SMED30024424

Overview
NameSMED30024424
Smed IDSMED30024424
Length (bp)3480
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 SMED30024424 (SMED30024424) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024424 (SMED30024424) 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 SMED30024424 (SMED30024424) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024424 (SMED30024424) 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




SMED30024424

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30024424SMESG000023315.1 SmedASXL_005919SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymal cellSMED30024424SMESG000023315.1 SMESG000018460.1 dd_Smed_v4_4409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30024424 vs. Planmine SMEST
Match: SMESG000023315.1 (SMESG000023315.1)

HSP 1 Score: 1985.69 bits (5143), Expect = 0.000e+0
Identity = 986/989 (99.70%), Postives = 988/989 (99.90%), Query Frame = 1
Query:   91 MDDSKYNINNLKEKVTQFYFNGSNHQELVDFVNDDKTTRFCFDLYLDNNQCIKHFGITGLINKLKKQSINEEDFNWLHSQINQRFYEEKNNLLYFIKLSAYIKLSYIYQNENKSFIQVLKELQNDDENCVCRNQTLISNMIEIFSNRDLPVFVLGALSQVLYKEGNDLLTFILETSTRFAGNLNLHQLTLKSISYLYNYCTVNGRSIPNLQQFVMHCVHKPELFSDAVDLLTNILVGTGLSNATMEYVIKFTLMCNPVIEKIIQDHKEAVRNNIEWKERDNNSKQMVYALCEYVGSIINLSFDGIVSFFTSTNDITESEKEAVEYXXXXXXXXXSIEGNIPKYNDIFIGIVNNVHNLLEELAEIYENNSECVIAFQRNLIDIFFDKLKHPFSYGDKDVDMDEFLDNRDNVGYAFASINHDMQVDWLKQKLYFYSQSENLNVSDIETVLYFYSQIPEFSFEILPFEQLHNIFKMAFLSAGDFQETLIDTYVGLLKELFQILKENDLNLLIGFLWDVLKNYEPAMGAAACLLSSVYQSEHLSLSAITTERETQTILLIKDIIDCSNWRESNIILYSIVGRLACICRNNEELNSLSNAFISSIFVQLTESIQRIVNKKVDINQNQQPIECKDELIIANQLSLISSFLTPISKFSNNCSQFIQEMIDALLQLLSQLAETVLLSVEFYSALLKLVHSALLTKIIENPTIVQKFSEILMVFMNTVYRLNTGQSRCSCFDLMIATLNIAFQLIVPLHQELATFIYKYFSDLLLDYTFNRFRSNYYMPAFISRCIKFVHSILIEHGLSNRIRNSESLCFDHTPNISRPNLSTQKLEWFEKNSVVLKQINWSSIFFIPSFYLGDLTPDVNRASIKLLISAIKCRSQLPDYISQALINNLQLVIFNVVKLFSFGVSELGDMVSLITAFRENMCAECVKMLSLVNNEPIVQANQYLQTVTKLVHYLLTGSKLSSSTMRIYISNFQENVKLLQPPAQCLQS 3057
            MDDSKYNINN+KEKVTQFYFNGSNHQ+LVDFVNDDKTTRFCFDLYLDNNQCIKHFGITGLINKLKKQSINEEDFNWLHSQINQRFYEEKNNLLYFIKLSAYIKLSYIYQNENKSFIQVLKELQNDDENCVCRNQTLISNMIEIFSNRDLPVFVLGALSQVLYKEGNDLLTFILETSTRFAGNLNLHQLTLKSISYLYNYCTVNGRSIPNLQQFVMHCVHKPELFSDAVDLLTNILVGTGLSNATMEYVIKFTLMCNPVIEKIIQDHKEAVRNNIEWKERDNNSKQMVYALCEYVGSIINLSFDGIVSFFTSTNDITESEKEAVEYLLKLILQLLSIEGNIPKYNDIFIGIVNNVHNLLEELAEIYENNSECVIAFQRNLIDIFFDKLKHPFSYGDKDVDMDEFLDNRDNVGYAFASINHDMQVDWLKQKLYFYSQSENLNVSDIETVLYFYSQIPEFSFEILPFEQLHNIFKMAFLSAGDFQETLIDTYVGLLKELFQILKENDLNLLIGFLWDVLKNYEPAMGAAACLLSSVYQSEHLSLSAITTERETQTILLIKDIIDCSNWRESNIILYSIVGRLACICRNNEELNSLSNAFISSIFVQLTESIQRIVNKKVDINQN