SMED30035944

Overview
NameSMED30035944
Smed IDSMED30035944
Length (bp)837
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30035944 (SMED30035944) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035944 (SMED30035944) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30035944 (SMED30035944) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035944 (SMED30035944) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30035944

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035944 SmedASXL_066122SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30035944 dd_Smed_v4_53733_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035944 dd_Smed_v4_53733_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035944 dd_Smed_v4_53733_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
SMED30035944 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012433:20365..21186 -3049
v31.003648:33699..34555 -2956
v31.020152:6961..7761 -2938
v31.022288:5506..6362 +2920
v31.000321:109805..110531 -2711
Homology
[Close]
BLAST of SMED30035944 vs. TrEMBL
Match: J9LPK8 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 59.3066 bits (142), Expect = 9.720e-9
Identity = 37/115 (32.17%), Postives = 66/115 (57.39%), Query Frame = -1 
Query:  400 LEQYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 744
            +E +L   NN++  ++R+++LFLDN + HP+LN SN++L +L  NTTS  Q +    +   K   +    +++   +++  SV+ L  KI++L  I +L  +   I P T+ KC 
Sbjct:  252 MEDWLHTFNNKLKKQNRRVILFLDNATCHPHLNLSNVRLAWLPANTTSLTQPMDQGIIYSIKVNYRKMVLQSLLASMDSIKSVNELSNKINVLDAIYWLNKSVNLIKPDTVKKCF 366

HSP 2 Score: 29.261 bits (64), Expect = 9.720e-9
Identity = 17/31 (54.84%), Postives = 18/31 (58.06%), Query Frame = -3 
Query:  755 VIGKAAQPRCFKN----*M*II*MLNKKTWM 835
            VIGKA +PRCFKN       II   N K WM
Sbjct:  217 VIGKAQKPRCFKNVDPTKFPIIWRANNKAWM 247
[Close]
BLAST of SMED30035944 vs. TrEMBL
Match: J9LFH9 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 57.3806 bits (137), Expect = 1.740e-8
Identity = 40/115 (34.78%), Postives = 63/115 (54.78%), Query Frame = -1 
Query:  400 LEQYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 744
            +E +L   NN+++ E+RKI+LFLDN S HP L  SN++L +   NTTS  Q +    +   K   +    +++   I+  NS S +  KI++L  IQ+L  A + +   TI  C 
Sbjct:  231 MENWLIQFNNRLIRENRKIILFLDNASSHPKLILSNLKLAWFPPNTTSLTQPMDQGIIYCVKIYDRRFLMQSLIANIDQINSTSEISKKITVLDAIQWLDGAVKLLKRETIKACF 345

HSP 2 Score: 30.4166 bits (67), Expect = 1.740e-8
Identity = 16/31 (51.61%), Postives = 20/31 (64.52%), Query Frame = -3 
Query:  755 VIGKAAQPRCFKN----*M*II*MLNKKTWM 835
            VIGK+ +PRCFKN     + +I   NKK WM
Sbjct:  196 VIGKSVKPRCFKNLDVSKLPVIWCANKKAWM 226
[Close]
BLAST of SMED30035944 vs. TrEMBL
Match: A0A3Q2XIU4 (HTH CENPB-type domain-containing protein OS=Hippocampus comes OX=109280 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 2.196e-7
Identity = 36/113 (31.86%), Postives = 65/113 (57.52%), Query Frame = -1 
Query:  400 QYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 738
            ++L  LNN+MV ++RKILLF+DN   H     SNI++ +   NTTS +  +    ++  K   +    +++ + ++ CN VS L  KI++   +++++ A  ++  STI KC 
Sbjct:  273 KWLHQLNNKMVIQNRKILLFMDNCGAHVPATLSNIKIIFFPPNTTSHLHPMDAGVIQNVKLQYRKSMLKSILLNMDECNKVSDLVKKITVRDALEWIEAAWMKLESSTIGKCF 385

HSP 2 Score: 28.4906 bits (62), Expect = 2.196e-7
Identity = 15/31 (48.39%), Postives = 18/31 (58.06%), Query Frame = -3 
Query:  755 VIGKAAQPRCF----KN*M*II*MLNKKTWM 835
            VIGK+A PRCF    K  M +    N+K WM
Sbjct:  236 VIGKSANPRCFTKDYKQQMRVTYEANRKAWM 266
[Close]
BLAST of SMED30035944 vs. TrEMBL
Match: A0A2B4R4Z9 (Tigger transposable element-derived protein 6 OS=Stylophora pistillata OX=50429 GN=TIGD6 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 4.787e-7
Identity = 39/113 (34.51%), Postives = 63/113 (55.75%), Query Frame = -1 
Query:  400 QYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 738
            ++L I+NNQM   +RKI+L +DN + HP +  SNI+L +L  NTT+K+Q      ++  K   +    R +    +   S S+L  K++I   I +L+ A   +P +TI KC 
Sbjct:  248 EWLDIVNNQMRNSNRKIILIVDNCAAHPQVERSNIKLVFLPPNTTAKLQPCDAGIIQAVKLQYRKKLLRKIAFAFDEVESASSLAKKVTIFDAIMWLRHAWSLLPETTIQKCF 360

HSP 2 Score: 26.5646 bits (57), Expect = 4.787e-7
Identity = 15/31 (48.39%), Postives = 18/31 (58.06%), Query Frame = -3 
Query:  755 VIGKAAQPRCFK----N*M*II*MLNKKTWM 835
            VIGK+ +PRCFK      + II   N K WM
Sbjct:  211 VIGKSKKPRCFKGKDIGALNIIYRHNSKAWM 241
[Close]
BLAST of SMED30035944 vs. TrEMBL
Match: A0A3Q2XZU1 (HTH CENPB-type domain-containing protein OS=Hippocampus comes OX=109280 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 4.875e-7
Identity = 36/113 (31.86%), Postives = 65/113 (57.52%), Query Frame = -1 
Query:  400 QYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 738
            ++L  LNN+MV ++RKILLF+DN   H     SN+++ +   NTTS +Q +    ++  K   +    +++ + ++ CN  S L  KI++   I++++ A  ++  STI KC 
Sbjct:  246 KWLHQLNNKMVIQNRKILLFMDNCGAHVPATLSNMKIIFFPPNTTSHLQPMDAGVIQNVKLQYRKSMLKSILLNMDECNKASDLVKKITVRDAIEWIEAAWMKLESSTISKCF 358

HSP 2 Score: 28.4906 bits (62), Expect = 4.875e-7
Identity = 15/31 (48.39%), Postives = 18/31 (58.06%), Query Frame = -3 
Query:  755 VIGKAAQPRCF----KN*M*II*MLNKKTWM 835
            VIGK+A PRCF    K  M +    N+K WM
Sbjct:  209 VIGKSANPRCFTKDYKQQMRVTYEANRKAWM 239
[Close]
BLAST of SMED30035944 vs. Planmine SMEST
Match: SMESG000070537.1 (SMESG000070537.1)

HSP 1 Score: 102.834 bits (255), Expect = 3.641e-27
Identity = 62/118 (52.54%), Postives = 70/118 (59.32%), Query Frame = -3 
Query:  239 TIDAKIIENIKVNNQKLMLQNYVHGN*KLQXXXXXXXXXXXXXXXXXFKSCASTNSTIYDNKMFINCGFGFKDECEESLLEDEKQPNSQIIEVLNLIQCAFGSTIYNTADYVGVDYNI 592
             +DA II NIKVN +KLMLQN                +    +     K      S     K F+NCGFG K+EC+ESL EDEKQPNSQIIEV NL Q AFGS IY+ ADYVGVDYNI
Sbjct:    9 PLDAGIIANIKVNYRKLMLQNLHMEIENCNSVSGLTMKILILDAIQFLKVACQQISPYTIIKCFLNCGFGVKNECKESLSEDEKQPNSQIIEVQNLNQSAFGSKIYSAADYVGVDYNI 126

HSP 2 Score: 63.1586 bits (152), Expect = 3.225e-12
Identity = 32/45 (71.11%), Postives = 34/45 (75.56%), Query Frame = -1 
Query:  400 RTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 534
            + + MEIENCNSVS L MKI IL  IQFLKVA QQI P TIIKC 
Sbjct:   28 QNLHMEIENCNSVSGLTMKILILDAIQFLKVACQQISPYTIIKCF 72
[Close]
BLAST of SMED30035944 vs. Planmine SMEST
Match: SMESG000070576.1 (SMESG000070576.1)

HSP 1 Score: 103.605 bits (257), Expect = 1.770e-26
Identity = 62/118 (52.54%), Postives = 70/118 (59.32%), Query Frame = -3 
Query:  239 TIDAKIIENIKVNNQKLMLQNYVHGN*KLQXXXXXXXXXXXXXXXXXFKSCASTNSTIYDNKMFINCGFGFKDECEESLLEDEKQPNSQIIEVLNLIQCAFGSTIYNTADYVGVDYNI 592
             +DA II NIKVN +KLMLQN                +    +     K      S     K F+NCGFG K+EC+ESL EDEKQPNSQIIEV NL Q AFGS IY+ ADYVGVDYNI
Sbjct:   87 PLDAGIIANIKVNYRKLMLQNLHMEIENCNRVSGLTMKILILDAIKFLKVACQQISPYTIIKCFLNCGFGVKNECKESLSEDEKQPNSQIIEVQNLNQSAFGSKIYSAADYVGVDYNI 204

HSP 2 Score: 58.9214 bits (141), Expect = 3.263e-10
Identity = 30/45 (66.67%), Postives = 33/45 (73.33%), Query Frame = -1 
Query:  400 RTMFMEIENCNSVSALRMKISILIVIQFLKVARQQIPPSTIIKCL 534
            + + MEIENCN VS L MKI IL  I+FLKVA QQI P TIIKC 
Sbjct:  106 QNLHMEIENCNRVSGLTMKILILDAIKFLKVACQQISPYTIIKCF 150
[Close]
BLAST of SMED30035944 vs. Planmine SMEST
Match: SMESG000002710.1 (SMESG000002710.1)

HSP 1 Score: 90.5077 bits (223), Expect = 6.485e-23
Identity = 58/96 (60.42%), Postives = 70/96 (72.92%), Query Frame = -1 
Query:  457 LEQYLKILNNQMVAEDRKILLFLDNVSPHPNLNFSNIQLKYLHHNXXXXXXXXXXXXXXXXXXXXXS*CCRTMFMEIENCNSVSALRMKISILIVI 744
             EQYL+ LNNQM+AEDRKILLFLDN S HPNL+FS IQLKYL  NTTSK+Q L +  +   K   +    + +FMEI+NCNSVSAL +K+S L  I
Sbjct:    6 FEQYLRNLNNQMIAEDRKILLFLDNDSSHPNLSFSYIQLKYLSPNTTSKLQPLDVGIIANIKVNYRKLMLQNLFMEIDNCNSVSALMIKLSFLDAI 101
The following BLAST results are available for this feature:
BLAST of SMED30035944 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
J9LPK89.720e-932.17Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
J9LFH91.740e-834.78Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
A0A3Q2XIU42.196e-731.86HTH CENPB-type domain-containing protein OS=Hippoc... [more]
A0A2B4R4Z94.787e-734.51Tigger transposable element-derived protein 6 OS=S... [more]
A0A3Q2XZU14.875e-731.86HTH CENPB-type domain-containing protein OS=Hippoc... [more]
back to top
BLAST of SMED30035944 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30035944 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000070537.13.641e-2752.54SMESG000070537.1[more]
SMESG000070576.11.770e-2652.54SMESG000070576.1[more]
SMESG000002710.16.485e-2360.42SMESG000002710.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035944 ID=SMED30035944|Name=SMED30035944|organism=Schmidtea mediterranea sexual|type=transcript|length=837bp
TGAATAATTCATATTCCTTGCAAATAGAAAACATCCTACACATCCTACAC
TTAAAATCGTCGTTCCAAGACTGACGTCCATAAGTTCCCAGTGTTTTAAA
ATCATTCAAAACATCTATATTTCTTATTTTTTCTTCCTCATTTGATTTAT
CTTCACTCACGACACCCACATTTTCAACCAATAACAGATTGTTGTTTGCA
ATTATATTATCCAAATCAATTGAATTAGTTTCTGTAGCGATATTATAATC
TACTCCAACATAATCTGCTGTATTGTAAATTGTTGATCCGAATGCACACT
GAATCAAATTTAGAACTTCTATAATTTGACTATTAGGCTGTTTCTCATCC
TCTAATAGGGATTCTTCGCATTCATCCTTAAATCCAAATCCACAATTTAT
AAACATTTTATTATCGTAGATGGTGGAATTTGTTGACGCGCAACTTTTAA
AAATTGAATTACAATTAGAATTGAAATTTTCATTCTAAGAGCAGATACAC
TATTGCAATTTTCAATTTCCATGAACATAGTTCTGCAGCATTAGCTTTTG
ATTGTTGACTTTTATATTTTCAATTATTTTAGCGTCAATAGTTGTATTTT
AGAGGTTGTGTTATGATGCAAATATTTCAGCTGTATATTTGAAAAGTTAA
GATTCGGATGTGGTGATACATTATCCAAAAATAAAAGGATTTTCCGATCT
TCGGCTACCATTTGATTGTTCAATATTTTTAAATATTGTTCAAGTCATTT
CCATCATCCATGTCTTTTTATTCAACATCTAGATTATTCACATTTAATTT
TTAAAACAACGAGGTTGAGCTGCTTTTCCAATCACGA
back to top

protein sequence of SMED30035944-orf-1

>SMED30035944-orf-1 ID=SMED30035944-orf-1|Name=SMED30035944-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MFINCGFGFKDECEESLLEDEKQPNSQIIEVLNLIQCAFGSTIYNTADYV
GVDYNIATETNSIDLDNIIANNNLLLVENVGVVSEDKSNEEEKIRNIDVL
NDFKTLGTYGRQSWNDDFKCRMCRMFSICKEYELF
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR004875DDE_SF_endonuclease_dom
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding