SMED30008261

Overview
NameSMED30008261
Smed IDSMED30008261
Length (bp)2469
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 SMED30008261 (SMED30008261) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008261 (SMED30008261) 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 SMED30008261 (SMED30008261) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008261 (SMED30008261) 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




SMED30008261

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30008261h1SMcG0019739 SmedASXL_008740SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30008261h1SMcG0019739 SmedASXL_008740SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30008261h1SMcG0019739 dd_Smed_v4_11410_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30008261h1SMcG0019739 dd_Smed_v4_11410_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30008261h1SMcG0019739 dd_Smed_v4_5737_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
SMED30008261 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002641:33928..36552 +12190
Homology
BLAST of SMED30008261 vs. Planmine SMEST
Match: SMESG000014357.1 (SMESG000014357.1)

HSP 1 Score: 677.552 bits (1747), Expect = 0.000e+0
Identity = 345/347 (99.42%), Postives = 347/347 (100.00%), Query Frame = 3
Query: 1335 GHSNDIYESTNYKYKDKIIKKRLRSNTLESGEYTRNSDESTTTSVTIKPPGASSGNTRTVKIVQETDIAVTVKQESECVSTPEELFSSDPGSQAMETSDIQPISLAMGDRAISPDDSDIKLERALNXXXXXXXXXXXALGKHKRDLLIEKRRLQLRAEKQKNSVTSKLKRVSDSMLHYKSILEALILEFKSCDKSKRVTLVPKIKENHARFMQLKELHGKLNASKEVTLKRSRDPVEGQINELETNLVDRLNVSEKETNAMEQEEASDSKSIFIHVPTDIVLYQDQLQSIIGDQLEIASFDMSGYSNTSVLYVITMKSHSCACQALKTMTLSKETTNWQMSLTFKEQ 2375
            GHSNDIY+STNYKYKDKIIKKRLRSNTLESGEYTRNSDESTTTSVTIKPPGA+SGNTRTVKIVQETDIAVTVKQESECVSTPEELFSSDPGSQAMETSDIQPISLAMGDRAISPDDSDIKLERALNDSDVDSLDSDDALGKHKRDLLIEKRRLQLRAEKQKNSVTSKLKRVSDSMLHYKSILEALILEFKSCDKSKRVTLVPKIKENHARFMQLKELHGKLNASKEVTLKRSRDPVEGQINELETNLVDRLNVSEKETNAMEQEEASDSKSIFIHVPTDIVLYQDQLQSIIGDQLEIASFDMSGYSNTSVLYVITMKSHSCACQALKTMTLSKETTNWQMSLTFKEQ
Sbjct:  416 GHSNDIYDSTNYKYKDKIIKKRLRSNTLESGEYTRNSDESTTTSVTIKPPGANSGNTRTVKIVQETDIAVTVKQESECVSTPEELFSSDPGSQAMETSDIQPISLAMGDRAISPDDSDIKLERALNDSDVDSLDSDDALGKHKRDLLIEKRRLQLRAEKQKNSVTSKLKRVSDSMLHYKSILEALILEFKSCDKSKRVTLVPKIKENHARFMQLKELHGKLNASKEVTLKRSRDPVEGQINELETNLVDRLNVSEKETNAMEQEEASDSKSIFIHVPTDIVLYQDQLQSIIGDQLEIASFDMSGYSNTSVLYVITMKSHSCACQALKTMTLSKETTNWQMSLTFKEQ 762          
The following BLAST results are available for this feature:
BLAST of SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 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 SMED30008261 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000014357.10.000e+099.42SMESG000014357.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008261 ID=SMED30008261|Name=SMED30008261|organism=Schmidtea mediterranea sexual|type=transcript|length=2469bp
AATATATTTACTATTGATTAGTTTTAAGCATTAATTAAAAATGTATTATT
TTCATTTCTCTACATGAGCCTAACTAACTGGATGCAAATATGGAGATAAA
AATGGCAATCAAAATGTTACTACTAAGAATTATGGATTAATACTGGTCCG
ACTATTCACATCATCCGCCTTTGTATCACTAGCATTCATGGTAACATAGC
CAGGTAAAATAGCAACATGCAGCCTTAATTACTTTAATAAGTTAGAAAAT
ATGTATTCGTGAAATTTGAAATTAACAATTATTGATCTGACTCCAAAGCG
TGTTTTGGATGGCAACAATGATGAAACCCAAACAATATAAGCTTTTGTTA
ATCATCACAATTGAATACCGATGTACAATTTGAGTGCTTATTACAATCCA
TTAATAAACTTGGAATATCCGGCCACTTGGTTACTGCAGCTTTTTTCGAC
AACCGGTATAGTTGCTTTCTTTTTCCAACTTGAAAGCACTCGGAACTCGA
CACAAATAACTTAAATTACTGATATTAATTGTTTTCAATCTGATGATGTT
TTCTTCAATAATTTCCTACCCGTATTTATCCACCTCTTTTCACTTATCGT
TTTTCTCTTTTCAAACTTTTTAAAAACTCAATATAAAATTTCTCTTTTTC
CAAGTTGTATTTCGCTCTTTTAGATTTTTTCCTTCCCTGTATTCCCTCCA
GTTAGCTCCAGTTTCTTTATTATCTCGTATGGCTGTCGTGATATATAATT
TTTAATGGACTGCTGTCGATTTCCCCAATAATACATTTTCTTTATCTCGG
ACAGACTATCGAAATATACATATTTAATTTCGGCTTATACTCTTTATTTT
ATCCTCCTCCCTCTTATTTTTTTATTTTTTAGGTAACCCCAAGATATTTA
ATACTAAAGTCATTTAACTTATTCATTTTCGTTTATCTACACTCAATAAA
TTTCCATTAACTATCATTTCGTTGAGCTTTCGTTGATGATATTTCTCGGG
TTTACTTCATCTTTTCATTGTATTTCCACTGAATCTTTTGTACCAGAATT
AACTTTAGATTCCCGTGAGTTCTGGCAACTTAGTAAACCACTAGATAAAA
CCTTCAGCGCTCTGGGTTTGAATGGTACCTGGAGCATTTTTAATTGAATT
TTATTACAGTTTCATTAAAACTCGGGCTTATAAGAAAAAGAAATCCAAGA
AGACCTTGAAGAAATGCAAAAGAAGTCCTAGTCGATCCAATAAAGATCGG
AGTCGTTCTAGAAATAGCAATAGTCGCTCTAAACATAGTCGCAGCGATAG
TAAAAAATATCGAAGACGAACTAAGAGTAGTCGAGGTCACTCAAATGATA
TTTACGAGAGCACGAATTACAAATATAAAGATAAAATTATCAAGAAAAGG
TTAAGAAGCAATACCTTGGAATCGGGAGAATATACCAGGAATTCAGACGA
ATCTACAACCACGTCAGTTACAATAAAACCCCCAGGCGCGAGTAGTGGTA
ATACGAGAACCGTTAAAATTGTCCAGGAAACAGACATAGCTGTAACCGTT
AAGCAGGAATCAGAATGCGTGTCGACACCCGAAGAATTGTTCTCCAGTGA
TCCTGGAAGTCAGGCAATGGAAACGAGCGATATACAACCAATTTCATTGG
CCATGGGAGATCGAGCAATTTCACCGGATGATTCCGACATAAAATTGGAG
CGAGCACTCAATGATAGTGATGTAGATTCTTTGGATTCTGATGACGCGCT
TGGCAAGCACAAACGGGACTTGCTGATTGAGAAGCGAAGACTCCAACTTC
GCGCAGAGAAACAGAAAAATAGCGTCACCTCGAAACTGAAGCGGGTTTCC
GATTCCATGTTGCATTACAAGAGCATATTGGAGGCGTTGATCCTAGAGTT
CAAGTCATGCGACAAGTCTAAGCGAGTCACTCTCGTTCCGAAGATCAAGG
AAAACCACGCGAGATTTATGCAGCTGAAGGAGTTGCATGGGAAACTTAAC
GCGTCGAAAGAAGTGACATTGAAGCGGAGCAGAGATCCCGTGGAAGGGCA
AATCAATGAATTGGAAACGAATCTTGTGGACCGGCTGAATGTTAGTGAGA
AGGAAACGAACGCAATGGAGCAGGAGGAAGCGTCTGATTCCAAATCGATA
TTTATCCACGTTCCGACTGATATCGTTCTCTATCAGGATCAGCTGCAATC
GATAATTGGGGACCAGTTGGAAATCGCCAGCTTTGACATGTCGGGATATT
CCAATACCAGCGTGCTCTACGTTATCACCATGAAATCCCATTCCTGCGCT
TGTCAGGCACTCAAAACAATGACTCTGTCCAAGGAGACCACCAACTGGCA
GATGAGTCTAACTTTCAAGGAGCAGATTTAAATAGGAATCATATTGATTG
TCTTTATTGTCTAGAATTATTCTTTGTACATTTCGATTGTAAATTTATCA
ATAAATATTTGTATTTTTC
back to top

protein sequence of SMED30008261-orf-1

>SMED30008261-orf-1 ID=SMED30008261-orf-1|Name=SMED30008261-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=420bp
MVPGAFLIEFYYSFIKTRAYKKKKSKKTLKKCKRSPSRSNKDRSRSRNSN
SRSKHSRSDSKKYRRRTKSSRGHSNDIYESTNYKYKDKIIKKRLRSNTLE
SGEYTRNSDESTTTSVTIKPPGASSGNTRTVKIVQETDIAVTVKQESECV
STPEELFSSDPGSQAMETSDIQPISLAMGDRAISPDDSDIKLERALNDSD
VDSLDSDDALGKHKRDLLIEKRRLQLRAEKQKNSVTSKLKRVSDSMLHYK
SILEALILEFKSCDKSKRVTLVPKIKENHARFMQLKELHGKLNASKEVTL
KRSRDPVEGQINELETNLVDRLNVSEKETNAMEQEEASDSKSIFIHVPTD
IVLYQDQLQSIIGDQLEIASFDMSGYSNTSVLYVITMKSHSCACQALKTM
TLSKETTNWQMSLTFKEQI*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 214..234
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 23..38
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 23..79
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 39..56
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 100..129