SMED30030047

Overview
NameSMED30030047
Smed IDSMED30030047
Length (bp)2569
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




SMED30030047

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
testis primordiumSMED30030047SMESG000024879.1 Contig2495_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030047 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011661:8157..10725 +12791
Homology
BLAST of SMED30030047 vs. Planmine SMEST
Match: SMESG000024879.1 (SMESG000024879.1)

HSP 1 Score: 562.377 bits (1448), Expect = 0.000e+0
Identity = 287/288 (99.65%), Postives = 288/288 (100.00%), Query Frame = 3
Query:  867 MKTISADEISYRLSSEMSRTKASFESNRIPQNLDNSQIDTYNTVYNPNSANILKSEKAEFFAKGNSASDLIYEPFSNYVRNQRFNSNQKNEIQNSTVLFKGINYNLVSVIADQTYAYILCKNSRFRLTESNEKDLKSFKLDETXXXXXXXXXXXXRFETLKGILKTEILETFTQSFYGVALNQIPTGQLCVVQCMVEGRITERETVLNQILIHHTICGKIINKEYKLEVHGHGDLNFVMHLHGNERHIRKCSDQLKKEGLARNFKLIHPQYGRIFEEKILLPYSDARE 1730
            MKTISADEISYRLSSEMSRTKASFESNRIPQNLDNSQIDTYNTVYNPNSANILKSEKAEFFAKGNSASDLIYEPFSNYVRNQRFNSNQKNEIQN+TVLFKGINYNLVSVIADQTYAYILCKNSRFRLTESNEKDLKSFKLDETNQSYNNQSNSSNRFETLKGILKTEILETFTQSFYGVALNQIPTGQLCVVQCMVEGRITERETVLNQILIHHTICGKIINKEYKLEVHGHGDLNFVMHLHGNERHIRKCSDQLKKEGLARNFKLIHPQYGRIFEEKILLPYSDARE
Sbjct:    1 MKTISADEISYRLSSEMSRTKASFESNRIPQNLDNSQIDTYNTVYNPNSANILKSEKAEFFAKGNSASDLIYEPFSNYVRNQRFNSNQKNEIQNTTVLFKGINYNLVSVIADQTYAYILCKNSRFRLTESNEKDLKSFKLDETNQSYNNQSNSSNRFETLKGILKTEILETFTQSFYGVALNQIPTGQLCVVQCMVEGRITERETVLNQILIHHTICGKIINKEYKLEVHGHGDLNFVMHLHGNERHIRKCSDQLKKEGLARNFKLIHPQYGRIFEEKILLPYSDARE 288          
BLAST of SMED30030047 vs. Planmine SMEST
Match: SMESG000024859.1 (SMESG000024859.1)

HSP 1 Score: 370.548 bits (950), Expect = 2.242e-118
Identity = 228/553 (41.23%), Postives = 343/553 (62.03%), Query Frame = 3
Query:   78 VDKANFTSNLSLNSHFMFTNCQNSTKLVKSALKISSQEKLTSYIIDKVITCRNV-----NMILSENPTENISAIDSRPKNYCNPHXXXXXXXXXXKIQKNFRKNKIEKLGLYPIYSNNITTYFSGVIYLPEGPLIISHYITLHKLRLDSLSEKEFQNWCFTIGHMKTAFKYFQFQEVYQDLKLNHFKESYTINKILSKQNVHLRISDIFGTSGSNL-RALVVVGCRHHIVQSIIDFYCFETQGKVSFIIKNIEDYNHLRRISNKKSLDTMKTISADEISYRL----SSEMSRT--KASFESNRIPQNLDNSQIDTYNTVYNPNSANILKSEKAEFFAKGNSASDLIYEPFSNYVRNQRFNSNQKNEIQNSTVLFKGINYNLVSVIADQTYAYILCKNSRFRLTESNEKDLKSFKL-DETXXXXXXXXXXXXRFETLKGILKTEILETFTQSFYGVALNQIPTGQLCVVQCMVEGRITERETVLNQILIHHTICGKIINKEYKLEVHGHGDLNFVMHLHGNERHIRKCSDQLKKEGLARNFKLIHPQYGRIFEE 1697
            +DK NFTSNLSL S+    N   S   +KSALK +S EK+ S+++D+V +  NV     NM     P ++I  + +  K                +I+ N     IEKLGL+ I ++  T  F G+ Y PE  +I+SHYITL++L++D+L E++F+ WC +I H  T+ K+ Q ++VY+ +K NHF+ES+ INKI+SK+NV L ISD FG     L RALVVVG R   V++++D +C+  + KVSFIIK+ +DY ++ +         +K+   D+I+ +     + ++ R   K+S  +   P N+    I+  N   +PNS N  ++       K NS     +EPF NY+R ++ N+N  +   NS+V+  G  YNLVS+I+D+T+AYILCKNS   L+ S+E DL S  + D       NQSNS+N  ++L  I+K EI E+  + +YGV+L+Q+P G+  VVQCM++  ++E++++L++IL  HT+CGK+++KEY LE     DLN ++HLHGNER+I  CS++LK EGL R+FKLIHPQ G+ FEE
Sbjct:    2 IDKGNFTSNLSLESNIFIKNISTSLVPLKSALKSTSNEKIISFVLDQVTSNGNVAQRPCNMSEKTPPNKDIPEVIADKK----------------EIKFNQCIYPIEKLGLHEISAS--TPCFRGIAYFPECYIILSHYITLNRLKIDTLCERDFKAWCSSISHYATSKKFSQLKDVYEKMKSNHFQESFIINKIISKKNVDLAISDCFGDDEDKLFRALVVVGKRSCTVRNVLDCFCYNVKEKVSFIIKSEDDYRNIMKSYESNGKVELKSSKLDDINIKGVLKNTGKLLRPIKKSSLPTRYTPLNI----IEVLNI--HPNSVN--ETNLNGTPRKSNSE----FEPFMNYMRYEKCNTNFSSVCYNSSVISNGCTYNLVSIISDKTHAYILCKNSHSSLSYSSENDLHSIIMEDSLEDLNQNQSNSTNSLKSLLKIMKIEIYESCVEKYYGVSLSQVPCGEFYVVQCMIDSEMSEKKSLLDEILFRHTVCGKVVSKEYSLESQNRYDLNLIVHLHGNERNIVNCSNELKIEGLTRSFKLIHPQIGKTFEE 524          
BLAST of SMED30030047 vs. Planmine SMEST
Match: SMESG000024878.1 (SMESG000024878.1)

HSP 1 Score: 268.085 bits (684), Expect = 8.131e-85
Identity = 143/143 (100.00%), Postives = 143/143 (100.00%), Query Frame = 3
Query:   30 MGLTIMKFIHKSKTKTVDKANFTSNLSLNSHFMFTNCQNSTKLVKSALKISSQEKLTSYIIDKVITCRNVNMILSENPTENISAIDSRPKNYCNPHXXXXXXXXXXKIQKNFRKNKIEKLGLYPIYSNNITTYFSGVIYLPEG 458
            MGLTIMKFIHKSKTKTVDKANFTSNLSLNSHFMFTNCQNSTKLVKSALKISSQEKLTSYIIDKVITCRNVNMILSENPTENISAIDSRPKNYCNPHSSSLSLQNSSKIQKNFRKNKIEKLGLYPIYSNNITTYFSGVIYLPEG
Sbjct:    1 MGLTIMKFIHKSKTKTVDKANFTSNLSLNSHFMFTNCQNSTKLVKSALKISSQEKLTSYIIDKVITCRNVNMILSENPTENISAIDSRPKNYCNPHSSSLSLQNSSKIQKNFRKNKIEKLGLYPIYSNNITTYFSGVIYLPEG 143          
BLAST of SMED30030047 vs. Planmine SMEST
Match: SMESG000022282.1 (SMESG000022282.1)

