SMED30033299

Overview
NameSMED30033299
Smed IDSMED30033299
Length (bp)1581
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30033299 (SMED30033299) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033299 (SMED30033299) 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



SMED30033299

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
nervous systemSMED30033299SMESG000059210.1 dd_Smed_v4_70903_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30033299SMESG000059210.1 dd_Smed_v4_70903_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
SMED30033299 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002449:13201..14781 -7860
Homology
[Close]
BLAST of SMED30033299 vs. Planmine SMEST
Match: SMESG000059210.1 (SMESG000059210.1)

HSP 1 Score: 744.577 bits (1921), Expect = 0.000e+0
Identity = 420/422 (99.53%), Postives = 421/422 (99.76%), Query Frame = 1 
Query:    1 NDGYIVHKSSMGVIDLLEYDVKEYSPFSQNSRYIYSPLNILTRIKINQLQAFDKASFISYPLIFYWTEIIKKRSSPXXXXXXXXXXXXXXXXXXXXXPALYYDIYESELAYLKGGNSKLTLPGSPRNNCGVVNITMAFENWLSKNYRPXXXXXXXXXXXXXVKYGFVSSMFIFSIYRDMFTTSKIDKEFGIKSYRQPYALTQYFWTLINVILFIDLLAMETMGTLFSKIDSNYIFAVDLFIVLLAGLLMVDVILHLSMFPPFDKPFQRILRSIPVFVCMSSIYIMSLLVFGLIFVKFMPCSNYKMYYPSNSYVSGAIAVFHLNLNIIDFPYKDFERIWXXXXXXXXXXXXFIVNSIMTTMNEEIAIISSNSFLFQYLHSLQFHTIFDSFYFLSPVRFIARVVFKVHPSNMLVFAKKSHIFEH 1266
            NDGYIVHKSSMGVIDLLEYDVKEYSPFSQNSRYIYSPLNILTRIKINQLQAFDKASFISYPLIFYWTEIIKKRSSPLIVLDTLLTLSISIIFILYYIPALYYDIYESELAYLKGGNSKLTLPGSPRNNCGVVNITMAFENWLSKNYRPKYIINYIIKTISIVKYGFVSSMFIFSIYRDMFTTSKIDKEFGIKSYRQPYALTQYFWTLINVILFIDLLAMETMGTLFSKIDSNYIFAVDLFIV+LAGLLMVDVILHLSMFPPFDKPFQRILRSIPVFVCMSSIYIMSLLVFGLIFVKFMPCSNYKMYYPSNSYVSGAIAVFHLNLNIIDFPYKDFERIWPLQLCLVLVLPLFIVNSIMTTMNEEIAIISSNSFLFQYLH LQFHTIFDSFYFLSPVRFIARVVFKVHPSNMLVFAKKSHIFEH
Sbjct:  185 NDGYIVHKSSMGVIDLLEYDVKEYSPFSQNSRYIYSPLNILTRIKINQLQAFDKASFISYPLIFYWTEIIKKRSSPLIVLDTLLTLSISIIFILYYIPALYYDIYESELAYLKGGNSKLTLPGSPRNNCGVVNITMAFENWLSKNYRPKYIINYIIKTISIVKYGFVSSMFIFSIYRDMFTTSKIDKEFGIKSYRQPYALTQYFWTLINVILFIDLLAMETMGTLFSKIDSNYIFAVDLFIVILAGLLMVDVILHLSMFPPFDKPFQRILRSIPVFVCMSSIYIMSLLVFGLIFVKFMPCSNYKMYYPSNSYVSGAIAVFHLNLNIIDFPYKDFERIWPLQLCLVLVLPLFIVNSIMTTMNEEIAIISSNSFLFQYLHLLQFHTIFDSFYFLSPVRFIARVVFKVHPSNMLVFAKKSHIFEH 606
The following BLAST results are available for this feature:
BLAST of SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 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 SMED30033299 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000059210.10.000e+099.53SMESG000059210.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033299 ID=SMED30033299|Name=SMED30033299|organism=Schmidtea mediterranea sexual|type=transcript|length=1581bp
AATGATGGATATATTGTACACAAATCATCAATGGGGGTGATCGACCTTTT
GGAGTATGACGTGAAAGAATATTCACCGTTCAGTCAAAATTCCCGCTATA
TTTATTCGCCTCTCAATATTTTGACGAGAATCAAAATAAATCAGCTTCAG
GCTTTTGATAAGGCTTCTTTCATCAGTTACCCTTTGATTTTTTATTGGAC
AGAAATCATCAAGAAGCGCTCATCGCCTCTAATAGTTTTAGACACTCTCT
TAACTTTGTCCATTAGTATAATTTTTATCCTTTACTACATTCCTGCTCTG
TATTACGATATTTATGAATCAGAGTTAGCATATTTAAAAGGAGGAAACTC
TAAATTAACTCTTCCTGGTTCTCCAAGAAACAATTGCGGCGTAGTGAATA
TAACAATGGCTTTTGAAAATTGGTTATCAAAAAACTATCGGCCCAAATAC
ATTATCAATTATATTATCAAGACGATCTCCATTGTCAAATACGGATTTGT
CTCGTCGATGTTTATATTTTCCATATATAGAGACATGTTCACAACGAGCA
AGATTGACAAAGAATTCGGTATCAAATCCTACAGACAGCCATACGCTCTT
ACTCAATACTTTTGGACTCTCATCAATGTCATCCTATTCATAGATCTGTT
AGCAATGGAAACAATGGGAACTCTTTTTTCAAAAATCGATTCGAATTATA
TTTTTGCAGTAGATCTTTTCATTGTTCTTTTGGCAGGACTTCTAATGGTC
GATGTCATTTTGCATTTGAGTATGTTTCCGCCATTCGACAAGCCGTTTCA
AAGAATTCTTCGTTCGATTCCGGTGTTTGTTTGCATGAGTTCAATTTATA
TTATGAGTTTGTTAGTGTTTGGATTGATATTTGTAAAATTTATGCCTTGT
AGCAACTACAAAATGTATTATCCTTCCAATTCATATGTATCAGGTGCCAT
TGCAGTTTTTCATCTTAATCTTAACATCATAGACTTCCCTTATAAAGATT
TCGAAAGAATTTGGCCTCTTCAATTGTGTTTGGTTTTGGTGCTGCCCTTG
TTCATTGTTAACAGCATTATGACGACAATGAATGAAGAAATCGCCATCAT
CTCAAGCAATTCCTTTCTTTTTCAATATCTTCATTCACTGCAATTTCATA
CCATTTTCGATTCTTTCTATTTTCTAAGTCCGGTTCGATTTATCGCCCGA
GTAGTTTTCAAAGTCCATCCGTCTAATATGTTAGTTTTCGCCAAAAAGAG
TCACATTTTTGAACATTAATATGACACACAAATAAATGTGAAAAAAACAA
AAATATTTTATTTATTGTATCCATTTCCGAAATAAATTCAATAGATAATG
CGATGATAATATTTTCATTCATGACAAAATCAGTGCCGAAATGGTTTTGT
AGAGATTTCTCCCTAAAAACCGAGGCATTACAGAGTGGAGAATAATTGAA
CCATGTATTTGATGTTCTATTTATTATATTATTTTATGGAAATATTAGCG
GATGTTGTTCATAATTTCTTTTATTTTTTTCATCTCACGAATTGTATGTT
TCAGTGTGAAATATTTTCAGTGGTTTTCTCA
back to top

protein sequence of SMED30033299-orf-1

>SMED30033299-orf-1 ID=SMED30033299-orf-1|Name=SMED30033299-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=423bp
NDGYIVHKSSMGVIDLLEYDVKEYSPFSQNSRYIYSPLNILTRIKINQLQ
AFDKASFISYPLIFYWTEIIKKRSSPLIVLDTLLTLSISIIFILYYIPAL
YYDIYESELAYLKGGNSKLTLPGSPRNNCGVVNITMAFENWLSKNYRPKY
IINYIIKTISIVKYGFVSSMFIFSIYRDMFTTSKIDKEFGIKSYRQPYAL
TQYFWTLINVILFIDLLAMETMGTLFSKIDSNYIFAVDLFIVLLAGLLMV
DVILHLSMFPPFDKPFQRILRSIPVFVCMSSIYIMSLLVFGLIFVKFMPC
SNYKMYYPSNSYVSGAIAVFHLNLNIIDFPYKDFERIWPLQLCLVLVLPL
FIVNSIMTTMNEEIAIISSNSFLFQYLHSLQFHTIFDSFYFLSPVRFIAR
VVFKVHPSNMLVFAKKSHIFEH*
back to top
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 77..99
NoneNo IPR availableTMHMMTMhelixcoord: 234..256
NoneNo IPR availableTMHMMTMhelixcoord: 197..219
NoneNo IPR availableTMHMMTMhelixcoord: 337..356
NoneNo IPR availableTMHMMTMhelixcoord: 154..176
NoneNo IPR availableTMHMMTMhelixcoord: 273..295