SMED30017214

Overview
NameSMED30017214
Smed IDSMED30017214
Length (bp)3410
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 SMED30017214 (SMED30017214) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017214 (SMED30017214) 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 SMED30017214 (SMED30017214) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017214 (SMED30017214) 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




SMED30017214

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30017214SMESG000068350.1 SmedASXL_000592SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
headSMED30017214SMESG000068350.1 SmedASXL_012846SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30017214SMESG000068350.1 dd_Smed_v4_18752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30017214SMESG000068350.1 dd_Smed_v4_18752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
medial muscle cellSMED30017214 dd_Smed_v4_17528_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30017214SMESG000068350.1 dd_Smed_v6_18752_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30017214 dd_Smed_v6_17528_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30017214SMESG000068350.1 dd_Smed_v4_18752_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30017214 vs. Planmine SMEST
Match: SMESG000068350.1 (SMESG000068350.1)

HSP 1 Score: 600.127 bits (1546), Expect = 0.000e+0
Identity = 328/328 (100.00%), Postives = 328/328 (100.00%), Query Frame = -1
Query: 2289 MFYEIEYKSLNRNDVFLFNENEIWTRWLKYSFNKRKRWEILKCIHYHMNIFEKKVILSVKNVNNSNGVFFGIFNQSNPISLNEHRNFDLMKSDFCRNNTKGFLNIQSLENEIHSKIFIKKPNNIVRRPKLSTRKNHRQIFVNNFKGKXXXXXXXXXXXXXXXXXYIHFSVTVDTMGSCKPRKSKFQKNKLKALNKKSIEYEIKESLSEYLFDKENKIKYGSLKISTEQPQTVTNVKGLITELPSNQLLSEAQSKVEIETQSTNVERNRPYTSKELQILIGEALGQAFIQLFEERPRDPISHLAKILYSLSKEPKYSRNLLDSHLDSVT 3272
            MFYEIEYKSLNRNDVFLFNENEIWTRWLKYSFNKRKRWEILKCIHYHMNIFEKKVILSVKNVNNSNGVFFGIFNQSNPISLNEHRNFDLMKSDFCRNNTKGFLNIQSLENEIHSKIFIKKPNNIVRRPKLSTRKNHRQIFVNNFKGKNDFYYNEDYNNDSDSDSYIHFSVTVDTMGSCKPRKSKFQKNKLKALNKKSIEYEIKESLSEYLFDKENKIKYGSLKISTEQPQTVTNVKGLITELPSNQLLSEAQSKVEIETQSTNVERNRPYTSKELQILIGEALGQAFIQLFEERPRDPISHLAKILYSLSKEPKYSRNLLDSHLDSVT
Sbjct:    1 MFYEIEYKSLNRNDVFLFNENEIWTRWLKYSFNKRKRWEILKCIHYHMNIFEKKVILSVKNVNNSNGVFFGIFNQSNPISLNEHRNFDLMKSDFCRNNTKGFLNIQSLENEIHSKIFIKKPNNIVRRPKLSTRKNHRQIFVNNFKGKNDFYYNEDYNNDSDSDSYIHFSVTVDTMGSCKPRKSKFQKNKLKALNKKSIEYEIKESLSEYLFDKENKIKYGSLKISTEQPQTVTNVKGLITELPSNQLLSEAQSKVEIETQSTNVERNRPYTSKELQILIGEALGQAFIQLFEERPRDPISHLAKILYSLSKEPKYSRNLLDSHLDSVT 328          
BLAST of SMED30017214 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 101.293 bits (251), Expect = 1.230e-24
Identity = 62/107 (57.94%), Postives = 79/107 (73.83%), Query Frame = 3
Query: 1374 SYNSAQPRWPNVDYRYSISTPGDVA*PTQPGLIGDMNLPSIAIKREPGRNPAKEARQKIEFXXXXXXXXXXXXXXXXXXXXMKLENINRDIAT*RIPCSDGYAPSYD 1694
            S  SAQ R    DY YS+STPGD   P +PGLI D+++P IAIKREPGRNPA+E RQK+EF LL L E++R L HRR++ +++L+ INRDIA  RI C+  YAP Y+
Sbjct:   34 STASAQCRHILWDYEYSVSTPGDSTLPARPGLIEDLDIPGIAIKREPGRNPARETRQKVEFYLLLLVEEERRLQHRRRMPQVELDKINRDIAAGRILCTGVYAPDYN 140          
BLAST of SMED30017214 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 90.1225 bits (222), Expect = 4.871e-20
Identity = 59/135 (43.70%), Postives = 84/135 (62.22%), Query Frame = 3
Query: 1374 SYNSAQPRWPNVDYRYSISTPGDVA*PTQPGLIGD-MNLPSIAIKREPGRNPAKEARQKIEFXXXXXXXXXXXXXXXXXXXXMKLENINRDIAT*RIPCSDGYAPSYDTSFELDDPALKTLMVPIPNGLIHPSKL 1775
            S ++A+ R    D  Y +ST GD + P +     + + LPSIAIKREPG NPA+EARQ+ E+  ++++E +R    +  LAR +L  +NRDIA+  IP +DG+ P Y  SFELDDP L  + +  P  L+ P KL
Sbjct:   48 SASAARYRQVLWDNGYLLSTYGDSSWPRRSKYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRL--MQMTAPTKLVLPEKL 180          
BLAST of SMED30017214 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 89.3521 bits (220), Expect = 4.024e-19
Identity = 56/128 (43.75%), Postives = 78/128 (60.94%), Query Frame = 3
Query: 1410 DYRYSISTPGDVA*PTQPGLIGD-MNLPSIAIKREPGRNPAKEARQKIEFXXXXXXXXXXXXXXXXXXXXMKLENINRDIAT*RIPCSDGYAPSYDTSFELDDPALKTLMVPIPNGLIHPSKLKRLEL 1790
            D  Y +ST GD + P +     + + LPS+AIKREPG NPA+EARQ+ E+  ++ +E +R    +  LAR +L  +NRDIA+  IP +DG+ P Y  SFELDDP L  +  P    ++ P KL R  L
Sbjct:  113 DNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTK--MVIPEKLVRSTL 238          
BLAST of SMED30017214 vs. Planmine SMEST
Match: SMESG000056869.1 (SMESG000056869.1)

HSP 1 Score: 86.6557 bits (213), Expect = 6.744e-19
Identity = 52/107 (48.60%), Postives = 71/107 (66.36%), Query Frame = 3
Query: 1476 DMNLPSIAIKREPGRNPAKEARQKIEFXXXXXXXXXXXXXXXXXXXXMKLENINRDIAT*RIPCSDGYAPSYDTSFELDDPALKTLMVP----IPNGLIHPSKLKRL 1784
            ++ LPSIAIKREPGRNPA+E RQ+ E+ +++++E +R    +  LAR +L  INRDIA+  IP +D + P+Y+ SFELDDP L  +  P    IP  LI P    RL
Sbjct:   62 EVELPSIAIKREPGRNPAREVRQQAEYTVMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYEVSFELDDPRLLQMTAPTKLVIPEELIQPVLRNRL 168          
The following BLAST results are available for this feature:
BLAST of SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 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 SMED30017214 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068350.10.000e+0100.00SMESG000068350.1[more]
SMESG000004514.11.230e-2457.94SMESG000004514.1[more]
SMESG000027782.14.871e-2043.70SMESG000027782.1[more]
SMESG000004883.14.024e-1943.75SMESG000004883.1[more]
SMESG000056869.16.744e-1948.60SMESG000056869.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017214 ID=SMED30017214|Name=SMED30017214|organism=Schmidtea mediterranea sexual|type=transcript|length=3410bp
AAAGGACACTAAAATAGAACGATAATGGTAAAAATAATAAGTATATGTAA
TGATCTTAATAACGGATGTAGTATTAAAAACAAAAATCATAAGAATAACG
GCATTTTGACATTGACGGTAATAATACCTATTTTATGATATGATAACAAT
AACAATTTTGATGATAAAATGTTACACATAACAATAGCTCGATAATAATA
ATAGTGTTTAAAATAATAATAATATTGGTAATTATAACCAAAACAAAAAT
AAGAAAATTCGATACCGATAGACGCAAATGACAAATCCAATCATGAACAA
TTAAACCTAGAACTAACTGGTGAGATCAGGGATTCAACCATAGTAATATT
ATAAATGGCTTGACCAAGATACCAAAACCGATCTAATAAAAAACGACCAA
AGTCCTTTTATTAAAAATATCACGATGATTCCGATACGTTCATATTGATG
CAGTTGTAGTTGTAGTTCCCGAGATGATATTACCAACATAAGAAACCTCC
ATGGTAGAACATTCCTTCCTTGAATTACGAATATCTGGAATACTATGACT
TCCTGGTTACCGAGTACCGTTATAAACCTAATTACTAATAAAAATTACCT
GAAAAATTATCTCCCTCACTGGTCAAATATCAATACCATGTATTTTCCAA
CGACTTCATCAATCAATTATTTGACTGTACACAAGACGCGATTAACCTCG
TAAATAAATAATGACCAATTGACAATGATAAGTACAACAATTTACTAATG
AGAACGAAATATTTATAACATGATGGAGCTGATAATAAAGAACCATTATC
ATAACCATAATAATGATAATACGTACAACAGTGACCAGAATAATACCGGT
AAGGGGAACGATAGAAATATTACAAATAAGCATAACCCGTAAAAATCACA
TGACAGTAATGATAAGAATAGTAATACCAACTATCAAAATAAGAATGAAT
ATGAATACAATCACAATAAGAATTAACTATAATAATGACGTGGCGAATGG
CACTATATAAACCATATCAACAATTACGGTCACATCATTGATATGAACTT
TCAACCGAATCCTCAATACCAGAGTCGAAGACCTGAGAAACGAATTCGAG
GCCAGCAGATACCAGAAGTCCGCCAGAAGAACTTATGCGAATTAAATCCA
CACCCAATGATGCCCGAATTAACGTCTCAATGGTTGGTAAATGAAAGTAA
GAGGACATTAATTATTTTGTAGTATATCATAGTATCATTTGGTTCTTGAA
CCATAGCCGACCTGAACGAGTATCGCTCAGCATCCCGAATGAATATTATA
CCCTATTAATTTCTCTCTTCAATTATAGAACAATCCATTCCAAGAAGACC
GATACCGGAACAAGAAAGGCAGATCGTACAATTCAGCACAACCGCGGTGG
CCCAATGTCGACTACCGCTACTCGATTTCTACGCCAGGAGATGTAGCATA
GCCGACCCAACCGGGGCTGATAGGAGACATGAACCTTCCCAGTATCGCAA
TTAAAAGGGAGCCTGGCAGAAACCCAGCCAAAGAAGCTCGCCAGAAAATC
GAATTCCTATTACTCCGCCTGGACGAGCAAGACCGGTAATTGTGACACCG
ACGACAACTAGCCAGAATGAAGCTGGAAAATATCAACCGCGATATAGCGA
CATGAAGAATTCCCTGTTCAGATGGCTATGCCCCGAGCTACGATACTTCG
TTCGAGCTCGACGATCCTGCTCTGAAGACGCTAATGGTCCCGATTCCAAA
CGGATTAATCCATCCAAGTAAGCTAAAACGCCTGGAGCTCCCACATGCGA
AGAGAACCCTGAGTGATGAGAGATTTTAACTGGCAAGGTCTCGATTCCCC
AAGCAATAATATAGAGAAGGAAATAATCCATGTATAGCGTTTTTTTTGTG
AGACAAATAAATGGTACGTTTTTAAAAAACATTTTTTTCACTTTGTTCGA
ATGATTTTTTACCTATCACATTTTGATGATTATAATCTAAAGCAACACAA
CCAACCAATAGATATTGTAAGAAAACGGCTTCGTGATGCAAATATGAATC
AATTTCACAATTTAATTCTTATCTAGAAAAATCGTTAGGAGTTTTCATTT
AAATAAATATAACATAAGAGAGCTAGATATCAAGTAAAGGCAATAATTTC
TATTGTTGCTAAAATCCAACAATGATATCAAATTAAAACAAAGAAATATA
GTGAAAAAACATTAGAAATAGTCAATAGGTAAAATAAGTAATAAAAATTC
CAAAATAGGTTGAATATAAATATAAATCATGGCAAATTAGTGACAGAATC
TAAATGACTGTCTAATAAATTTCTAGAATATTTCGGTTCTTTGGACAGTG
AATAAAGTATTTTTGCTAAGTGGCTAATAGGATCCCTCGGTCGTTCTTCA
AATAATTGAATAAACGCTTGCCCGAGAGCTTCTCCGATTAGAATTTGTAA
TTCTTTACTGGTATAAGGACGATTTCGTTCAACATTGGTACTCTGTGTTT
CTATTTCTACCTTTGATTGAGCTTCACTTAAAAGTTGATTGCTCGGTAAT
TCTGTGATTAAACCTTTAACATTTGTCACTGTTTGTGGTTGTTCAGTACT
TATTTTTAGTGAACCATATTTTATTTTATTTTCCTTGTCAAACAAATATT
CACTGAGGCTCTCTTTAATTTCGTATTCAATTGATTTCTTATTCAGTGCT
TTTAATTTATTCTTTTGGAATTTGGATTTCCTCGGTTTGCATGAGCCCAT
CGTATCGACAGTGACACTGAAATGAATGTAAGAATCGGAATCGGAATCAT
TATTGTAATCCTCGTTATAATAAAAGTCATTCTTTCCTTTAAAGTTATTC
ACAAAAATTTGTCGATGATTTTTCCTCGTTGATAATTTTGGTCGTCTAAC
GATGTTATTAGGTTTTTTAATAAATATTTTTGAATGAATTTCATTTTCTA
GGCTTTGAATGTTAAGGAAACCTTTCGTATTGTTACGGCAAAAATCACTT
TTCATTAGATCAAAATTCCTATGTTCATTTAATGAAATTGGGTTTGATTG
ATTAAAAATTCCGAAAAATACTCCATTTGAATTGTTAACGTTTTTTACCG
ACAATATAACTTTTTTCTCAAATATGTTCATGTGGTAATGAATGCATTTC
AATATTTCCCATCGTTTTCTTTTATTAAATGAATATTTCAACCAGCGTGT
CCATATTTCGTTTTCGTTAAACAAGAATACATCATTTCTATTTAATGATT
TGTATTCAATTTCATAAAACATAGAAAACACAATATTCTAATTATAATGA
TAATTATAGCAATATCATATCAAAAATTAATTGGAAAATCTTTTCAGAAA
GATATTTTAAGAAATATCTATTATTATAATATAAAATAACGTTGTCACTG
ACAACACAAA
back to top

protein sequence of SMED30017214-orf-1

>SMED30017214-orf-1 ID=SMED30017214-orf-1|Name=SMED30017214-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=332bp
MFYEIEYKSLNRNDVFLFNENEIWTRWLKYSFNKRKRWEILKCIHYHMNI
FEKKVILSVKNVNNSNGVFFGIFNQSNPISLNEHRNFDLMKSDFCRNNTK
GFLNIQSLENEIHSKIFIKKPNNIVRRPKLSTRKNHRQIFVNNFKGKNDF
YYNEDYNNDSDSDSYIHFSVTVDTMGSCKPRKSKFQKNKLKALNKKSIEY
EIKESLSEYLFDKENKIKYGSLKISTEQPQTVTNVKGLITELPSNQLLSE
AQSKVEIETQSTNVERNRPYTSKELQILIGEALGQAFIQLFEERPRDPIS
HLAKILYSLSKEPKYSRNLLDSHLDSVTNLP*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002056medial muscle cell