SMED30012973

Overview
NameSMED30012973
Smed IDSMED30012973
Length (bp)843
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 SMED30012973 (SMED30012973) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012973 (SMED30012973) 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 SMED30012973 (SMED30012973) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012973 (SMED30012973) 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



SMED30012973

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
head regionSMED30012973h1SMcG0020972 SmedASXL_051340SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012973 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015040:2676..3548 +3932
Homology
[Close]
BLAST of SMED30012973 vs. Planmine SMEST
Match: SMESG000016780.1 (SMESG000016780.1)

HSP 1 Score: 251.136 bits (640), Expect = 3.837e-85
Identity = 123/128 (96.09%), Postives = 125/128 (97.66%), Query Frame = 2 
Query:  314 MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRHSGSTVQLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNEELPSGISLKDQSVKNNDTIKVLMKTRGG 697
            MHIRELRRKLK KFNVDIQSIQFNNQLL+DDRHSGSTV LTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYL HHNEELPSGISLKDQ+VKNNDTIKVLMKTRGG
Sbjct:    1 MHIRELRRKLKYKFNVDIQSIQFNNQLLSDDRHSGSTVSLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLTHHNEELPSGISLKDQNVKNNDTIKVLMKTRGG 128
[Close]
BLAST of SMED30012973 vs. Planmine SMEST
Match: SMESG000016811.1 (SMESG000016811.1)

HSP 1 Score: 215.698 bits (548), Expect = 6.934e-71
Identity = 104/135 (77.04%), Postives = 121/135 (89.63%), Query Frame = 2 
Query:  314 MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRH-------SGSTVQLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNEELPSGISLKDQSVKNNDTIKVLMKTRGG 697
            M +R+++R   DK+NVDIQS+++NNQ+L+D+ +       +GSTVQL  ++SDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYL+HHNEELPSG+SLKDQSVKNNDTIKVLMKTRGG
Sbjct:   23 MSLRDVKRNWSDKYNVDIQSVRYNNQILSDENNCNFYKIRTGSTVQLISNESDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLSHHNEELPSGVSLKDQSVKNNDTIKVLMKTRGG 157
[Close]
BLAST of SMED30012973 vs. Planmine SMEST
Match: SMESG000016811.1 (SMESG000016811.1)

HSP 1 Score: 215.698 bits (548), Expect = 8.250e-71
Identity = 104/135 (77.04%), Postives = 121/135 (89.63%), Query Frame = 2 
Query:  314 MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRH-------SGSTVQLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNEELPSGISLKDQSVKNNDTIKVLMKTRGG 697
            M +R+++R   DK+NVDIQS+++NNQ+L+D+ +       +GSTVQL  ++SDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYL+HHNEELPSG+SLKDQSVKNNDTIKVLMKTRGG
Sbjct:   21 MSLRDVKRNWSDKYNVDIQSVRYNNQILSDENNCNFYKIRTGSTVQLISNESDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLSHHNEELPSGVSLKDQSVKNNDTIKVLMKTRGG 155
[Close]
BLAST of SMED30012973 vs. Planmine SMEST
Match: SMESG000016810.1 (SMESG000016810.1)

HSP 1 Score: 173.711 bits (439), Expect = 2.914e-54
Identity = 88/135 (65.19%), Postives = 111/135 (82.22%), Query Frame = 2 
Query:  314 MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRH-------SGSTVQLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNEELPSGISLKDQSVKNNDTIKVLMKTRGG 697
            + I+EL++K  DKFN+ IQS++FNNQ+L+DD +       +GSTV+L  DKS+DQI LLVELQS+N NQRS QI VNPNITTEELMSVIRN++ FD+GSAYL HH ++L S +SLKDQ+VKNND I+VLM+TRGG
Sbjct:   29 ISIKELKKKWSDKFNIAIQSVKFNNQILSDDSNCSSCSIINGSTVKLIQDKSNDQITLLVELQSINTNQRSIQIPVNPNITTEELMSVIRNRISFDLGSAYLTHHGQQLRSAVSLKDQNVKNNDRIQVLMRTRGG 163
[Close]
BLAST of SMED30012973 vs. Planmine SMEST
Match: SMESG000016785.1 (SMESG000016785.1)

