SMED30029247

Overview
NameSMED30029247
Smed IDSMED30029247
Length (bp)362
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



SMED30029247

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
prepharyngeal regionSMED30029247 SmedASXL_069668SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30029247 Contig43909newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029247 Contig43909uc_Smed_v2PMID: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
SMED30029247 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018650:7396..7803 +1727
Homology
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BLAST of SMED30029247 vs. Planmine SMEST
Match: SMESG000043422.1 (SMESG000043422.1)

HSP 1 Score: 177.178 bits (448), Expect = 4.170e-59
Identity = 95/96 (98.96%), Postives = 96/96 (100.00%), Query Frame = 1 
Query:   13 MKVFYXXXXXXXXXSVYGKHGYMELVEHENDFEVKNLVEDQEKISDEDQSSETKRVARGIFCGTRQCRILFRSWITCTIYLYRIGRICKPRSFRCT 300
            MKVFYLTVLLTLVLSVYGKHGYMELVEHENDFEVKNLVEDQEKISDE+QSSETKRVARGIFCGTRQCRILFRSWITCTIYLYRIGRICKPRSFRCT
Sbjct:    1 MKVFYLTVLLTLVLSVYGKHGYMELVEHENDFEVKNLVEDQEKISDENQSSETKRVARGIFCGTRQCRILFRSWITCTIYLYRIGRICKPRSFRCT 96
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BLAST of SMED30029247 vs. Planmine SMEST
Match: SMESG000043393.1 (SMESG000043393.1)

HSP 1 Score: 69.3218 bits (168), Expect = 2.073e-16
Identity = 34/83 (40.96%), Postives = 54/83 (65.06%), Query Frame = 1 
Query:   55 SVYGKHGYMELVEHENDFEVKNLVEDQ-EKISDEDQSSETKRVARGIFCGTRQCRILF-RSWITCTIYLYRIGRICKPRSFRC 297
            S+Y      E + ++  F+VK+L E++ E+ +D+++ ++TK   +  +CG R CR+ F R W TCT+  YRIGR+CKPR F C
Sbjct:   15 SIYCAEEENEALTNDESFDVKSLKEEEIEEGNDKEEENDTKLFIKHRYCGLRTCRLYFGRRWFTCTVRFYRIGRLCKPRRFAC 97
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BLAST of SMED30029247 vs. Planmine SMEST
Match: SMESG000043388.1 (SMESG000043388.1)

HSP 1 Score: 67.3958 bits (163), Expect = 9.343e-16
Identity = 33/83 (39.76%), Postives = 54/83 (65.06%), Query Frame = 1 
Query:   55 SVYGKHGYMELVEHENDFEVKNLVEDQ-EKISDEDQSSETKRVARGIFCGTRQCRILF-RSWITCTIYLYRIGRICKPRSFRC 297
            S+Y      E + ++  F+VK+L E++ E+ +D+++ ++TK + +  +CG R CR+ F R W TCT+  YRIGR+CKP  F C
Sbjct:   15 SIYCAEEENEALTNDESFDVKSLKEEEIEEGNDKEEENDTKLLIKHRYCGLRTCRLHFGRRWFTCTVRFYRIGRLCKPSRFNC 97
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BLAST of SMED30029247 vs. Planmine SMEST
Match: SMESG000040596.1 (SMESG000040596.1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.721e-12
Identity = 32/83 (38.55%), Postives = 50/83 (60.24%), Query Frame = 1 
Query:   55 SVYGKHGYMELVEHENDFEVKNLVEDQEKI-SDEDQSSETKRVARGIFCGTRQCRILF-RSWITCTIYLYRIGRICKPRSFRC 297
            S+Y      E + ++  F+VK+L E++ +  +D+++ ++TK   R  +CG R CR  F R W TCT+  YR  R+CKPR F C
Sbjct:   15 SIYCAEEENEALTNDESFDVKSLKEEELEEGNDKEEENDTKLFKRRRYCGLRTCRFFFGRRWFTCTVRFYRSRRLCKPRRFSC 97
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BLAST of SMED30029247 vs. Planmine SMEST
Match: SMESG000043411.1 (SMESG000043411.1)

HSP 1 Score: 55.4546 bits (132), Expect = 5.129e-11
Identity = 27/83 (32.53%), Postives = 47/83 (56.63%), Query Frame = 1 
Query:   55 SVYGKHGYMELVEHENDFEVKNLVEDQEKISDEDQSSETKRVARGIFCGTRQCRILF-RSWITCTIYLYRIGRICKPRSFRCT 300
            S++    + ++  +E+D EVK+  E +  ++++ + +E+K   +  FCG R+C + F R    CTI  YR    CKPR F C+
Sbjct:   15 SIFCSEDHHDVAANEDDLEVKDFSEME--VNEDKEENESKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSTCKPRRFSCS 95
The following BLAST results are available for this feature:
BLAST of SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 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 SMED30029247 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043422.14.170e-5998.96SMESG000043422.1[more]
SMESG000043393.12.073e-1640.96SMESG000043393.1[more]
SMESG000043388.19.343e-1639.76SMESG000043388.1[more]
SMESG000040596.11.721e-1238.55SMESG000040596.1[more]
SMESG000043411.15.129e-1132.53SMESG000043411.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029247 ID=SMED30029247|Name=SMED30029247|organism=Schmidtea mediterranea sexual|type=transcript|length=362bp
ATGGGCATAATGATGAAGGTCTTTTATCTAACTGTTCTTCTTACCCTCGT
TTTGTCGGTTTATGGTAAGCATGGATATATGGAACTAGTAGAACACGAAA
ATGATTTCGAAGTGAAAAACTTAGTTGAAGATCAAGAAAAAATAAGCGAT
GAAGATCAATCGAGTGAAACGAAACGAGTAGCTAGAGGAATATTTTGTGG
AACAAGGCAGTGTCGGATCCTTTTCCGGAGTTGGATCACTTGCACGATAT
ATCTCTACCGCATTGGACGGATATGTAAACCTCGCTCTTTTCGTTGCACC
TAGACTGGAACTATAGACATCATTATTGCTTTAATAAATTATGGTGATTC
ACTAAAAAAAAA
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protein sequence of SMED30029247-orf-1

>SMED30029247-orf-1 ID=SMED30029247-orf-1|Name=SMED30029247-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MGIMMKVFYLTVLLTLVLSVYGKHGYMELVEHENDFEVKNLVEDQEKISD
EDQSSETKRVARGIFCGTRQCRILFRSWITCTIYLYRIGRICKPRSFRCT
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region
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..20
score: 0.88