SMED30028655

Overview
NameSMED30028655
Smed IDSMED30028655
Length (bp)1536
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



SMED30028655

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30028655 SmedASXL_078416SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X2 cellSMED30028655 SmedASXL_076841SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30028655SMESG000000385.1 Contig34259newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028655 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000435:103167..104702 +6439
v31.003415:13935..23046 +6284
v31.000396:47846..49403 +6154
v31.011191:11494..13022 +5889
v31.017768:10062..11588 -5881
v31.008574:13589..14950 +5406
v31.000493:115719..116985 -4925
v31.001456:9745..11231 -3904
Homology
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BLAST of SMED30028655 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 189.119 bits (479), Expect = 4.292e-57
Identity = 100/187 (53.48%), Postives = 126/187 (67.38%), Query Frame = 2 
Query:  737 YPSDESWIDESRVTVQFPARSAAKCRQAMWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEHILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYELDSPMLGELSKSMKV-----VLPKEMRSSEQSPREDQDHPYARMRPKH---NQIPRYRS 1273
            Y  ++SWID  RV  +FPA +AA+CRQAMWDAGFS+S VRE+R G Q    D +LPYVAIKRE G N ARE R +AE +L RLEE QK T  Q+  A+ +L +VN DIA GRIPSTD  APSY +S+ELD P L    ++M V     VLP+E+R+ E++    QDH +AR R      N+IPR+ S
Sbjct:    9 YNLEDSWIDAPRVIARFPAHAAARCRQAMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKREPGGNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSFELDDPSLCNRLETMNVILPRRVLPRELRNVEENSDSRQDHSFARNRQSQRYGNEIPRFNS 195
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BLAST of SMED30028655 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 189.889 bits (481), Expect = 1.448e-56
Identity = 99/171 (57.89%), Postives = 118/171 (69.01%), Query Frame = 2 
Query:  743 SDESWIDESRVTVQFPARSAAKCRQAMWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEHILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYELDSPMLGELSKSMKV-----VLPKEMRSSEQSPREDQDHPYARMR 1240
            S +SWID SRV  +FPA SAA+CRQAMWDAGFS+ PVRE+R G Q D  + DL YVAIKRE GR+ ARE R +AE++LARLE  Q  TN QVE A+ +L RVN DIAAGRIPSTD  AP Y +S+ELD P L      M+V     +LPKEMR+        ++H YAR R
Sbjct:   88 SHDSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRSPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQREHSYARER 258
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BLAST of SMED30028655 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 184.882 bits (468), Expect = 1.297e-55
Identity = 95/171 (55.56%), Postives = 120/171 (70.18%), Query Frame = 2 
Query:  746 DESWIDESRVTVQFPARSAAKCRQAMWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEHILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYELDSPMLGELSKSMKVVLPKEMR-----SSEQSPREDQDHPYARMRP 1243
            + SWI  SRVT++FPA SA +CRQAMWDAGFS+SPVRESR G + +  D DLP+VAIKRE GRN ARE R +AE++LARLEE +++T+ +V+ A+ HL  +N DIAAG IPSTD  AP Y   + LD P L   S +MKVV+P+E        + +   E  DHPYAR RP
Sbjct:    6 ENSWIYASRVTLRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARERP 176
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BLAST of SMED30028655 vs. Planmine SMEST
Match: SMESG000075969.1 (SMESG000075969.1)

HSP 1 Score: 186.808 bits (473), Expect = 8.724e-55
Identity = 94/161 (58.39%), Postives = 117/161 (72.67%), Query Frame = 2 
Query:  749 ESWIDESRVTVQFPARSAAKCRQAMWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEHILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYELDSPMLGELSKSMKV-----VLPKEMRSSEQSPREDQ 1216
            +SW+DESR+T++FP+ SA +CRQAMWDAGFS+SPVRESR GRQ    D +LP+VAIKRE GRN ARE R R E ILAR E  Q+RTN QVE A+  L + N DIAAG IPSTD   PSYGIS++LD P + +  ++M V     VLP+EMR+  ++ R D 
Sbjct:    9 DSWVDESRITMRFPSHSAVRCRQAMWDAGFSISPVRESRFGRQGGTEDVELPFVAIKREPGRNPARELRSRVEEILARPEAHQRRTNKQVEKARRQLEQTNEDIAAGLIPSTDGYTPSYGISFQLDDPRVNQPVQAMTVSMPKEVLPREMRTETRNRRSDH 169
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BLAST of SMED30028655 vs. Planmine SMEST
Match: SMESG000027872.1 (SMESG000027872.1)

HSP 1 Score: 179.874 bits (455), Expect = 8.005e-54
Identity = 90/175 (51.43%), Postives = 125/175 (71.43%), Query Frame = 2 
Query:  743 SDESWIDESRVTVQFPARSAAKCRQAMWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEHILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYELDSPMLGELSKSMKVVLPKEMRS-----SEQSPREDQDHPYARMRPKHN 1252
            S++SWID SRVT++FPA SAA+CRQAMWDA FS+SPVRES+   Q+   D DLP+VAIKRE GRN ARE R +A+H+LARLEE Q++T  Q+  A+ HL  +N DIA G IPST+  AP Y  S+ LD P     ++++ VV+P+++ +     + ++P  +++HPYAR  P+ N
Sbjct:    7 SEDSWIDASRVTLRFPAHSAARCRQAMWDAEFSISPVRESQGKDQKISDDVDLPFVAIKREPGRNPAREIRGQAKHLLARLEEHQRQTAQQIRRAQRHLDEINRDIAVGLIPSTNGYAPPYNTSFNLDDPRFNRPTEAINVVVPRQLWTGRGERTYEAPTTNREHPYARGPPRTN 181
The following BLAST results are available for this feature:
BLAST of SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 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 SMED30028655 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065931.14.292e-5753.48SMESG000065931.1[more]
SMESG000013157.11.448e-5657.89SMESG000013157.1[more]
SMESG000032540.11.297e-5555.56SMESG000032540.1[more]
SMESG000075969.18.724e-5558.39SMESG000075969.1[more]
SMESG000027872.18.005e-5451.43SMESG000027872.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028655 ID=SMED30028655|Name=SMED30028655|organism=Schmidtea mediterranea sexual|type=transcript|length=1536bp
AACGGCCAACAGCGAGATAGCCAAGTGGAAGAAGTAACTATGGAGGAAAA
GATGCACGCACGAGCAGGTACTGATGTTAATAATTCTCAGTTAATTATCA
TGAGGGTCGAACGTAGACAATGAATTGGATTCGGAAATGTCCGGTTTCCC
CGATTGCGAAGACGCTCTTAGAATCAGTAAAGGCGTGGAGATAGAACTGT
ATACCAATTGTTATAAATCAGCAAATAAAAAAATCTAGTGTAATGTTGTT
CGTTGTCAATTACTTGTTGATGAAAATTTTACCGATGAATTAAAATGCAG
TCAAGCAGACTGAGATCCTAATAATAAACGTCAGGAGTAAATGCACATAA
CTTTAGATAATCGGATCAAAGCAAATAGACCTTTGTTACATGAACAACTT
ATAGCGTCATCTCGTGAAACTCAAATATTAAATCTACGAAACGAATCTGT
TGACTCTTAATTAACCATTCTCGCTCGAACATCCCACCAATCCCGTACTA
GAAATAGAATCCATCAAGTTTAGACACATACAGGCCACTAGCCATTACTC
ATGGAGAGTGAGAGCTCCTAAACAGTAGATTCTTGACGCCGTGAAGTTCG
ACTCACCACTTTTCAACCCACTGTCTCAGGTGGTATGACCCGCATCTAGG
CTCGATAATGACCGATTCCACGTACCACACACAGTTTAAATTCGAACAAC
TCAAGAAACAAATAAAAGATTCGATAAGTAACCATTTATCCTTCAGACGA
ATCGTGGATCGACGAGTCTCGGGTTACCGTACAATTTCCCGCACGATCAG
CTGCCAAATGCAGGCAGGCGATGTGGGACGCGGGCTTCTCAATGTCGCCC
GTAAGAGAATCGAGATCAGGACGTCAAGAGGACTTCGGAGATGCCGACTT
ACCATATGTGGCTATCAAAAGAGAGCTGGGTCGAAACACCGCTCGTGAAA
GTAGGCAACGCGCCGAGCATATTCTGGCCCGCCTTGAGGAGCGCCAGAAA
CGGACCAACTGGCAAGTGGAAATGGCGAAGCATCATCTGGTCAGAGTAAA
CTCTGATATTGCCGCGGGAAGGATCCCGAGTACGGATGTGAATGCCCCAT
CGTACGGCATTTCTTACGAACTCGATAGCCCAATGCTAGGAGAATTATCC
AAATCCATGAAAGTGGTGTTACCGAAAGAGATGCGGTCTAGTGAACAAAG
TCCGAGGGAAGACCAAGACCATCCGTATGCTAGAATGCGGCCGAAACATA
ACCAAATTCCACGTTACCGAAGTCCCATGCGGCGATAGTGTGTTACAAAA
TAAAAATTTGGATTTTATTTTTCTCCCCTTACTTATGAATTATTTTAAAT
TTTTGAAGCTGAGATAATAATAATGATAGAGCGGTAAAGGAATCAACGTA
ATACAGACGTGTGATAAGCTTAAATCAAAAACATAACTTGACGTTGTCAG
AGATAAGAAAATTTTTCCAAATTAAAATTAGACCAAAAGGTAATGATTTT
CGTTTTATTGTAGACATGAACCTAGTGAAAATGTTG
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protein sequence of SMED30028655-orf-1

>SMED30028655-orf-1 ID=SMED30028655-orf-1|Name=SMED30028655-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
MWDAGFSMSPVRESRSGRQEDFGDADLPYVAIKRELGRNTARESRQRAEH
ILARLEERQKRTNWQVEMAKHHLVRVNSDIAAGRIPSTDVNAPSYGISYE
LDSPMLGELSKSMKVVLPKEMRSSEQSPREDQDHPYARMRPKHNQIPRYR
SPMRR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..25
score: 0.461