SMED30030221

Overview
NameSMED30030221
Smed IDSMED30030221
Length (bp)939
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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Alignments
SMED30030221 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014926:12610..13522 +2943
v31.015591:5393..6304 -2897
Homology
BLAST of SMED30030221 vs. Planmine SMEST
Match: SMESG000071773.1 (SMESG000071773.1)

HSP 1 Score: 226.098 bits (575), Expect = 7.433e-74
Identity = 125/138 (90.58%), Postives = 131/138 (94.93%), Query Frame = -1
Query:   46 MSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRKLFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCSWAQGLNIIPA*HLLSNXXXXXXXXXPQNVVTESRPGVS 459
            M +LPRIPRLSPSIIATRQKLEQL++DH VLQAKYQKLKGTWSSPEATRKLFQK  RLS+ARDDLVV SRSQRILIA+QSAALRRIFT+AELRARLPGCSWAQGLNIIPA HL SNPTPPPTIEPPQNVVTESRPGVS
Sbjct:    1 MLDLPRIPRLSPSIIATRQKLEQLQKDHTVLQAKYQKLKGTWSSPEATRKLFQKSSRLSRARDDLVVESRSQRILIAKQSAALRRIFTEAELRARLPGCSWAQGLNIIPAQHLPSNPTPPPTIEPPQNVVTESRPGVS 138          
BLAST of SMED30030221 vs. Planmine SMEST
Match: SMESG000002079.1 (SMESG000002079.1)

HSP 1 Score: 219.55 bits (558), Expect = 2.842e-68
Identity = 121/158 (76.58%), Postives = 132/158 (83.54%), Query Frame = -1
Query:   43 CLHID--------PLRTANMSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRKLFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCSWAQGLNIIPA*HLLSNXXXXXXXXXPQNVVTESRPGVSQ 492
            C HI         P RT N +ELP+IPRLS SIIATRQ+LEQLE+DHAVLQ KYQKLKGTW SPEATRKLFQKI RLS+ARDDLVV SRSQRILIAEQS ALRRIFT+AELRAR+PGCSWAQ L+IIPA HL SNP PPPTIEP QN+  ESRPG++Q
Sbjct:  206 CYHIYREHVSYNIPHRTTNTTELPKIPRLSRSIIATRQRLEQLEKDHAVLQTKYQKLKGTWRSPEATRKLFQKISRLSRARDDLVVESRSQRILIAEQSDALRRIFTEAELRARVPGCSWAQSLDIIPAQHLFSNPIPPPTIEPSQNIRAESRPGIAQ 363          
BLAST of SMED30030221 vs. Planmine SMEST
Match: SMESG000070051.1 (SMESG000070051.1)

HSP 1 Score: 215.312 bits (547), Expect = 2.859e-68
Identity = 117/138 (84.78%), Postives = 125/138 (90.58%), Query Frame = -1
Query:   46 MSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRKLFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCSWAQGLNIIPA*HLLSNXXXXXXXXXPQNVVTESRPGVS 459
            MS+L  IPRLSPSIIATRQ+L+QLERDHAVLQ+KY+KLKGTWSSPE T+KLFQKI RLS+ARDDLVV SRSQRILIAEQSAALRRIFT+AELRARLPGCSWAQGLNIIPA HLLSN  P P  EPPQNVV E RPGVS
Sbjct:    1 MSDLHWIPRLSPSIIATRQRLKQLERDHAVLQSKYEKLKGTWSSPEFTQKLFQKISRLSRARDDLVVESRSQRILIAEQSAALRRIFTEAELRARLPGCSWAQGLNIIPAQHLLSN--PTPPNEPPQNVVIEPRPGVS 136          
BLAST of SMED30030221 vs. Planmine SMEST
Match: SMESG000041408.1 (SMESG000041408.1)

HSP 1 Score: 210.69 bits (535), Expect = 1.267e-66
Identity = 107/140 (76.43%), Postives = 121/140 (86.43%), Query Frame = -1
Query:   46 ANMSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRKLFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCSWAQGLNIIPA*HLLSNXXXXXXXXXPQNVVTESRPGVS 465
             NM+ELPRIPRLSPSI+ATRQ+LEQLE+DH VLQAKYQKLKGTWSSPE+T+KLFQKI RL++ARD+L++ SRSQRILIAEQS ALRRIFT+AELRARLPGCS AQ L+IIPA HL SNPTP    EP QN   +  PGVS
Sbjct:    2 TNMTELPRIPRLSPSIVATRQRLEQLEKDHTVLQAKYQKLKGTWSSPESTKKLFQKIARLTRARDELIIESRSQRILIAEQSTALRRIFTEAELRARLPGCSLAQSLDIIPAQHLPSNPTPSLPNEPSQNTTVDPTPGVS 141          
BLAST of SMED30030221 vs. Planmine SMEST
Match: SMESG000061686.1 (SMESG000061686.1)

HSP 1 Score: 182.57 bits (462), Expect = 1.350e-56
Identity = 86/115 (74.78%), Postives = 100/115 (86.96%), Query Frame = -1
Query:  121 ANMSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRKLFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCSWAQGLNIIPA*HL 465
            +N+S LPRIPRLS S IATRQKL+QLERDHA+LQAKY+ +KGTWSSPEA R L+QK+ RLS+ARDDL++ +RSQRI IAEQSAALR IFT+ ELR RLP CSWAQ +NIIPA HL
Sbjct:    2 SNLSNLPRIPRLSSSAIATRQKLDQLERDHAILQAKYRNIKGTWSSPEAARSLYQKVSRLSRARDDLIIETRSQRITIAEQSAALRPIFTENELRTRLPSCSWAQDINIIPAQHL 116          
The following BLAST results are available for this feature:
BLAST of SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 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 SMED30030221 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071773.17.433e-7490.58SMESG000071773.1[more]
SMESG000002079.12.842e-6876.58SMESG000002079.1[more]
SMESG000070051.12.859e-6884.78SMESG000070051.1[more]
SMESG000041408.11.267e-6676.43SMESG000041408.1[more]
SMESG000061686.11.350e-5674.78SMESG000061686.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030221 ID=SMED30030221|Name=SMED30030221|organism=Schmidtea mediterranea sexual|type=transcript|length=939bp
TCTTCCGATCTAGCGGCGACGGCGATTTCGATTTGGCCGCCGTTGGGATA
CTCCGGGCCTTGATTCTGTCACTACATTCTGTGGAGGTTCAATGGTTGGA
GGTGGAGTTGGATTTGAAAGGAGGTGCTAGGCTGGAATAATATTTAGGCC
CTGGGCCCAACTACATCCCGGTAAACGAGCTCTGAGCTCGGCATCCGTAA
ATATCCGCCTGAGTGCGGCACTCTGTTCAGCGATGAGAATTCGCTGGCTG
CGTGATACAACCACCAGATCATCTCTGGCCTGAGATAGGCGACAGATTTT
TTGGAATAATTTGCGGGTGGCTTCGGGCGAGCTCCAGGTGCCCTTTAATT
TTTGATATTTCGCTTGAAGGACTGCGTGGTCCCTTTCGAGTTGTTCCAGC
TTCTGACGGGTGGCAATTATTGAGGGAGACAATCGTGGTATTCTGGGAAG
CTCTGACATATTCGCTGTTCGGAGAGGATCTATATGTAAACAAAGATAGC
TTTATATACAATTGTCTGAGAATCATACTGGGACGTCGGTGAGGTAATCG
TGAGATAAATCGTAATCGAGATGACGGTATGAGTGGGGCATATATCAGTA
GTGGTATGGGGGTTGTAGAACCATCCTAGCACGGTGTAAATAATTAGAGG
GGGGTATTGATGCTAATGGTACGTATGAGTCGAGGTGAATTAATGATAAG
GTCAGTGGTCTCCCTAGTAATTAAATTAATCATGATTTGAACGGGGTTCG
GTTCAATTAATGTTGAGGTTTATCAATTAAGTATATTCTCTACTAATAAA
CAACCAAATTGTTAATAATCATATTCATAAGGTTGACTATAATATTCGTA
ACAGTACGCGCGGACATGTTAATAATATTAATACTAATAATTAACCATAA
TCATAATAAAACGGTAATAATAATAGTAATAATAACATT
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protein sequence of SMED30030221-orf-1

>SMED30030221-orf-1 ID=SMED30030221-orf-1|Name=SMED30030221-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MSELPRIPRLSPSIIATRQKLEQLERDHAVLQAKYQKLKGTWSSPEATRK
LFQKICRLSQARDDLVVVSRSQRILIAEQSAALRRIFTDAELRARLPGCS
WAQGLNIIPA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland