SMED30002986

Overview
NameSMED30002986
Smed IDSMED30002986
Length (bp)2111
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30002986 (SMED30002986) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002986 (SMED30002986) in cells (dots) of each of the 12 neoblast clusters.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30002986

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
parenchymaSMED30002986h1SMcG0018448 dd_Smed_v4_25770_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002986 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007646:2986..9574 +10081
Homology
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BLAST of SMED30002986 vs. Planmine SMEST
Match: SMESG000062044.1 (SMESG000062044.1)

HSP 1 Score: 339.347 bits (869), Expect = 1.340e-112
Identity = 228/229 (99.56%), Postives = 228/229 (99.56%), Query Frame = 2 
Query: 1025 MVYTSDTATVXXXXXXXXXXXXXXRSTKSKAKKQIDIKCATNISIGXXXXXXXXXXXXEFILNIPLHLLTSEKIINNENQTKTKPVYKIISNTKTKSKPKIENSLRXXXXXXXXXXXRAMETYKPKVSPIALQNPLKSDSKEVCESTDDDDEFSIRLSPEQIKSFYNNFDNNSEKLVEKPTDSKPISTNNIKTNWHLXXXXXXXXXXXXEEFTITIPTCAWNKTEKLFS 1711
            MVYTSDTATVKFLLKEKGFLKGKGRSTKSKAKKQIDIKCATNISIGSSSTVNDVSNDDEFILNIPLHLLTSEKIINNENQTKTKPVYKIISNTKTKSKPKIENSLRKPIKSPIKKSPRAMET KPKVSPIALQNPLKSDSKEVCESTDDDDEFSIRLSPEQIKSFYNNFDNNSEKLVEKPTDSKPISTNNIKTNWHLADSTASNDSDDDEEFTITIPTCAWNKTEKLFS
Sbjct:    1 MVYTSDTATVKFLLKEKGFLKGKGRSTKSKAKKQIDIKCATNISIGSSSTVNDVSNDDEFILNIPLHLLTSEKIINNENQTKTKPVYKIISNTKTKSKPKIENSLRKPIKSPIKKSPRAMETSKPKVSPIALQNPLKSDSKEVCESTDDDDEFSIRLSPEQIKSFYNNFDNNSEKLVEKPTDSKPISTNNIKTNWHLADSTASNDSDDDEEFTITIPTCAWNKTEKLFS 229
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BLAST of SMED30002986 vs. Planmine SMEST
Match: SMESG000000948.1 (SMESG000000948.1)

HSP 1 Score: 157.532 bits (397), Expect = 2.064e-44
Identity = 84/151 (55.63%), Postives = 100/151 (66.23%), Query Frame = 3 
Query:  297 GLDHMKPIFQDKQKLLPQCQMDRCKVCIFLNNCQKLLHSMRPLHTLTSAELW*LSNWQTKLIRTLLPQWELYQMITTTIFFEKDSTCDLLISGLHTSESRRNVYENYGQTLRLPNSLSARKKLVTLASGICNVCLKLSETLQSRLYVHNLR 749
             +D +K +F   QK+LP C MD+C VCI LN+C K LH M+P+HTLTSAEL+ LS W  KLI+ LLP+ ELYQMI TTI  E DST    I   +  ES +  YENYGQ L LPNSL  RK+L TLA  ICN C K  E LQS L   N++
Sbjct:   23 AIDAVKTLFHQNQKVLPMCPMDQCTVCILLNSCLKSLHLMKPIHTLTSAELYKLSCWLNKLIKNLLPRLELYQMIITTISLENDSTFGPSILASNIIESMKTHYENYGQILTLPNSLCVRKRLATLALDICNACWKKFEILQSVLSEPNIQ 173
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BLAST of SMED30002986 vs. Planmine SMEST
Match: SMESG000044627.1 (SMESG000044627.1)

HSP 1 Score: 66.2402 bits (160), Expect = 2.772e-16
Identity = 32/84 (38.10%), Postives = 53/84 (63.10%), Query Frame = 2 
Query:  308 HEAHIP-RQTKTITAMSNGSVQSMHISKQLSKASTLDETSAHLDKCRALVAQQLADQINKDSTSSVGTLPNDNYNNIFRKRFYL 556
            HE H+   +T T T + NG V  +H +KQ +  S ++E++ ++   R +    LA+QIN DS + +G++ ND  +NI+RKRFY+
Sbjct:   22 HETHVSGDETHTATDVPNGPVHCVHPTKQCTAVSKINESTQNIIAMREMETNSLAEQINNDSAAHLGSVSNDKKDNIYRKRFYI 105

HSP 2 Score: 38.5058 bits (88), Expect = 2.772e-16
Identity = 18/35 (51.43%), Postives = 25/35 (71.43%), Query Frame = 3 
Query:  564 LISGLHTSESRRNVYENYGQTLRLPNSLSARKKLV 668
            LI   H S++ R +YE+YGQT+ L +SL ARK+L 
Sbjct:  108 LILACHISQNMRTLYESYGQTMSLQDSLLARKRLA 142
[Close]
BLAST of SMED30002986 vs. Planmine SMEST
Match: SMESG000059232.1 (SMESG000059232.1)

HSP 1 Score: 54.299 bits (129), Expect = 3.755e-8
Identity = 32/106 (30.19%), Postives = 52/106 (49.06%), Query Frame = 2 
Query:  638 KFFVCQEEIGDSGFRHLQCMLETVRNFTISAVRAQFKIPFAKGHPASERQAIYDYCTKPETKVRDGL*IIYGKQKITLCVSMNFNHNPL---NNAINIQFLKKTSP 946
            KFF  Q+E+ + G  H +  L T  N ++ A+     I ++ G PA+E    +DYC+K  T+V DG+ +       TL  S +     L   N    +++LK+  P
Sbjct:   51 KFFYLQDEMSERGHHHCEVFLHTGNNMSVRALNNALGIQYSWGVPAAEFDREFDYCSKETTRVADGIILSIETPPKTLPQSKDLYRQLLAFDNPDDGMEYLKEKDP 156
The following BLAST results are available for this feature:
BLAST of SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 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 SMED30002986 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000062044.11.340e-11299.56SMESG000062044.1[more]
SMESG000000948.12.064e-4455.63SMESG000000948.1[more]
SMESG000044627.12.772e-1638.10SMESG000044627.1[more]
SMESG000059232.13.755e-830.19SMESG000059232.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002986 ID=SMED30002986|Name=SMED30002986|organism=Schmidtea mediterranea sexual|type=transcript|length=2111bp
GAAATAAAATTTTATTTGCATATTGGTTTATTCGTTCTTCCGAAATCAAA
TGGAATGGTGATGACGATAATATCTCAGTGTTTTTTATTGTTACACCACC
AGAATACGCATCACTAGTACCCTCACTGTCCTTCTATCATTACAGTTAAA
AGGCTCTGAAGCCCCTGACGTACTCAGTGGTGAGCGAGTGATACCATAAA
TAATGATGTACAGTTTAGGTGCTTATGTTATAAGGAAAATATTGATATTT
AATTTGCAATCGATTTACTCAAACGTAAGCACATTTATATCAAACGGGCT
TAGATCACATGAAGCCCATATTCCAAGACAAACAAAAACTATTACCGCAA
TGTCAAATGGATCGGTGCAAAGTATGCATATTTCTAAACAATTGTCAAAA
GCTTCTACACTCGATGAGACCTCTGCACACCTTGACAAGTGCAGAGCTCT
GGTAGCTCAGCAATTGGCAGACCAAATTAATAAGGACTCTACTTCCTCAG
TGGGAACTTTACCAAATGATAACTACAACAATATTTTTCGAAAAAGATTC
TACCTGTGATCTTTTAATCTCGGGATTGCATACATCAGAGAGCAGGAGGA
ATGTTTACGAAAACTATGGTCAAACGCTGAGATTACCAAATTCTTTGTCT
GCCAGGAAGAAATTGGTGACTCTGGCTTCCGGCATCTGCAATGTATGCTT
GAAACTGTCCGAAACTTTACAATCTCGGCTGTACGTGCACAATTTAAGAT
ACCCTTCGCTAAAGGGCATCCCGCTTCGGAGAGACAGGCCATCTACGACT
ATTGCACAAAGCCGGAGACAAAGGTCCGCGATGGCCTATAGATTATTTAT
GGAAAACAGAAAATAACACTTTGTGTTTCTATGAATTTTAATCATAATCC
ACTAAATAACGCTATCAACATTCAATTCCTAAAAAAAACTAGCCCCATTG
GGAGTTCTCAAATCAAACAGACGATTCAGTGAAATATATTCCTAAGCCTT
TCAAGCACGACATTGTCAAAAGTCATGGTCTACACAAGTGACACTGCTAC
AGTTAAGTTTTTGTTGAAAGAGAAAGGATTTCTAAAAGGCAAAGGGAGGT
CTACTAAATCTAAAGCGAAAAAACAAATCGACATTAAATGTGCTACTAAC
ATTTCTATCGGTTCAAGTTCCACTGTGAATGATGTCAGCAATGACGATGA
ATTTATCCTAAATATACCGCTACATTTATTAACTTCAGAGAAAATTATTA
ATAATGAAAATCAAACGAAAACTAAACCTGTTTATAAAATAATCAGTAAT
ACAAAGACAAAATCAAAACCCAAAATTGAAAATTCTTTAAGAAAACCTAT
CAAAAGTCCAATTAAAAAATCACCACGTGCAATGGAAACTTATAAACCAA
AAGTCTCTCCAATAGCTCTACAAAATCCTTTAAAATCTGACAGTAAAGAA
GTCTGTGAAAGCACCGACGACGACGATGAATTTTCTATTAGACTATCACC
AGAACAAATAAAATCTTTCTATAATAATTTTGACAATAATTCAGAGAAAC
TTGTAGAAAAGCCCACAGACAGTAAGCCAATTTCAACAAATAACATCAAA
ACCAATTGGCATTTAGCAGACAGCACTGCAAGTAACGATAGCGACGATGA
TGAGGAATTTACGATAACCATTCCAACTTGTGCATGGAATAAAACGGAAA
AATTATTTTCATAATAAAAAGTAGTCAAATTCATTACAGACAAAAGAGAA
TTCTAAAAACGTTCTTTTTCCCATTTTTTAAAAAAAAATTTTAGAGTCAA
TATTTCAAATGTATTTTTTTAAAGTTTATAAATGTTTTATTACAAAAACT
CATTTGAACTTAAATCGATATTTATAGTAATAAAATTTGAAAAAATCGAT
TTGCTATTAAAAAAGAAAAGATTTTTATTTCTTGGAAACACGTTTTAAAA
ATTTTACGGAACGGAATTCCATTGGATTACGTAATTGTTTGGAAATTATG
TGCCAATCAAATCACGGGGAAATCAAAACTATTATTGTTTTATTTTGTAA
CTTTTAATGTTTTTATAATATTAAAAAATTCAAGTAAAAACTATATTTTA
TTAATTTGTTT
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protein sequence of SMED30002986-orf-1

>SMED30002986-orf-1 ID=SMED30002986-orf-1|Name=SMED30002986-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MMYSLGAYVIRKILIFNLQSIYSNVSTFISNGLRSHEAHIPRQTKTITAM
SNGSVQSMHISKQLSKASTLDETSAHLDKCRALVAQQLADQINKDSTSSV
GTLPNDNYNNIFRKRFYL*
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protein sequence of SMED30002986-orf-2

>SMED30002986-orf-2 ID=SMED30002986-orf-2|Name=SMED30002986-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=230bp
MVYTSDTATVKFLLKEKGFLKGKGRSTKSKAKKQIDIKCATNISIGSSST
VNDVSNDDEFILNIPLHLLTSEKIINNENQTKTKPVYKIISNTKTKSKPK
IENSLRKPIKSPIKKSPRAMETYKPKVSPIALQNPLKSDSKEVCESTDDD
DEFSIRLSPEQIKSFYNNFDNNSEKLVEKPTDSKPISTNNIKTNWHLADS
TASNDSDDDEEFTITIPTCAWNKTEKLFS*
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