F+K  Q + Y  P   RI                     PN       +KFRLL INVN+VFHWF  EYQKSLPK+
Sbjct:  252 INRYVMETANEFKETEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQRSIIGISRDYKFQKCIPFMARKTNGQETTSTINTTPPTEENRLPMVIITPLEEPKIEHRRPEKRGASNDTIVLSDEEFPLLKRRTLPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIECKECGKVWENVRNGMNHLRQKHDFPNRTDVMVSCVRCEVPIKGAECVNHIKNHKKDDKEESQAGSLVANTQDIPNE--------------------KNQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCDSKTSVILDSDNQMTLQQRCNIKAKFDKFLEGTFEEKAVLGTLERNVPQQPNNFDCGVYVIQYISDFLKDPQRMDYHTPDSKRIRKEIGELILEEMKNPASKIKNPNKEIQSLLQKFRLLQINVNDVFHWFAEEYQKSLPKI 732
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BLAST of SMED30035076 vs. Planmine SMEST
Match: SMESG000031457.1 (SMESG000031457.1)

HSP 1 Score: 744.191 bits (1920), Expect = 0.000e+0
Identity = 385/501 (76.85%), Postives = 409/501 (81.64%), Query Frame = 3 
Query:    3 INRYVMETAKEFKEIEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQKSIIGISRDYKFQKFIPFMARKNXXXXXXXXXXXXXXXXQNRLPIVIITPMEEPKSEHRRPEKRGASNDTIVLSDEEFPLLKRRILPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIKCKKCGKVWENVRNGLNHLRQKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS*LSQAAIEVYLRNILKMKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCESKSSFILDSDSQMTLHQKCNIKAKFDKFFEGTFEEKTVLENLEIEYNQLTNNFDTSIAVYM*YQ*FIKIYQ*L-YKRPKKMRI---------------------PN---TGF*KKFRLL*INVNEVFHWFTTEYQKSLPKM 1430
            INRYVMETA EFKE EFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQ+EQTSVANFLHFFTQ+SIIGISRDYKFQK IPFMARK    ETTST++TT PTE+NRLP+VIITP+EEPK EHRRPEKRGASNDTIVLSDEEFPLLKRR LPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQI+CK+CGK+WENVRNG+NHLRQKHDF NRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNE                    +NQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANC+SK+S ILDSD+QMTL Q+CNIKAKFDKF EGTFEEKTVL  LE    Q  NNFD  + V      F+K  Q + Y  P   RI                     PN       +KFRLL INVN+VFHWF  EYQKSLPK+
Sbjct:   21 INRYVMETANEFKETEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQQEQTSVANFLHFFTQRSIIGISRDYKFQKCIPFMARKTNGQETTSTIITTPPTEENRLPMVIITPLEEPKIEHRRPEKRGASNDTIVLSDEEFPLLKRRTLPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIECKECGKLWENVRNGMNHLRQKHDFINRTDVMVSCVRCEVPIKGAECINHIKNHKKDDKEESQAGSLVANTQDIPNE--------------------KNQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCDSKTSVILDSDNQMTLQQRCNIKAKFDKFLEGTFEEKTVLGTLERNVPQQPNNFDCGVYVIQYISDFLKDPQRMDYHTPDSKRIRKEIGELILEEMKNPASKIKNPNKEIQSLLQKFRLLQINVNDVFHWFADEYQKSLPKI 501
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BLAST of SMED30035076 vs. Planmine SMEST
Match: SMESG000069571.1 (SMESG000069571.1)

HSP 1 Score: 495.352 bits (1274), Expect = 7.416e-165
Identity = 250/281 (88.97%), Postives = 261/281 (92.88%), Query Frame = 3 
Query:    3 INRYVMETAKEFKEIEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQKSIIGISRDYKFQKFIPFMARKNXXXXXXXXXXXXXXXXQNRLPIVIITPMEEPKSEHRRPEKRGASNDTIVLSDEEFP-LLKRRILPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIKCKKCGKVWENVRNGLNHLRQKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNE 842
            INRYVMETAKEFKE EFDMARFAKFF +PE WLKHLK +STATETSPADRIKVQKLVDLTC YPFKTQEEQTSVANFLHFFTQ+SIIGISRDYKFQKFIPFMAR+NTRPETTST VT S TEQN LPIVI+TP++EPK EHRRPEKRGASNDTIVLSDEEFP L K+R L TRKSK PTGAGNVPTE ECTDEVKFILNNEYQ++CK+CGKVWENVRNGLNHLRQKHDFPNRTD MVSCVRCEVP KGAEC NHIKNHKKDDKE SEAGSLVANTQDIPNE
Sbjct:   21 INRYVMETAKEFKEAEFDMARFAKFFMVPEKWLKHLKSFSTATETSPADRIKVQKLVDLTCIYPFKTQEEQTSVANFLHFFTQRSIIGISRDYKFQKFIPFMARRNTRPETTSTEVTASLTEQNSLPIVIVTPIKEPKVEHRRPEKRGASNDTIVLSDEEFPPLFKKRTLTTRKSKIPTGAGNVPTENECTDEVKFILNNEYQLECKECGKVWENVRNGLNHLRQKHDFPNRTDAMVSCVRCEVPFKGAECTNHIKNHKKDDKEASEAGSLVANTQDIPNE 301

HSP 2 Score: 104.76 bits (260), Expect = 2.301e-23
Identity = 68/137 (49.64%), Postives = 76/137 (55.47%), Query Frame = 3 
Query: 1095 FILDSDSQMTLHQKCNIKAKFDKFFEGTFEEKTVLENLEIEYNQLTNNFDTSIAVYM*YQ*FIKIYQ*L-YKRPKKMRI---------------------PN---TGF*KKFRLL*INVNEVFHWFTTEYQKSLPKM 1430
             ILDSD+QMTL QKCNIKAKFDKF EGTFEEKTVL  L+    Q  NNFD  I V      FIK  Q + Y+ P   RI                     PN       +KFRLL I+VN+VFHWFT E Q SL K+
Sbjct:  302 IILDSDNQMTLQQKCNIKAKFDKFLEGTFEEKTVLGTLDRIVPQQPNNFDCGIYVIQYISDFIKDPQRIDYQTPDSKRIRKEIGELILEEMKNPASKIKNPNKEIQSLLQKFRLLQISVNDVFHWFTAESQNSLSKL 438
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BLAST of SMED30035076 vs. Planmine SMEST
Match: SMESG000005302.1 (SMESG000005302.1)

HSP 1 Score: 318.546 bits (815), Expect = 8.534e-108
Identity = 162/181 (89.50%), Postives = 172/181 (95.03%), Query Frame = 3 
Query:  306 MARKNXXXXXXXXXXXXXXXXQNRLPIVIITPMEEPKSEHRRPEKRGASNDTIVLSDEEFPLLKRRILPTRKSKNPTGAGNVPTETECTDEVKFILNNEYQIKCKKCGKVWENVRNGLNHLRQKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS 848
            MARK    ETTST++TT PTE+NRLP+VIITP+EEPK EHRRPEKRGASNDTIVLSDEEFPLLKRR LP RKSKNPTGAGNVPTETECTDEVKFILNNEYQI+CK+CGKVWENVRNG+NHLRQKHDFPNRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNESS
Sbjct:    1 MARKTNGQETTSTIITTPPTEENRLPMVIITPLEEPKIEHRRPEKRGASNDTIVLSDEEFPLLKRRTLPNRKSKNPTGAGNVPTETECTDEVKFILNNEYQIECKECGKVWENVRNGMNHLRQKHDFPNRTDVMVSCVRCEVPIKGAECVNHIKNHKKDDKEESQAGSLVANTQDIPNESS 181
[Close]
BLAST of SMED30035076 vs. Planmine SMEST
Match: SMESG000056391.1 (SMESG000056391.1)

HSP 1 Score: 201.06 bits (510), Expect = 5.347e-62
Identity = 97/107 (90.65%), Postives = 101/107 (94.39%), Query Frame = 3 
Query:    3 INRYV-METAKEFKEIEFDMARFAKFFTIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQKSIIGISRDYKFQKFIPFMARKN 320
            + RY+  ETAKEFKE EFDMARFAKFF IPENWLKHLKPYSTATETSPADRIKVQKLVDLTC YPFKTQEEQTSVANFLHFFTQ+SIIGISRDYKFQKFIPFMAR+N
Sbjct:    4 VQRYINWETAKEFKETEFDMARFAKFFKIPENWLKHLKPYSTATETSPADRIKVQKLVDLTCIYPFKTQEEQTSVANFLHFFTQRSIIGISRDYKFQKFIPFMARRN 110
The following BLAST results are available for this feature:
BLAST of SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 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 SMED30035076 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047667.10.000e+077.25SMESG000047667.1[more]
SMESG000031457.10.000e+076.85SMESG000031457.1[more]
SMESG000069571.17.416e-16588.97SMESG000069571.1[more]
SMESG000005302.18.534e-10889.50SMESG000005302.1[more]
SMESG000056391.15.347e-6290.65SMESG000056391.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035076 ID=SMED30035076|Name=SMED30035076|organism=Schmidtea mediterranea sexual|type=transcript|length=1490bp
TAATTAATCGGTATGTCATGGAGACAGCAAAAGAATTCAAAGAAATTGAA
TTTGACATGGCTCGCTTTGCCAAATTCTTCACAATCCCGGAGAATTGGTT
AAAACATCTAAAACCATACTCTACAGCTACCGAAACATCACCGGCTGATA
GAATCAAAGTACAAAAATTAGTGGATCTCACATGCAGATATCCATTCAAA
ACTCAAGAAGAACAAACAAGTGTAGCAAACTTCCTACATTTCTTCACCCA
AAAATCAATAATTGGAATCTCAAGGGATTACAAATTCCAAAAATTCATAC
CATTTATGGCCAGAAAAAACACCAGGCCGGAGACAACCTCCACTATGGTT
ACGACTTCTCCAACAGAACAAAACAGACTACCAATAGTAATCATCACTCC
AATGGAAGAACCAAAAAGTGAACATCGTAGACCAGAGAAAAGAGGCGCAA
GCAATGACACAATTGTGCTTAGCGACGAAGAGTTCCCACTACTTAAAAGG
AGAATTCTTCCAACCAGAAAATCCAAAAATCCTACTGGTGCAGGAAATGT
ACCTACAGAAACCGAATGCACTGATGAAGTTAAATTCATCCTCAACAATG
AATACCAAATAAAATGTAAAAAGTGTGGAAAAGTGTGGGAAAACGTTCGA
AATGGACTAAACCACCTTCGTCAAAAGCACGATTTCCCAAACCGAACAGA
TGTTATGGTATCTTGCGTGAGATGTGAAGTACCGGTCAAAGGAGCAGAAT
GTGCAAATCACATTAAAAATCACAAAAAAGATGACAAAGAAGAAAGTGAA
GCTGGGAGTCTTGTAGCTAACACTCAAGACATCCCAAATGAAAGTAGCTG
ACTATCACAAGCCGCAATCGAAGTATATCTGAGGAATATTCTGAAAATGA
AAGAAAACCAAGAAAGAAATATTCAATATCTTGAACCTAGTACTGCGAAT
TTCCTCATAAATAGAAACCTCAGAGCATTCTATCAAAACGTCAAAATCGA
AAAGCTTATCGGATGGGAACAAGTTATCTGGCTTATACATTGGAACAAAT
GTCATTGGATTGTCTACCTAGCTAATTGTGAATCTAAATCCTCATTTATC
TTAGATTCGGACAGTCAAATGACATTACACCAAAAATGCAACATAAAAGC
CAAATTTGACAAATTTTTTGAAGGTACCTTCGAAGAAAAAACAGTGTTAG
AGAACCTAGAAATAGAATATAATCAGCTAACAAATAACTTCGATACATCG
ATTGCGGTATATATGTGATATCAGTGATTTATAAAAATATATCAGTGACT
TTATAAAAGACCCAAAAAGATGAGAATACCAAACACCGGATTCTAAAAGA
AATTCAGACTGCTATAAATCAATGTGAATGAAGTATTCCATTGGTTTACA
ACTGAATATCAAAAGTCTCTCCCAAAAATGGGCGAATTATTTTTAATTTT
CAAAATTAAATTTTTCAATAGAATATAAATCAGTATATTT
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protein sequence of SMED30035076-orf-1

>SMED30035076-orf-1 ID=SMED30035076-orf-1|Name=SMED30035076-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWN
KCHWIVYLANCESKSSFILDSDSQMTLHQKCNIKAKFDKFFEGTFEEKTV
LENLEIEYNQLTNNFDTSIAVYM*
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protein sequence of SMED30035076-orf-2

>SMED30035076-orf-2 ID=SMED30035076-orf-2|Name=SMED30035076-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=283bp
INRYVMETAKEFKEIEFDMARFAKFFTIPENWLKHLKPYSTATETSPADR
IKVQKLVDLTCRYPFKTQEEQTSVANFLHFFTQKSIIGISRDYKFQKFIP
FMARKNTRPETTSTMVTTSPTEQNRLPIVIITPMEEPKSEHRRPEKRGAS
NDTIVLSDEEFPLLKRRILPTRKSKNPTGAGNVPTETECTDEVKFILNNE
YQIKCKKCGKVWENVRNGLNHLRQKHDFPNRTDVMVSCVRCEVPVKGAEC
ANHIKNHKKDDKEESEAGSLVANTQDIPNESS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding