SMED30033333

Overview
NameSMED30033333
Smed IDSMED30033333
Length (bp)1480
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 SMED30033333 (SMED30033333) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033333 (SMED30033333) 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.
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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
SMED30033333 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008155:6860..8383 -7250
v31.028942:1201..3080 -7100
v31.000709:29215..30743 +5802
v31.000189:152083..153518 +5129
v31.000047:251412..252934 +4904
Homology
BLAST of SMED30033333 vs. Planmine SMEST
Match: SMESG000059844.1 (SMESG000059844.1)

HSP 1 Score: 224.557 bits (571), Expect = 3.537e-68
Identity = 112/189 (59.26%), Postives = 137/189 (72.49%), Query Frame = 1
Query:  670 GTIRSNWTDDSRSTLTIPSRFAGRYSQALWDRGYSLSTYGSQEWPFRNRD-QDKDV*MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARINADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPV---------QPDTLDILTDRASEEHAYSRRPLRREANDRTYRKQI 1206
            G   ++W ++ ++TLTIPS+FAGRY QALWD  YSLST+G+ EWP+RN++  D+D+ + SLAIKR+P RNPAREI HE E  LQ F  LERKY WKA+LQ RRL +IN DI+ GRIPSSDG+L +Y V FNP+DPA L  + PV         QPD L+ LTDR  EEHAYSRRPL REA  R Y  +I
Sbjct:   43 GNPSTHWMENDQNTLTIPSKFAGRYRQALWDPRYSLSTHGTSEWPYRNKNRHDEDMELLSLAIKREPGRNPAREIRHEAEVALQQFVHLERKYHWKASLQLRRLVKINKDIAGGRIPSSDGYLLEYNVTFNPEDPAFLELNTPVHLALPKRLLQPDILEALTDRTYEEHAYSRRPLNREAPPRNYGHKI 231          
BLAST of SMED30033333 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 221.476 bits (563), Expect = 4.671e-68
Identity = 115/190 (60.53%), Postives = 137/190 (72.11%), Query Frame = 1
Query:  667 SGTIRSNWTDDSRSTLTIPSRFAGRYSQALWDRGYSLSTYGSQEWPFRNR-DQDKDV*MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARINADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPV---------QPDTLDILTDRASEEHAYSRRPLRREANDRTYRKQI 1206
            SG   + W DD R+TL IPS+FAGRY QALWD  YSLSTYG+ EWP R+R   D+DV +PSLAIKR+P RN AR+I HE E  LQ F+ LERKYRWKA+LQR+RL RIN DI+SGRI SSDG+L DY + F+P+DPALL   APV         Q D L+ L DR SEEHAYS+RPL+RE   R +  +I
Sbjct:   52 SGNSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKFGHRI 241          
BLAST of SMED30033333 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 219.935 bits (559), Expect = 1.936e-67
Identity = 115/194 (59.28%), Postives = 137/194 (70.62%), Query Frame = 1
Query:  655 YLLASGTIRSNWTDDSRSTLTIPSRFAGRYSQALWDRGYSLSTYGSQEWPFRNR-DQDKDV*MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARINADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPV---------QPDTLDILTDRASEEHAYSRRPLRREANDRTYRKQI 1206
            Y    G   + W DD R+TL IPS+FAGRY QALWD  YSLSTYG+ EWP R+R   D+DV +PSLAIKR+P RN AR+I HE E  LQ F+ LERKYRWKA+LQR+RL RIN DI+SGRI SSDG+L DY + F+P+DPALL   APV         Q D L+ L DR SEEHAYS+RPL+RE   R +  +I
Sbjct:   50 YPSVIGNSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKFGHRI 243          
BLAST of SMED30033333 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1)

HSP 1 Score: 203.371 bits (516), Expect = 1.104e-57
Identity = 103/173 (59.54%), Postives = 125/173 (72.25%), Query Frame = 1
Query:  688 WTDDSRSTLTIPSRFAGRYSQALWDRGYSLSTYGSQEWPFR-NRDQDKDV*MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARINADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPV---------QPDTLDILTDRASEEHAYSRRPLRRE 1176
            W D   +TLT+PSRFAGRY QALWD+GY++ST+G+ EWP R + + D+D  +PSL IKR+P RNPAREI  E E +L  +E+LERKYR+ AN +RRRLARIN DI++G IPSSDGHL  Y V  +P DPALL  DAPV         QPD  DIL DR +EEH YSRR L R+
Sbjct:   93 WRDMESTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDGHLPSYRVAHDPSDPALLELDAPVHLVFPKLLLQPDIKDILEDRVTEEHVYSRRRLSRK 265          
BLAST of SMED30033333 vs. Planmine SMEST
Match: SMESG000044253.1 (SMESG000044253.1)

HSP 1 Score: 200.675 bits (509), Expect = 1.659e-56
Identity = 112/168 (66.67%), Postives = 121/168 (72.02%), Query Frame = 1
Query:  724 SRFAGRYSQALWDRGYSLSTYGSQEWPFRNRDQDKDV*MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARINADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPV---------QPDTLDILTDRASEEHAYSRRPLRREANDRTYRK 1200
            S +  RY QALWD  Y LSTYGSQEWP RN++QDK + +PSLAIKR+P RNPA E  HE EFMLQ FE LERKYRWKANLQR+RLARI A ISS RI SSDGHL DYGV F PD+PALLS  APV         QPD LDIL DR SEEHAY+RR      ND  Y K
Sbjct:   51 SGYIRRYRQALWDSRYLLSTYGSQEWPNRNQEQDKHIEIPSLAIKREPGRNPAWETRHEAEFMLQQFEHLERKYRWKANLQRQRLARITASISSSRILSSDGHLPDYGVAFKPDEPALLSIGAPVHLVVPKQLIQPDILDILADRNSEEHAYARR------NDYNYNK 212          

HSP 2 Score: 49.2914 bits (116), Expect = 5.838e-6
Identity = 26/48 (54.17%), Postives = 33/48 (68.75%), Query Frame = 2
Query:  425 ITFNMSNLNTKKMKR-DINYIEIRRLEKVDQNFGQEDHT*GSG*ISNF 565
            + FNMSN   KK+K+ DINY EI  +EKV Q++ QEDH  GSG I  +
Sbjct:   10 LYFNMSNQIPKKLKKKDINYHEISHVEKVSQSYAQEDHAQGSGYIRRY 57          
The following BLAST results are available for this feature:
BLAST of SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 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 SMED30033333 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000059844.13.537e-6859.26SMESG000059844.1[more]
SMESG000010307.14.671e-6860.53SMESG000010307.1[more]
SMESG000010307.11.936e-6759.28SMESG000010307.1[more]
SMESG000008335.11.104e-5759.54SMESG000008335.1[more]
SMESG000044253.11.659e-5666.67SMESG000044253.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033333 ID=SMED30033333|Name=SMED30033333|organism=Schmidtea mediterranea sexual|type=transcript|length=1480bp
TCCATAACTACCGATAGTTTCGTAGGAAGTAGCGAATCAGTTATGAATTA
ACTAACCTCATCATGTCGACAATATCAATATAACCAATTCCAAAGTCCAT
TCCAAAGTGGACGATCTCAGCGACCGAATATACACACCAGTGACGTAACT
AGTGGAATTCTATAACTGTTTCCAAATCAGACAGACAAATGAGTCATAAA
CGTAAATCCAAAAAAGTAATCAAGCGATGGCTTGCAGATTACTCATGTAC
ACCGGATAGGCAGGTAAAATTATCTAAAATTGTCAGAAACAGCCACTGCA
ATAAATAAATTAATTAACTCTAATAAACATACCGCACATACAACTTCTAG
AGCGACGACAAACCATACGCAGTCAGCCTCTCGTCAATTAATATAAATAT
GCGTGGAATATACATAACAGCATCATTACATTCAACATGTCAAATTTGAA
CACGAAAAAGATGAAGAGGGATATCAACTACATTGAGATCCGCCGATTGG
AGAAGGTCGACCAGAACTTTGGCCAAGAAGACCACACATAAGGTAGTGGA
TAGATCAGTAACTTTATTCTTTAAATATGACCATTAATAATTCCATTAAA
ACTGATTCATCCTAAAACTAACATAAGATTTATCTACGTAATATTTTATC
CGTATATCTATTAGCATCTGGCACCATTCGAAGCAATTGGACGGATGATT
CACGCAGTACTCTGACGATCCCCAGCAGATTCGCAGGAAGATACAGTCAA
GCGCTGTGGGATCGTGGATATTCGCTATCTACGTACGGAAGCCAGGAATG
GCCCTTCCGAAACCGGGATCAAGATAAGGATGTCTAGATGCCCAGCCTCG
CCATAAAGAGGAAGCCCGATCGGAATCCGGCTCGGGAGATTCACCATGAA
GTAGAATTCATGTTACAACCGTTCGAACGCCTTGAAAGAAAATATCGATG
GAAGGCGAACCTCCAGCGCCGACGATTGGCGAGAATCAATGCTGATATCT
CCAGCGGTCGTATTCCTAGTTCTGATGGCCATCTTGCTGATTATGGAGTA
GGTTTTAATCCGGACGACCCAGCTCTCCTAAGCACAGACGCACCAGTACA
GCCTGACACCCTAGATATTCTAACGGACCGAGCAAGTGAGGAGCATGCTT
ATTCACGACGTCCTCTGAGGCGCGAAGCTAATGATAGGACCTACAGAAAA
CAAATCCCGAAATGAATGCCTATTGAAATGTACCGGTAATGCTGAAAATA
AATGTTTTGTTGTTAGTTTAAATTTTACCGATCGAAAAATTCCACTGAAA
ATGTTAGAAATTGGATAATGTTATAGGTGAAAATAAATAAATAAATAAAA
TTTTAGATTAACAGCTAATTAAAATTTAGATAAGGTTGAAAATTAGATTT
TTAAATAAGTAAAAGAAATTCTAACTCAACCGGTAAATTAATAGTTAATA
AAAACAAGAATATATTTAGGTAAAAGCTAG
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protein sequence of SMED30033333-orf-1

>SMED30033333-orf-1 ID=SMED30033333-orf-1|Name=SMED30033333-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=126bp
MPSLAIKRKPDRNPAREIHHEVEFMLQPFERLERKYRWKANLQRRRLARI
NADISSGRIPSSDGHLADYGVGFNPDDPALLSTDAPVQPDTLDILTDRAS
EEHAYSRRPLRREANDRTYRKQIPK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000070intestinal phagocyte