SMED30011891

Overview
NameSMED30011891
Smed IDSMED30011891
Length (bp)736
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



SMED30011891

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
parapharyngeal regionSMED30011891 SmedASXL_021652SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011891 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000242:103566..104417 +3108
Homology
[Close]
BLAST of SMED30011891 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 78.9518 bits (193), Expect = 5.531e-32
Identity = 37/63 (58.73%), Postives = 47/63 (74.60%), Query Frame = -1 
Query:  374 DDSRVTLTVSTQYAARYHQALCDHGYSLSTY*KDDWP*RTMSRDDEMELPSVAVKR*PCRKPA 562
            DDS++TL +S   AARY QAL D+GY+LSTY +  WP R   R+DE+ELPS+A+KR P R PA
Sbjct:  672 DDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPA 734

HSP 2 Score: 77.0258 bits (188), Expect = 5.531e-32
Identity = 40/78 (51.28%), Postives = 54/78 (69.23%), Query Frame = -2 
Query:  160 NRAENRRQRAEFTLRRLENLKKTF*WQANMAWRQLACINADITSRAIPSTDSFAPDYGVSFKLDDTALSKMEAPTQLV 393
            N A    QRAE+T  ++E +++ +  +A +A ++LA IN DI S  IPSTDSF P YGVSF+LDD  L +M APT+LV
Sbjct:  732 NPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLV 809
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BLAST of SMED30011891 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 78.9518 bits (193), Expect = 5.670e-32
Identity = 37/63 (58.73%), Postives = 47/63 (74.60%), Query Frame = -1 
Query:  374 DDSRVTLTVSTQYAARYHQALCDHGYSLSTY*KDDWP*RTMSRDDEMELPSVAVKR*PCRKPA 562
            DDS++TL +S   AARY QAL D+GY+LSTY +  WP R   R+DE+ELPS+A+KR P R PA
Sbjct:  676 DDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPA 738

HSP 2 Score: 77.0258 bits (188), Expect = 5.670e-32
Identity = 40/78 (51.28%), Postives = 54/78 (69.23%), Query Frame = -2 
Query:  160 NRAENRRQRAEFTLRRLENLKKTF*WQANMAWRQLACINADITSRAIPSTDSFAPDYGVSFKLDDTALSKMEAPTQLV 393
            N A    QRAE+T  ++E +++ +  +A +A ++LA IN DI S  IPSTDSF P YGVSF+LDD  L +M APT+LV
Sbjct:  736 NPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLV 813
[Close]
BLAST of SMED30011891 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 78.5666 bits (192), Expect = 8.932e-32
Identity = 37/63 (58.73%), Postives = 47/63 (74.60%), Query Frame = -1 
Query:  374 DDSRVTLTVSTQYAARYHQALCDHGYSLSTY*KDDWP*RTMSRDDEMELPSVAVKR*PCRKPA 562
            DDS++TL +S   AARY QAL D+GY+LSTY +  WP R   R+DE+ELPS+A+KR P R PA
Sbjct:  620 DDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPA 682

HSP 2 Score: 76.6406 bits (187), Expect = 8.932e-32
Identity = 40/78 (51.28%), Postives = 54/78 (69.23%), Query Frame = -2 
Query:  160 NRAENRRQRAEFTLRRLENLKKTF*WQANMAWRQLACINADITSRAIPSTDSFAPDYGVSFKLDDTALSKMEAPTQLV 393
            N A    QRAE+T  ++E +++ +  +A +A ++LA IN DI S  IPSTDSF P YGVSF+LDD  L +M APT+LV
Sbjct:  680 NPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLV 757
[Close]
BLAST of SMED30011891 vs. Planmine SMEST
Match: SMESG000053255.1 (SMESG000053255.1)

HSP 1 Score: 79.337 bits (194), Expect = 2.220e-31
Identity = 37/63 (58.73%), Postives = 47/63 (74.60%), Query Frame = -1 
Query:  374 DDSRVTLTVSTQYAARYHQALCDHGYSLSTY*KDDWP*RTMSRDDEMELPSVAVKR*PCRKPA 562
            DDSR+TL +S+  A RY QALCD+GY LSTY +  WP R+  R+DE+ELPS+A+KR   R PA
Sbjct:  318 DDSRITLQISSTSATRYRQALCDNGYPLSTYGESSWPGRSEDREDEVELPSIAIKRELGRNPA 380

HSP 2 Score: 74.3294 bits (181), Expect = 2.220e-31
Identity = 39/78 (50.00%), Postives = 55/78 (70.51%), Query Frame = -2 
Query:  160 NRAENRRQRAEFTLRRLENLKKTF*WQANMAWRQLACINADITSRAIPSTDSFAPDYGVSFKLDDTALSKMEAPTQLV 393
            N A   +QRAE+T  ++E +++    +A +A ++LA IN DI +  IPSTDSF+P YGVSF+LDD  L +M APT+LV
Sbjct:  378 NPAREVQQRAEYTAMKMEEMERKNHRKAVLARQRLAQINRDIANGIIPSTDSFSPPYGVSFELDDPRLLQMTAPTKLV 455
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BLAST of SMED30011891 vs. Planmine SMEST
Match: SMESG000066595.1 (SMESG000066595.1)

HSP 1 Score: 68.5514 bits (166), Expect = 5.134e-24
Identity = 32/68 (47.06%), Postives = 45/68 (66.18%), Query Frame = -1 
Query:  362 TDDSRVTLTVSTQYAARYHQALCDHGYSLSTY*KDDWP*RTMSRDDEMELPSVAVKR*PCRKPATKSR 565
             D+SRVTL + +   ARY Q L D+GY LSTY    WP R+  + +E+ELPS+A+KR P + P  ++R
Sbjct:  220 NDNSRVTLQIPSASVARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGKNPVREAR 287

HSP 2 Score: 60.8474 bits (146), Expect = 5.134e-24
Identity = 29/56 (51.79%), Postives = 41/56 (73.21%), Query Frame = -2 
Query:  208 RQRAEFTLRRLENLKKTF*WQANMAWRQLACINADITSRAIPSTDSFAPDYGVSFK 375
            RQRAEFT   +E L++ +  +A +A ++LA +N +I S AIPSTD F P+YGVSF+
Sbjct:  287 RQRAEFTAMMMEELERKYHRKAVLARQRLAQVNRNIASGAIPSTDGFPPEYGVSFE 342
The following BLAST results are available for this feature:
BLAST of SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 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 SMED30011891 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046313.15.531e-3258.73SMESG000046313.1[more]
SMESG000046313.15.670e-3258.73SMESG000046313.1[more]
SMESG000046313.18.932e-3258.73SMESG000046313.1[more]
SMESG000053255.12.220e-3158.73SMESG000053255.1[more]
SMESG000066595.15.134e-2447.06SMESG000066595.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011891 ID=SMED30011891|Name=SMED30011891|organism=Schmidtea mediterranea sexual|type=transcript|length=736bp
TGAACTAAAAACATTTATTTTATATTAAATTTCTCCAATAGTGTCTTCGA
TTTATCGTTCAGGAAATTTGTTATATTTTTTTCCGAGCATAGGTGTGATC
GTCCCGTTGCCGATGGCCCAAACAATCCAATAAGGCCAGCTGGATTAATC
GGGTTTCCTGACTAGCTGTGTTGGTGCCTCCATCTTGGATAACGCGGTAT
CGTCTAACTTGAATGAGACCCCGTAATCCGGAGCGAAGCTGTCAGTGCTT
GGTATCGCTCTACTCGTGATATCGGCGTTTATGCAAGCCAATTGCCTCCA
AGCCATGTTTGCTTGCCATCAGAATGTTTTTTTCAGGTTCTCCAGGCGAC
GCAGCGTAAATTCTGCTCTTTGTCGCCGGTTTTCTGCACGGTTATCGCTT
GACGGCCACGCTAGGTAGCTCCATCTCGTCATCTCGGCTCATCGTTCGTC
ATGGCCAGTCATCTTTTCAATAGGTAGATAGTGAGTATCCGTGGTCGCAG
AGTGCTTGGTGGTACCGTGCAGCATACTGAGTTGAAACTGTTAAGGTGAC
TCTGGAATCATCTGTCTATCATGACTCTGACGTGTTACGTACTTGTCTTT
GGTGGACCATCTCGAATTCTGGATCTACTTCCACTGTGAGTCGACGATGT
ATGGATCGGTCCCTGTCCACGTCTCTTTCCTGACAGTGTAATCTGATTAT
TTCTAGTATCTTCGTGCCGACAGTATAGTTGTTTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region