HSP 1 Score: 146.747 bits (369), Expect = 1.034e-43
Identity = 71/135 (52.59%), Postives = 97/135 (71.85%), Query Frame = 2 
Query:  314 MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRHS-------GSTVQLTLDKSDDQINLLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNEELPSGISLKDQSVKNNDTIKVLMKTRGG 697
            M I  L+    DK+ VDIQS++FN Q L+DD++        G+T++L   KSD +INL+VE+QS+NP QR  Q+RVNP+I TE+LM VI+ K+ F+  SAYL HH E L  G+SL+DQ VKNND I+VL++T+GG
Sbjct:   29 MSISVLKGNWSDKYGVDIQSVRFNGQTLSDDKNCNFYNIRDGATLELISSKSDSEINLIVEVQSINPGQRPIQVRVNPSIKTEDLMKVIKEKIYFNFDSAYLTHHGETLREGVSLRDQCVKNNDMIQVLVRTKGG 163
The following BLAST results are available for this feature:
BLAST of SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 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 SMED30012973 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016780.13.837e-8596.09SMESG000016780.1[more]
SMESG000016811.16.934e-7177.04SMESG000016811.1[more]
SMESG000016811.18.250e-7177.04SMESG000016811.1[more]
SMESG000016810.12.914e-5465.19SMESG000016810.1[more]
SMESG000016785.11.034e-4352.59SMESG000016785.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012973 ID=SMED30012973|Name=SMED30012973|organism=Schmidtea mediterranea sexual|type=transcript|length=843bp
TGAAAATTTGTGGATGTGCAGTAAATATTAATAGAATAAATGATAAAAAA
GAGAACAAAGAAGTTGTAATTGAAAATTAATTTACGAAATTAATTAATTT
AATTGAAATTAGTATGTTATCATCTAATGTATTGAAATATATTTGTTATA
CTCACTATTCTCATAATGACTGCGTCGACCCTCCCCAATTTCCCATTCTA
AGTGATTATTGTAACGCTCATGTTCATGTGTAGCACAGTTTGTGAGTTTT
GTCGTTACGGATAAACACAAAAAACAGTATTGAATAAGAAATGTGGGGGT
TGGTATAAATTGAATGCACATAAGAGAATTGAGAAGGAAATTGAAGGATA
AATTCAATGTAGACATTCAATCCATTCAGTTCAACAATCAACTACTTACC
GATGACAGACATTCTGGTTCAACTGTGCAGCTCACCTTGGATAAATCAGA
CGATCAGATCAATTTGCTTGTGGAACTGCAATCAGTAAATCCCAACCAAA
GATCATGTCAAATCCGAGTGAACCCAAATATCACAACCGAAGAGCTGATG
AGCGTTATCCGAAATAAAGTTCCATTCGATGTAGGGTCGGCATATCTAGC
TCATCACAACGAAGAACTTCCTTCTGGGATCAGTTTAAAAGACCAAAGTG
TCAAAAATAACGACACAATCAAAGTTTTAATGAAAACCAGAGGCGGATAA
ATTAATTTATTCAAATTATTATCATTTGTTTGTAAACAATTCAATTTTGT
AGTGATTTAATAAAATGTTTCCATTGTAAACAATTCATTTTCAATACATT
TTCCAATCAGATTCATTTGATATTAATTTCAAGATCGGAAGAG
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protein sequence of SMED30012973-orf-1

>SMED30012973-orf-1 ID=SMED30012973-orf-1|Name=SMED30012973-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MHIRELRRKLKDKFNVDIQSIQFNNQLLTDDRHSGSTVQLTLDKSDDQIN
LLVELQSVNPNQRSCQIRVNPNITTEELMSVIRNKVPFDVGSAYLAHHNE
ELPSGISLKDQSVKNNDTIKVLMKTRGG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 48..128
e-value: 3.7E-8
score: 35.0
NoneNo IPR availableCDDcd17039Ubl_ubiquitin_likecoord: 58..122
e-value: 2.83831E-4
score: 34.8794
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 51..128
score: 10.441
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 30..128