QPIECKDELIIANQLSLISSFLTPISKFSNNCSQFIQEMIDALLQLLSQLAETVLLSVEFYSALLKLVHSALLTKIIENPTIVQKFSEILMVFMNTVYRLNTGQSRCSCFDLMIATLNIAFQLIVPLHQELATFIYKYFSDLLLDYTFNRFRSNYYMPAFISRCIKFVHSILIEHGLSNRIRNSESLCFDHTPNISRPNLSTQKLEWFEKNSVVLKQINWSSIFFIPSFYLGDLTPDVNRASIKLLISAIKCRSQLPDYISQALINNLQLVIFNVVKLFSFGVSELGDMVSLITAFRENMCAECVKMLSLVNNEPIVQANQYLQTVTKLVHYLLTGSKLSSSTMRIYISNFQENVKLLQPPAQCLQS
Sbjct:    1 MDDSKYNINNVKEKVTQFYFNGSNHQDLVDFVNDDKTTRFCFDLYLDNNQCIKHFGITGLINKLKKQSINEEDFNWLHSQINQRFYEEKNNLLYFIKLSAYIKLSYIYQNENKSFIQVLKELQNDDENCVCRNQTLISNMIEIFSNRDLPVFVLGALSQVLYKEGNDLLTFILETSTRFAGNLNLHQLTLKSISYLYNYCTVNGRSIPNLQQFVMHCVHKPELFSDAVDLLTNILVGTGLSNATMEYVIKFTLMCNPVIEKIIQDHKEAVRNNIEWKERDNNSKQMVYALCEYVGSIINLSFDGIVSFFTSTNDITESEKEAVEYLLKLILQLLSIEGNIPKYNDIFIGIVNNVHNLLEELAEIYENNSECVIAFQRNLIDIFFDKLKHPFSYGDKDVDMDEFLDNRDNVGYAFASINHDMQVDWLKQKLYFYSQSENLNVSDIETVLYFYSQIPEFSFEILPFEQLHNIFKMAFLSAGDFQETLIDTYVGLLKELFQILKENDLNLLIGFLWDVLKNYEPAMGAAACLLSSVYQSEHLSLSAITTERETQTILLIKDIIDCSNWRESNIILYSIVGRLACICRNNEELNSLSNAFISSIFVQLTESIQRIVNKKVDINQNHQPIECKDELIIANQLSLISSFLTPISKFSNNCSQFIQEMIDALLQLLSQLAETVLLSVEFYSALLKLVHSALLTKIIENPTIVQKFSEILMVFMNTVYRLNTGQSRCSCFDLMIATLNIAFQLIVPLHQELATFIYKYFSDLLLDYTFNRFRSNYYMPAFISRCIKFVHSILIEHGLSNRIRNSESLCFDHTPNISRPNLSTQKLEWFEKNSVVLKQINWSSIFFIPSFYLGDLTPDVNRASIKLLISAIKCRSQLPDYISQALINNLQLVIFNVVKLFSFGVSELGDMVSLITAFRENMCAECVKMLSLVNNEPIVQANQYLQTVTKLVHYLLTGSKLSSSTMRIYISNFQENVKLLQPPAQCLQS 989          
The following BLAST results are available for this feature:
BLAST of SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 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 SMED30024424 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000023315.10.000e+099.70SMESG000023315.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024424 ID=SMED30024424|Name=SMED30024424|organism=Schmidtea mediterranea sexual|type=transcript|length=3480bp
TCTATATAAATCTTATATGGTTTCTTTAATTTACTTTTATTTATTTGATA
ACATTTTGAAAAGAATTTATATTTATATCAAAATTTTGTAATGGACGATT
CTAAATATAATATTAATAATCTGAAGGAGAAAGTAACCCAATTTTACTTT
AATGGCAGTAATCATCAAGAATTGGTGGATTTTGTTAATGATGATAAAAC
TACTCGATTTTGTTTTGATTTATATCTGGACAATAACCAATGTATAAAGC
ATTTCGGTATAACTGGATTGATAAATAAGCTCAAAAAACAATCTATCAAC
GAAGAGGATTTTAATTGGTTGCATTCTCAAATTAATCAGCGATTTTATGA
AGAGAAAAACAATTTACTATATTTTATCAAGCTGTCAGCTTACATAAAGC
TGTCGTATATTTACCAGAATGAAAACAAATCATTTATCCAAGTGTTGAAA
GAGCTGCAAAATGATGATGAGAACTGCGTCTGTCGCAATCAAACTCTAAT
TAGCAACATGATAGAGATATTCAGCAATCGTGACTTGCCAGTGTTTGTAT
TGGGCGCTCTCAGCCAGGTGCTCTACAAGGAGGGCAATGATTTGCTGACA
TTTATCCTTGAGACGAGCACGCGATTCGCTGGTAACCTTAATCTGCATCA
ATTGACCCTGAAATCCATCAGTTACTTGTATAACTATTGCACAGTCAACG
GGCGTTCTATTCCCAATCTACAGCAATTCGTTATGCATTGTGTTCACAAA
CCAGAACTGTTCTCTGATGCAGTTGATCTATTGACGAATATTCTTGTCGG
TACCGGACTATCAAACGCCACAATGGAGTATGTCATCAAGTTCACATTGA
TGTGCAATCCAGTCATTGAGAAAATTATCCAAGACCATAAAGAGGCCGTT
AGGAATAATATCGAATGGAAGGAACGGGATAATAATAGCAAACAGATGGT
GTATGCCCTTTGTGAGTATGTTGGCTCGATTATTAACTTGTCATTTGATG
GAATCGTGAGCTTTTTTACATCGACCAATGATATCACAGAATCGGAAAAG
GAGGCGGTGGAGTATTTGTTAAAGTTGATTTTGCAATTGTTGAGTATTGA
AGGAAATATTCCCAAATATAATGATATTTTTATTGGCATTGTTAATAATG
TTCATAATCTGTTGGAGGAGCTTGCAGAAATATATGAAAATAATTCAGAA
TGCGTTATTGCTTTCCAGAGGAACTTGATCGATATTTTTTTTGATAAATT
GAAACATCCGTTTTCATACGGCGATAAAGATGTAGATATGGATGAGTTTC
TCGATAATAGGGACAATGTCGGCTATGCCTTTGCCAGCATTAATCACGAC
ATGCAAGTCGACTGGTTGAAACAGAAACTCTATTTTTATTCTCAGTCAGA
AAATCTCAATGTTTCTGACATCGAAACGGTGCTTTATTTCTACAGTCAGA
TACCCGAGTTCTCCTTTGAGATTTTGCCGTTTGAACAACTGCATAATATC
TTCAAAATGGCCTTTTTATCTGCTGGAGATTTTCAGGAAACTTTAATTGA
CACATATGTTGGATTGCTAAAGGAACTTTTTCAAATACTAAAGGAGAATG
ATTTAAATCTGCTTATTGGATTCTTGTGGGATGTGTTAAAAAATTATGAG
CCGGCAATGGGAGCAGCAGCTTGTTTACTTAGTAGTGTTTACCAATCGGA
ACATCTTTCTCTCTCTGCTATTACTACCGAACGAGAAACTCAGACCATTC
TTTTAATAAAAGATATAATTGACTGCTCAAATTGGAGAGAATCTAATATC
ATTCTTTATTCAATTGTTGGCCGATTGGCGTGCATTTGTCGGAATAATGA
AGAATTAAACAGTCTCTCCAATGCATTTATCAGCTCGATTTTTGTCCAGC
TCACCGAGTCGATCCAGCGCATTGTCAACAAGAAAGTCGATATCAATCAA
AATCAGCAGCCAATAGAATGCAAGGATGAATTAATAATAGCTAATCAACT
TTCCTTGATATCTAGTTTTCTCACTCCAATAAGCAAGTTTTCTAACAATT
GCTCCCAATTTATACAAGAAATGATTGATGCGCTCTTGCAACTTTTATCA
CAGTTAGCAGAAACTGTTCTTTTATCAGTTGAATTTTATTCTGCGTTGCT
CAAATTAGTCCATAGTGCTCTGCTCACTAAAATTATCGAAAATCCAACAA
TTGTACAAAAGTTTTCTGAGATTTTGATGGTATTTATGAACACAGTTTAT
CGATTAAACACTGGCCAATCGCGTTGTTCATGTTTTGATTTGATGATCGC
AACACTTAATATTGCATTCCAATTAATAGTTCCTTTGCACCAAGAACTCG
CCACTTTCATCTATAAATATTTCTCAGACCTCTTACTCGATTACACATTC
AATCGATTCAGAAGCAATTACTACATGCCCGCATTTATATCCCGTTGCAT
CAAATTTGTCCATTCCATTCTCATAGAGCACGGTCTGTCGAATCGGATAC
GGAACAGTGAATCTCTTTGTTTCGATCACACTCCCAATATTTCTCGCCCG
AATTTGTCCACTCAAAAATTGGAATGGTTCGAGAAAAACTCAGTAGTGCT
CAAGCAAATCAATTGGTCTAGTATATTTTTCATTCCTTCATTCTATCTCG
GCGATCTTACTCCCGACGTGAATCGAGCCTCAATCAAGTTGCTGATATCC
GCAATAAAATGCCGGTCTCAATTACCCGACTATATATCTCAGGCTTTAAT
CAATAATCTTCAATTGGTCATATTCAATGTTGTCAAATTGTTCAGTTTTG
GTGTGTCAGAATTGGGCGATATGGTATCTCTGATTACGGCATTCAGAGAG
AACATGTGTGCTGAATGCGTCAAAATGTTAAGCTTGGTCAACAATGAACC
TATTGTCCAAGCAAACCAGTATCTGCAAACGGTCACCAAACTTGTACATT
ACCTTCTGACCGGTTCGAAACTCAGTAGCTCGACAATGAGAATTTACATC
AGTAACTTCCAGGAAAATGTGAAATTATTACAACCTCCCGCTCAATGTCT
TCAATCGTGAAACAGTTCAAATGATGATCTATGTTGTTGTGTGCAATTTT
GATTGGTGCCCCGTGTGGGCTGGCCACATGTCTTGATGTTGTATTTTATC
TGGACAATAATATTACCTACCATATTGTTATTATTATTTTTGTTATCATA
ATTATTATTGTCACCGTCGGCATCATTGCCGTTATTATTATTATTATTAT
TGTCATCCATCCAATCCATGCGTGCTCTACTCTCTCTCTCTCATTCTGCA
ATTCATCTACCTTGTGGCCATTTGTTGCCAGGGCTGTTGATGTATTTTAA
TAAATATTTATTTGATAATTGCACGTTTATCAAGGATCATTTCTACTATT
TTTTGATTAATTCGATAAAATTTGTTTTGCTCTGATCTCTGTTAATTTAT
GTTTTGATAACTAAATTGCTATTTTATTGC
back to top

protein sequence of SMED30024424-orf-1

>SMED30024424-orf-1 ID=SMED30024424-orf-1|Name=SMED30024424-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=990bp
MDDSKYNINNLKEKVTQFYFNGSNHQELVDFVNDDKTTRFCFDLYLDNNQ
CIKHFGITGLINKLKKQSINEEDFNWLHSQINQRFYEEKNNLLYFIKLSA
YIKLSYIYQNENKSFIQVLKELQNDDENCVCRNQTLISNMIEIFSNRDLP
VFVLGALSQVLYKEGNDLLTFILETSTRFAGNLNLHQLTLKSISYLYNYC
TVNGRSIPNLQQFVMHCVHKPELFSDAVDLLTNILVGTGLSNATMEYVIK
FTLMCNPVIEKIIQDHKEAVRNNIEWKERDNNSKQMVYALCEYVGSIINL
SFDGIVSFFTSTNDITESEKEAVEYLLKLILQLLSIEGNIPKYNDIFIGI
VNNVHNLLEELAEIYENNSECVIAFQRNLIDIFFDKLKHPFSYGDKDVDM
DEFLDNRDNVGYAFASINHDMQVDWLKQKLYFYSQSENLNVSDIETVLYF
YSQIPEFSFEILPFEQLHNIFKMAFLSAGDFQETLIDTYVGLLKELFQIL
KENDLNLLIGFLWDVLKNYEPAMGAAACLLSSVYQSEHLSLSAITTERET
QTILLIKDIIDCSNWRESNIILYSIVGRLACICRNNEELNSLSNAFISSI
FVQLTESIQRIVNKKVDINQNQQPIECKDELIIANQLSLISSFLTPISKF
SNNCSQFIQEMIDALLQLLSQLAETVLLSVEFYSALLKLVHSALLTKIIE
NPTIVQKFSEILMVFMNTVYRLNTGQSRCSCFDLMIATLNIAFQLIVPLH
QELATFIYKYFSDLLLDYTFNRFRSNYYMPAFISRCIKFVHSILIEHGLS
NRIRNSESLCFDHTPNISRPNLSTQKLEWFEKNSVVLKQINWSSIFFIPS
FYLGDLTPDVNRASIKLLISAIKCRSQLPDYISQALINNLQLVIFNVVKL
FSFGVSELGDMVSLITAFRENMCAECVKMLSLVNNEPIVQANQYLQTVTK
LVHYLLTGSKLSSSTMRIYISNFQENVKLLQPPAQCLQS*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell