SMED30029048

Overview
NameSMED30029048
Smed IDSMED30029048
Length (bp)1220
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 SMED30029048 (SMED30029048) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029048 (SMED30029048) 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 SMED30029048 (SMED30029048) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029048 (SMED30029048) 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



SMED30029048

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30029048h1SMcG0002502 SmedASXL_015985SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30029048h1SMcG0002502 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029048h1SMcG0002502 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029048h1SMcG0002502 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30029048h1SMcG0002502 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
photoreceptor neuronSMED30029048h1SMcG0002502 SMED30001792smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
photoreceptor neuronSMED30029048h1SMcG0002501 SMED30001792smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30029048h1SMcG0002502 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029048 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.028981:2143..7908 -4511
Homology
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BLAST of SMED30029048 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 271.937 bits (694), Expect = 2.877e-154
Identity = 128/128 (100.00%), Postives = 128/128 (100.00%), Query Frame = 3 
Query:  540 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKET 923
            KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKET
Sbjct:  203 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKET 330

HSP 2 Score: 261.151 bits (666), Expect = 2.877e-154
Identity = 158/162 (97.53%), Postives = 160/162 (98.77%), Query Frame = 2 
Query:   65 QEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKRFQ 550
            +EYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEK  Q
Sbjct:   18 EEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQ 179

HSP 3 Score: 54.299 bits (129), Expect = 2.877e-154
Identity = 24/24 (100.00%), Postives = 24/24 (100.00%), Query Frame = 1 
Query: 1021 TCQFEDLESILCRTIDPNINKKLK 1092
            TCQFEDLESILCRTIDPNINKKLK
Sbjct:  330 TCQFEDLESILCRTIDPNINKKLK 353
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BLAST of SMED30029048 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 269.626 bits (688), Expect = 8.302e-144
Identity = 127/128 (99.22%), Postives = 127/128 (99.22%), Query Frame = 3 
Query:  540 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKET 923
            KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKE 
Sbjct:  203 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVVSIYNKEV 330

HSP 2 Score: 260.766 bits (665), Expect = 8.302e-144
Identity = 158/162 (97.53%), Postives = 160/162 (98.77%), Query Frame = 2 
Query:   65 QEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKRFQ 550
            +EYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEK  Q
Sbjct:   18 EEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQ 179
[Close]
BLAST of SMED30029048 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 261.151 bits (666), Expect = 4.670e-140
Identity = 158/162 (97.53%), Postives = 160/162 (98.77%), Query Frame = 2 
Query:   65 QEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKRFQ 550
            +EYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEK  Q
Sbjct:   18 EEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQ 179

HSP 2 Score: 256.529 bits (654), Expect = 4.670e-140
Identity = 120/121 (99.17%), Postives = 121/121 (100.00%), Query Frame = 3 
Query:  540 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVV 902
            KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSV+
Sbjct:  203 KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVI 323

HSP 3 Score: 80.1073 bits (196), Expect = 3.321e-16
Identity = 62/85 (72.94%), Postives = 67/85 (78.82%), Query Frame = 2 
Query:  833 FQKKTFFQYRFFKWIFYTLFKRC*YLQ*RDLKLFTFLHQSLHLLLXXXXXXXXXXXXXXXXXLLVNSKIWKAFCAGQSIQILTKN 1087
            F+KK FF        ++  F    + Q  DLKLFTFLHQSLH+LLIFGRISRIIPRIIQSTILLVNSKIWKAFCAGQSIQILTKN
Sbjct:  301 FRKKRFFNTDSLNG-YFIHFSSVIFFQ-SDLKLFTFLHQSLHILLIFGRISRIIPRIIQSTILLVNSKIWKAFCAGQSIQILTKN 383
The following BLAST results are available for this feature:
BLAST of SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 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 SMED30029048 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000045022.12.877e-154100.00SMESG000045022.1[more]
SMESG000045022.18.302e-14499.22SMESG000045022.1[more]
SMESG000045022.14.670e-14097.53SMESG000045022.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029048 ID=SMED30029048|Name=SMED30029048|organism=Schmidtea mediterranea sexual|type=transcript|length=1220bp
TCGGAACAGTGATTTTAATTCATCATTAGATGAACGAAAAATAAAAATTT
ACTATGAATTATATCAGGAATACAAAACGCAATTGGAAGGTCTTCGAAAA
ACTATTGACATTCTACAATTTGAATCTAAAGAACAACTTCTAAAAGGCGC
GGAATTAGAAGAAAAATTAAAAAAGTATAAAGATCGAGAAAAAGAGCTGG
AAGATGGTATGAATATGAACAAAGCAAATGAACAGAAGGTTTATGAAATG
AAAATTTTATTAAAAGACTCAAGAAAGCAAAATATAAATTATTCCAATCA
AATTAAAGAATTGAGAAAAGACGAGTCTATAATTCAACAATTGAGAGAGG
AAATGTCATATTTACAACAGGAAAATATGACATTGAAAGCTTATATAGTT
TCCCAAAATAAAATGAGCCATTATGGAAATGCTTTTAAAAATTTCAAACT
TGAACAATTTTGTCCAATTTGCTCCAATTCAAAGATGGAATTATGCCAAA
GACATTATTTGGAAAATTTTTCATCCGAAAATCCAGAAAAAAGATTTCAA
TCAAACAAATGCGCCGCTGCCGAAATCCAACAAACAGCGAATAAAGCAAT
TAATGGATAAGTGTGATTTATCCAATGATGCGATTGAAGCGGCTGTGAAA
ACCATTTTCCATTTGGGAGACCAAGTGGAAATAGTTGTTGATTCGGAATC
AGGAAAGATATGCGCAAAAGCCACAGTGAAATATATGGGAAATCTTGATG
ATAGATATCACAGCAGCTTTTTCTTAGGGGTGAAATTACATCAAATTGGT
AATGAGAGATTAGTTAATTACTGCAATGGGAGTTTCAGAAAAAAACGTTT
TTTCAATACAGATTCTTTAAATGGATATTTTATACACTTTTCAAGCGTTG
TTAGTATTTACAATAAAGAGACCTAAAACTATTTACCTTCCTTCACCAAT
CACTACACCTATTGTTGATATTTGGCCGCATTTCAAGAATCATACCAAGA
ATCATACAAAGTACAATTTTACTTGTCAATTCGAAGATCTGGAAAGCATT
TTGTGCCGGACAATCGATCCAAATATTAACAAAAAACTGAAATAGTATAT
TTGATAAGTTATGAAAAATGTAATCCATTAAAACAAACAAATTATATTTG
AAATTCTTTGTGATTTATATAAATTTTGGATCGTATTGTAAATACTCCTA
TATTGCATTCTTTGCCAAGC
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protein sequence of SMED30029048-orf-1

>SMED30029048-orf-1 ID=SMED30029048-orf-1|Name=SMED30029048-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=168bp
MEMLLKISNLNNFVQFAPIQRWNYAKDIIWKIFHPKIQKKDFNQTNAPLP
KSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKA
TVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLN
GYFIHFSSVVSIYNKET*
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protein sequence of SMED30029048-orf-2

>SMED30029048-orf-2 ID=SMED30029048-orf-2|Name=SMED30029048-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp
RNSDFNSSLDERKIKIYYELYQEYKTQLEGLRKTIDILQFESKEQLLKGA
ELEEKLKKYKDREKELEDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQ
IKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKL
EQFCPICSNSKMELCQRHYLENFSSENPEKRFQSNKCAAAEIQQTANKAI
NG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR000938CAP-Gly_domain
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 19..67
NoneNo IPR availableCOILSCoilCoilcoord: 85..129