HSP 1 Score: 56.225 bits (134), Expect = 4.393e-8
Identity = 45/152 (29.61%), Postives = 77/152 (50.66%), Query Frame = 3
Query:  384 KLGLYPIYSNNITTYFSGVIYLPEGPLIISHYITLHKLRLDSLSEKEFQNWCFTIGHMKTAFKYFQFQEVYQDLKLNHFKESYTINKILSKQNVHLRISDIFGTSGSN-LRALVVVGCRHHIVQSIIDFYCFE-TQGKVSFIIKNIEDYNHL 833
            K G++  Y N+I+ +F  +I++ E  +    +++ + L L  + + EFQ+WC   G+ KT  +YF F ++     L+ F  S  +N +  K NV   ISD+F   G    RA+      H+++   ++ Y    T+ KV + I    D NHL
Sbjct:   75 KPGIF--YDNDISMWFR-LIFVLEDDITRKQFLSFYGLNLKYMEKDEFQSWCDKNGYPKTK-EYFDFFKL-----LDAFPYSRLLNGLSHKYNVKFHISDLFLYKGKGPFRAITCCARNHNVIDKALNEYENRITKKKVIYTINKHWD-NHL 216          
The following BLAST results are available for this feature:
BLAST of SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 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 SMED30030047 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000024879.10.000e+099.65SMESG000024879.1[more]
SMESG000024859.12.242e-11841.23SMESG000024859.1[more]
SMESG000024878.18.131e-85100.00SMESG000024878.1[more]
SMESG000022282.14.393e-829.61SMESG000022282.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030047 ID=SMED30030047|Name=SMED30030047|organism=Schmidtea mediterranea sexual|type=transcript|length=2569bp
GTAGTAACAATTAAAAATAATAATTATAAATGGGACTGACAATTATGAAA
TTCATCCACAAATCAAAAACCAAAACTGTCGACAAGGCGAATTTCACGTC
AAATTTGTCTCTAAATTCCCATTTTATGTTCACGAATTGTCAGAACTCTA
CAAAACTTGTCAAATCGGCTTTAAAAATCTCCAGTCAAGAAAAGTTGACG
TCGTACATTATTGACAAGGTGATTACGTGCAGAAACGTCAACATGATTCT
GTCAGAAAACCCAACGGAAAACATTTCTGCTATCGACTCTCGGCCGAAAA
ATTACTGTAATCCTCACTCATCAAGTCTTTCGCTTCAGAACTCTTCGAAA
ATTCAAAAGAATTTCCGAAAGAATAAAATTGAAAAGCTAGGATTATATCC
AATTTATTCCAATAACATAACTACTTACTTTAGTGGAGTTATTTATTTAC
CGGAAGGTCCTTTGATTATATCTCATTATATTACCCTTCACAAACTTAGG
TTGGATAGCCTTTCAGAAAAAGAATTTCAAAATTGGTGTTTCACTATCGG
ACATATGAAAACGGCATTTAAATATTTTCAATTTCAAGAAGTGTACCAAG
ATTTGAAATTAAACCATTTCAAGGAATCGTACACCATCAATAAGATACTC
TCCAAGCAAAATGTACACTTAAGGATTTCTGACATTTTTGGGACGAGTGG
GAGCAATCTACGCGCTCTAGTAGTCGTCGGTTGTCGACACCACATAGTTC
AAAGTATAATTGACTTTTATTGTTTCGAAACACAGGGGAAAGTATCTTTT
ATTATAAAAAACATCGAAGACTACAATCATTTGAGACGAATTTCAAATAA
AAAGAGTCTAGACACCATGAAGACGATTTCGGCGGACGAGATCAGTTATA
GGTTATCATCAGAAATGTCTCGCACTAAAGCTTCATTCGAATCGAACCGG
ATTCCACAGAACCTTGATAATTCTCAAATCGACACTTACAACACTGTATA
TAACCCGAATTCCGCTAACATATTAAAATCTGAAAAAGCCGAATTCTTTG
CGAAAGGAAATTCTGCATCCGACCTTATATATGAGCCGTTTTCCAATTAT
GTTAGAAATCAAAGATTTAATTCTAACCAAAAGAATGAAATTCAAAACTC
CACTGTCTTATTTAAAGGGATTAATTATAATCTTGTGTCAGTTATTGCTG
ATCAAACATACGCTTACATCCTTTGCAAAAATTCTAGATTCAGACTCACG
GAAAGTAATGAAAAAGATCTAAAATCATTCAAGCTAGATGAAACAAACCA
ATCTTACAACAATCAGTCTAACTCATCAAACCGTTTTGAAACATTAAAAG
GAATACTGAAAACTGAAATCTTAGAGACCTTCACTCAAAGTTTTTATGGG
GTTGCATTGAACCAGATACCTACTGGGCAATTGTGTGTCGTACAATGCAT
GGTTGAAGGTCGAATCACCGAACGAGAAACAGTGTTGAATCAAATTCTTA
TCCATCACACTATCTGTGGGAAAATAATTAACAAAGAGTATAAGTTAGAG
GTTCATGGACACGGTGATTTAAACTTCGTTATGCATCTGCATGGTAATGA
AAGACATATCCGCAAATGCTCGGATCAACTTAAGAAAGAAGGTTTAGCTC
GAAATTTCAAACTAATTCATCCTCAGTATGGACGAATCTTTGAAGAAAAG
ATTCTTTTACCATATTCTGATGCTAGAGAGTAACATCTAAATTTGCAAAA
TCTATTGAAGTTTCTAACTGGCGTTAACGGGTCCCATGTAGTTATGTTTT
GGGCTTTTGGAAACCGAAATAACTTATTAAATATTCAATTAGAATATTAT
TGCCAGCTTCTGATCTGAATTTTTATTGTCTTGCACTTGTCTTGCACTTA
TGTTGCACTCATTTGCAATATTCATGGCACATCATAAATAAACAAAATTA
ATTTGTATTTTGTTGACTAAGTATCTTAATAAAACTCAAATTTGAGGTGA
TTACGATTAAAGAGATCCTTGTGGCAAAGAATAATAACTATTATAATGGA
CCCCACTGAAATTGATCCTTGAAACACGATTCTTGAAGAGATACAAATAT
GATGTTGTTAGTGAAATATTCGCCTTGACAATTTTTCAAAATTCTCAAAC
TGTCGAACGACAGTGTGATAAAACAAAAACACAATAATGTACTTTTTTGA
ACATTTCTAAAATCAATATTAGTACTTTTTAAGAGTGCAAAGTGCACCTT
AGAACTGAATGTGTGTTCACTGTACCCTCAAATAACATAAAATAATGCCT
CACTATTGGTAGGTGTCCTTATAATCAATCGACCGTTGATTCTGTTACAG
TTTTCATCCACATTTCCACAGTACCCAGTTAACAGGGCAGAGACTCGAAA
TAGCTGCGACCTCTTCATAAATTTCCGCATATAATTTTGATTTAATTATT
TTCAGTTATTCTTTTTTTTATCGAGTTGGATTTACACACCAGCTGGTATA
AAAGAAATTGTCATTCATTTGAACAAATTACATCACCAAACATGTAACTG
TATGTCCTATAATATAAGC
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protein sequence of SMED30030047-orf-1

>SMED30030047-orf-1 ID=SMED30030047-orf-1|Name=SMED30030047-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=568bp
MGLTIMKFIHKSKTKTVDKANFTSNLSLNSHFMFTNCQNSTKLVKSALKI
SSQEKLTSYIIDKVITCRNVNMILSENPTENISAIDSRPKNYCNPHSSSL
SLQNSSKIQKNFRKNKIEKLGLYPIYSNNITTYFSGVIYLPEGPLIISHY
ITLHKLRLDSLSEKEFQNWCFTIGHMKTAFKYFQFQEVYQDLKLNHFKES
YTINKILSKQNVHLRISDIFGTSGSNLRALVVVGCRHHIVQSIIDFYCFE
TQGKVSFIIKNIEDYNHLRRISNKKSLDTMKTISADEISYRLSSEMSRTK
ASFESNRIPQNLDNSQIDTYNTVYNPNSANILKSEKAEFFAKGNSASDLI
YEPFSNYVRNQRFNSNQKNEIQNSTVLFKGINYNLVSVIADQTYAYILCK
NSRFRLTESNEKDLKSFKLDETNQSYNNQSNSSNRFETLKGILKTEILET
FTQSFYGVALNQIPTGQLCVVQCMVEGRITERETVLNQILIHHTICGKII
NKEYKLEVHGHGDLNFVMHLHGNERHIRKCSDQLKKEGLARNFKLIHPQY
GRIFEEKILLPYSDARE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium