SMED30001213

Overview
NameSMED30001213
Smed IDSMED30001213
Length (bp)371
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30001213

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
X2 cellSMED30001213 SmedASXL_079427SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001213 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002515:54090..54460 -1801
v31.002728:47719..48089 -1792
v31.001693:42200..42569 +1397
v31.001803:48551..48920 -1388
v31.001803:46668..47037 -1388
v31.011142:3385..3754 +1343
v31.006436:7979..8349 -1333
v31.003005:38841..39205 +1278
Homology
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BLAST of SMED30001213 vs. Planmine SMEST
Match: SMESG000042945.1 (SMESG000042945.1)

HSP 1 Score: 141.354 bits (355), Expect = 1.317e-41
Identity = 80/122 (65.57%), Postives = 92/122 (75.41%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRAEGEVILSNATNVL*DATVRVAE 366
            E VK LQ KIHRL+RC +DLI EN  Q+IIINDQS VLV SFTE EL KRL GR+LAL+LNL+PA H+P+   A   +TPRT KKHHP+KN RRRE RRAEG  IL+NA  VL +A   VAE
Sbjct:  156 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPAGHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAE 277
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BLAST of SMED30001213 vs. Planmine SMEST
Match: SMESG000028417.1 (SMESG000028417.1)

HSP 1 Score: 138.272 bits (347), Expect = 1.686e-41
Identity = 77/122 (63.11%), Postives = 93/122 (76.23%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRAEGEVILSNATNVL*DATVRVAE 366
            E VK LQ KIHRL+RC +DLI EN  Q+IIINDQS  LV SFTEVEL KRL GR+L ++LNL+P +H+P++  A   +TPRT KKHHP+KN RRRE RRAEG  +LSNA  VL +A + VAE
Sbjct:   48 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSADLVASFTEVELTKRLAGRDLVVKLNLIPVNHLPEETQAGPAQTPRTSKKHHPSKNCRRRERRRAEGLTLLSNAAQVLEEAAMLVAE 169
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BLAST of SMED30001213 vs. Planmine SMEST
Match: SMESG000059904.1 (SMESG000059904.1)

HSP 1 Score: 139.043 bits (349), Expect = 6.089e-41
Identity = 79/122 (64.75%), Postives = 92/122 (75.41%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRAEGEVILSNATNVL*DATVRVAE 366
            E VK LQ KIH L+RC +DLI EN  Q+IIINDQS VLV SFTE EL KRL GR+LAL+LNL+PA+H+P+   A   +TPRT KKHHP+KN RRRE RRAEG  IL+NA  VL +A   VAE
Sbjct:  129 EAVKILQDKIHELSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAE 250

HSP 2 Score: 98.5969 bits (244), Expect = 1.524e-25
Identity = 49/88 (55.68%), Postives = 63/88 (71.59%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHP 264
            E VKAL Q+IHRLTR  DDLI+EN  Q+IIINDQ  VL+ SFT+ EL KR+ GR+LA++LNL+P  H+P+K      K P+ +K   P
Sbjct:   12 EFVKALHQQIHRLTRYRDDLISENRAQRIIINDQIPVLIASFTKAELTKRIAGRDLAVKLNLIPPTHIPEKNEVGQAKPPKPVKNATP 99
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BLAST of SMED30001213 vs. Planmine SMEST
Match: SMESG000039380.1 (SMESG000039380.1)

HSP 1 Score: 135.191 bits (339), Expect = 2.786e-40
Identity = 78/122 (63.93%), Postives = 90/122 (73.77%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRAEGEVILSNATNVL*DATVRVAE 366
            E VK LQ KIHRL+RC +DLI EN  Q+IIINDQS VLV SFTE EL KRL GR+LAL+LNL+PA H+P+   A   +T RT KKHHP+KN RRRE RRAEG  IL+NA  VL +A   V E
Sbjct:   48 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPASHLPEPTQAGPAQTLRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVTE 169
[Close]
BLAST of SMED30001213 vs. Planmine SMEST
Match: SMESG000072638.1 (SMESG000072638.1)

HSP 1 Score: 137.502 bits (345), Expect = 1.224e-39
Identity = 79/122 (64.75%), Postives = 92/122 (75.41%), Query Frame = 1 
Query:    1 EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKRLYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRAEGEVILSNATNVL*DATVRVAE 366
            E VK LQ KIHRL+RC +DLI EN  Q+IIINDQS VLV SFTE EL KRL GR+LAL+LNL+PA+H+P+   A   + PRT KKHHP+KN RRRE RRAEG  IL+NA  VL +A   VAE
Sbjct:  237 EAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPEIAQAGPAQIPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAE 358
The following BLAST results are available for this feature:
BLAST of SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 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 SMED30001213 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042945.11.317e-4165.57SMESG000042945.1[more]
SMESG000028417.11.686e-4163.11SMESG000028417.1[more]
SMESG000059904.16.089e-4164.75SMESG000059904.1[more]
SMESG000039380.12.786e-4063.93SMESG000039380.1[more]
SMESG000072638.11.224e-3964.75SMESG000072638.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001213 ID=SMED30001213|Name=SMED30001213|organism=Schmidtea mediterranea sexual|type=transcript|length=371bp
GAAAAAGTCAAGGCGCTACAACAAAAAATTCACCGGCTAACGCGATGCTT
AGATGATTTGATTAATGAGAATGGCACCCAGAAAATAATAATAAACGATC
AAAGCACGGTGTTAGTAGGATCGTTCACTGAAGTAGAGTTGAAAAAGCGA
TTATATGGCCGAAACCTCGCATTGGAATTAAATTTGGTACCTGCCCATCA
TGTCCCTGATAAAGAACCGGCTCATATATACAAGACACCGAGGACCATCA
AAAAACACCATCCCAACAAGAACATGCGACGCCGTGAAAGTCGTCGGGCT
GAGGGAGAGGTGATCCTCTCCAACGCAACGAATGTTCTATAAGATGCCAC
CGTGCGAGTGGCCGAGATGCA
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protein sequence of SMED30001213-orf-1

>SMED30001213-orf-1 ID=SMED30001213-orf-1|Name=SMED30001213-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
EKVKALQQKIHRLTRCLDDLINENGTQKIIINDQSTVLVGSFTEVELKKR
LYGRNLALELNLVPAHHVPDKEPAHIYKTPRTIKKHHPNKNMRRRESRRA
EGEVILSNATNVL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 3..23