SMED30017918

Overview
NameSMED30017918
Smed IDSMED30017918
Length (bp)1262
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 SMED30017918 (SMED30017918) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017918 (SMED30017918) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30017918 (SMED30017918) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017918 (SMED30017918) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30017918

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30017918SMESG000047327.1 SmedASXL_009344SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30017918SMESG000047327.1 dd_Smed_v4_28678_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017918SMESG000047327.1 dd_Smed_v4_28678_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017918SMESG000047327.1 dd_Smed_v4_28678_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017918SMESG000047327.1 dd_Smed_v6_28678_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017918 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.021233:7697..11324 +5475
Homology
BLAST of SMED30017918 vs. TrEMBL
Match: A0A210PH67 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT04422 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 4.615e-9
Identity = 40/99 (40.40%), Postives = 58/99 (58.59%), Query Frame = 1
Query:  697 PIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEE 993
            P+++ T +   +D   T+EA EC  +   L A GV +S  TL+R L PPS  +   YE  ++ LP +   GLL+HP  WLP EY +LKSA+K + +  E
Sbjct:  957 PLYLNTVN--HSDYPETEEAQECTVMQAKLAAKGVTVSAKTLERALYPPSG-QTTYYEI-KANLPRSQSLGLLSHPKVWLPDEYRQLKSAEKALAKVNE 1051          
BLAST of SMED30017918 vs. TrEMBL
Match: A0A2T7NLV0 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_17943 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 8.554e-7
Identity = 31/91 (34.07%), Postives = 55/91 (60.44%), Query Frame = 1
Query:  706 IYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRM 978
            I  K ++ +D   T+ ++EC+++ + L   G+ +   TL+R L PPS   +  YE   + LP ++   LL+HP  WLP+E+ RL+ A+K++
Sbjct:  269 IVLKSKMPDDEFETETSMECREMQKRLACYGIDVKAETLERALFPPSGKTL-YYEVT-AKLPQSNSDRLLSHPRFWLPEEHKRLRLAEKKL 357          
BLAST of SMED30017918 vs. TrEMBL
Match: K1PHI7 (CutA-like protein OS=Crassostrea gigas OX=29159 GN=CGI_10012900 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 5.130e-6
Identity = 34/104 (32.69%), Postives = 58/104 (55.77%), Query Frame = 1
Query:  697 PIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQ 1008
            P++I++K  + +D   T+  +E   + + L ++ V I   TL+R L PPS   +  Y   ++ LP ++ + LL+HP  WLP EY + K A+K + +  E   RQ
Sbjct:  897 PLYIHSK--IPDDDVVTENEIEAHLIHERLASDNVYIRPETLERALYPPSGKTL--YYDIENKLPRSTSASLLSHPKVWLPVEYKQFKLAEKNLNKANEIIRRQ 996          
BLAST of SMED30017918 vs. Planmine SMEST
Match: SMESG000047327.1 (SMESG000047327.1)

HSP 1 Score: 610.142 bits (1572), Expect = 0.000e+0
Identity = 390/395 (98.73%), Postives = 390/395 (98.73%), Query Frame = 1
Query:   40 MSLHPPHSHKLVKRMSAVSFQENATVYEPXXXXXXXXXXXXXXXXXXXXXEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDSGCQTESKTSSYTNKLIIQEDFDCQTELKASSYKKKLTLQENYDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXINSANIELVQSFINSVPXXXXXXXXXXXXXXXXXXXXXXVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQRTIRPKTAG 1224
            MSLHPPHSHKLVKRMSAVSFQENATVYEPISDNNALKSNNNINNSISNGSEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDS CQTESKTSSYTNKLIIQEDFDCQTELKASSYK KLTLQENYDSQTESKQSSISSKLSR RRSIRRSKSAASSRESLSSCTRIN ANIELVQSFINSVPFKENKKKEKNKSNNSFKRKKKKVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQR IRPKTAG
Sbjct:    1 MSLHPPHSHKLVKRMSAVSFQENATVYEPISDNNALKSNNNINNSISNGSEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDSSCQTESKTSSYTNKLIIQEDFDCQTELKASSYKNKLTLQENYDSQTESKQSSISSKLSRHRRSIRRSKSAASSRESLSSCTRINYANIELVQSFINSVPFKENKKKEKNKSNNSFKRKKKKVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQRAIRPKTAG 395          
BLAST of SMED30017918 vs. Planmine SMEST
Match: SMESG000047327.1 (SMESG000047327.1)

HSP 1 Score: 578.941 bits (1491), Expect = 0.000e+0
Identity = 376/381 (98.69%), Postives = 376/381 (98.69%), Query Frame = 1
Query:   82 MSAVSFQENATVYEPXXXXXXXXXXXXXXXXXXXXXEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDSGCQTESKTSSYTNKLIIQEDFDCQTELKASSYKKKLTLQENYDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXINSANIELVQSFINSVPXXXXXXXXXXXXXXXXXXXXXXVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQRTIRPKTAG 1224
            MSAVSFQENATVYEPISDNNALKSNNNINNSISNGSEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDS CQTESKTSSYTNKLIIQEDFDCQTELKASSYK KLTLQENYDSQTESKQSSISSKLSR RRSIRRSKSAASSRESLSSCTRIN ANIELVQSFINSVPFKENKKKEKNKSNNSFKRKKKKVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQR IRPKTAG
Sbjct:    1 MSAVSFQENATVYEPISDNNALKSNNNINNSISNGSEQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDSSCQTESKTSSYTNKLIIQEDFDCQTELKASSYKNKLTLQENYDSQTESKQSSISSKLSRHRRSIRRSKSAASSRESLSSCTRINYANIELVQSFINSVPFKENKKKEKNKSNNSFKRKKKKVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLPKEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQYNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQRAIRPKTAG 381          
The following BLAST results are available for this feature:
BLAST of SMED30017918 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A210PH674.615e-940.40Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
A0A2T7NLV08.554e-734.07Uncharacterized protein OS=Pomacea canaliculata OX... [more]
K1PHI75.130e-632.69CutA-like protein OS=Crassostrea gigas OX=29159 GN... [more]
back to top
BLAST of SMED30017918 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017918 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000047327.10.000e+098.73SMESG000047327.1[more]
SMESG000047327.10.000e+098.69SMESG000047327.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017918 ID=SMED30017918|Name=SMED30017918|organism=Schmidtea mediterranea sexual|type=transcript|length=1262bp
AATTGAAATTATTTTTTTTTGAATAGAAATTTTTTATTTATGTCTTTACA
TCCACCTCATTCTCACAAACTAGTAAAACGGATGTCAGCAGTTTCTTTTC
AAGAAAACGCAACTGTTTACGAACCGATTTCAGATAACAATGCGCTTAAG
TCTAATAATAATATCAATAACTCCATTTCCAATGGCAGCGAACAAACATT
TAAATTTAGAACCATTCTTAAGAAAACAATGCCTAAAATAAAATGTATAT
CAAAATTTTCTGCTCTACATGAAAATGTTCAGCATAATAATTTGGAAAAA
GCCGTAATACAGGAAGACTCAGGCTGTCAAACAGAATCGAAAACAAGTTC
TTACACAAACAAATTAATAATCCAAGAAGACTTCGACTGTCAAACAGAAT
TGAAAGCAAGTTCTTACAAAAAAAAACTAACATTACAAGAGAACTATGAC
TCGCAAACTGAATCAAAGCAAAGTTCTATATCCTCAAAATTGTCGAGACC
TCGCAGATCAATTAGGCGTTCAAAGAGTGCAGCATCATCACGAGAGTCAT
TATCAAGTTGTACTAGAATCAATTCGGCGAATATTGAGTTAGTTCAATCG
TTTATTAATTCAGTACCTTTCAAAGAAAACAAAAAGAAAGAGAAAAATAA
ATCTAATAATTCATTCAAAAGAAAAAAGAAGAAAGTTCTTGTCGATCCCA
TCTTCATTTATACTAAAGATCGTCTGGAGAATGATTCTTGCAACACTGAT
GAAGCGCTTGAATGCCAGAAACTGTTTCAAATTCTTCAAGCAAATGGCGT
TAGGATTTCTCTGACGACTTTGAAAAGAGGTTTGTTGCCTCCTTCTGCTA
CTAGAATCGAAAGATATGAATTCAATCAATCCACATTGCCTTATAATAGT
TGTAGTGGATTATTAAATCATCCCTCAACCTGGTTACCAAAAGAATATGC
GCGACTAAAGTCTGCTAAAAAGAGAATGGAACAATTTGAAGAGGAAACAA
TTCGGCAATCTACGGTGGTAACAAGTGACGATGAAAGCCTCTCGTCAGAG
GAAGGCAGGAATCGACAAAGTCACAGTAAATTATCTCAATATAATGAGTT
TGCTCGTAGTATGAGTAAAGCATCAATTTCTCCAGTTGAATTAAAATCTA
AAAAGTCTATTATATTTACGAAAGCTAAAGCTGTATACAAATTTCAAAGA
ACTATTAGGCCTAAAACTGCCGGGTGAAAAACCGTTTGAATTTCCAACTT
TGATTACACACA
back to top

protein sequence of SMED30017918-orf-1

>SMED30017918-orf-1 ID=SMED30017918-orf-1|Name=SMED30017918-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=396bp
MSLHPPHSHKLVKRMSAVSFQENATVYEPISDNNALKSNNNINNSISNGS
EQTFKFRTILKKTMPKIKCISKFSALHENVQHNNLEKAVIQEDSGCQTES
KTSSYTNKLIIQEDFDCQTELKASSYKKKLTLQENYDSQTESKQSSISSK
LSRPRRSIRRSKSAASSRESLSSCTRINSANIELVQSFINSVPFKENKKK
EKNKSNNSFKRKKKKVLVDPIFIYTKDRLENDSCNTDEALECQKLFQILQ
ANGVRISLTTLKRGLLPPSATRIERYEFNQSTLPYNSCSGLLNHPSTWLP
KEYARLKSAKKRMEQFEEETIRQSTVVTSDDESLSSEEGRNRQSHSKLSQ
YNEFARSMSKASISPVELKSKKSIIFTKAKAVYKFQRTIRPKTAG*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 299..319
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 321..351
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 135..165