UPF0466 protein-like

Overview
NameUPF0466 protein-like
Smed IDSMED30016918
Length (bp)405
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 UPF0466 protein-like (SMED30016918) t-SNE clustered cells

Violin plots show distribution of expression levels for UPF0466 protein-like (SMED30016918) 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 UPF0466 protein-like (SMED30016918) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for UPF0466 protein-like (SMED30016918) 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



SMED30016918

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30016918 dd_Smed_v4_5792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30016918 dd_Smed_v4_5792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016918 dd_Smed_v4_5792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30016918 dd_Smed_v4_5792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016918 dd_Smed_v4_5792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016918 dd_Smed_v4_5792_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
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Zebrafish
Match: smdt1b (single-pass membrane protein with aspartate-rich tail 1b [Source:ZFIN;Acc:ZDB-GENE-141212-9])

HSP 1 Score: 50.0618 bits (118), Expect = 1.313e-8
Identity = 26/54 (48.15%), Postives = 39/54 (72.22%), Query Frame = 2 
Query:  173 TSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            T+V S TG+VL KP K+ F L R+TIV +  + +G++IS+  AALL ++ +FVP
Sbjct:   39 TAVSSTTGRVLPKPDKVPFGLTRMTIVVVPFLYVGTLISKNFAALLEEHEIFVP 92
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Zebrafish
Match: smdt1a (single-pass membrane protein with aspartate-rich tail 1a [Source:ZFIN;Acc:ZDB-GENE-110411-114])

HSP 1 Score: 43.8986 bits (102), Expect = 5.441e-6
Identity = 22/57 (38.60%), Postives = 37/57 (64.91%), Query Frame = 2 
Query:  164 NNFTSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
             + T+V + TG +L KP K  F L+R+  V    + +G++IS+  AALL ++++FVP
Sbjct:   61 QHRTAVNTATGAILAKPKKTAFGLLRIMTVVAPFLYVGTLISKNFAALLEEHDIFVP 117
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Xenopus
Match: steap1 (six transmembrane epithelial antigen of the prostate 1 [Source:Xenbase;Acc:XB-GENE-940653])

HSP 1 Score: 45.4394 bits (106), Expect = 9.537e-7
Identity = 22/54 (40.74%), Postives = 38/54 (70.37%), Query Frame = 2 
Query:  173 TSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            T++ ++ G VL KP K+ F L+RV  V +  + +G++IS+  AALL ++++FVP
Sbjct:   39 TAIATSAGTVLPKPEKVSFGLLRVFTVVIPFLYIGTLISKNFAALLEEHDIFVP 92
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Xenopus
Match: steap1 (six transmembrane epithelial antigen of the prostate 1 [Source:Xenbase;Acc:XB-GENE-940653])

HSP 1 Score: 45.4394 bits (106), Expect = 1.082e-6
Identity = 22/54 (40.74%), Postives = 38/54 (70.37%), Query Frame = 2 
Query:  173 TSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            T++ ++ G VL KP K+ F L+RV  V +  + +G++IS+  AALL ++++FVP
Sbjct:   39 TAIATSAGTVLPKPEKVSFGLLRVFTVVIPFLYIGTLISKNFAALLEEHDIFVP 92
[Close]
BLAST of UPF0466 protein-like vs. UniProt/SwissProt
Match: sp|Q28ED6|EMRE_XENTR (Essential MCU regulator, mitochondrial OS=Xenopus tropicalis OX=8364 GN=smdt1 PE=3 SV=1)

HSP 1 Score: 45.4394 bits (106), Expect = 5.382e-6
Identity = 22/54 (40.74%), Postives = 38/54 (70.37%), Query Frame = 2 
Query:  173 TSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            T++ ++ G VL KP K+ F L+RV  V +  + +G++IS+  AALL ++++FVP
Sbjct:   39 TAIATSAGTVLPKPEKVSFGLLRVFTVVIPFLYIGTLISKNFAALLEEHDIFVP 92
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Cavefish
Match: smdt1a (single-pass membrane protein with aspartate rich tail 1 [Source:NCBI gene;Acc:103036919])

HSP 1 Score: 45.4394 bits (106), Expect = 8.906e-7
Identity = 22/53 (41.51%), Postives = 38/53 (71.70%), Query Frame = 2 
Query:  176 SVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            +V +N+G +L KP K  F LIR+ +V +  + +G++IS+  AALL ++++FVP
Sbjct:   48 AVCTNSGALLPKPRKTPFGLIRICMVVVPFLYVGTLISKNFAALLEEHDIFVP 100
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Medaka
Match: smdt1b (essential MCU regulator, mitochondrial [Source:NCBI gene;Acc:110014938])

HSP 1 Score: 44.2838 bits (103), Expect = 8.804e-7
Identity = 22/52 (42.31%), Postives = 37/52 (71.15%), Query Frame = 2 
Query:  179 VYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            V +++G +L KP K  F LIR+T V +  + +G++IS+  AALL ++++FVP
Sbjct:    2 VSTSSGGILPKPDKTPFGLIRMTAVVVPFLYVGTLISKNFAALLEEHDIFVP 53
[Close]
BLAST of UPF0466 protein-like vs. Ensembl Medaka
Match: smdt1a (single-pass membrane protein with aspartate rich tail 1 [Source:NCBI gene;Acc:101156580])

HSP 1 Score: 43.8986 bits (102), Expect = 2.269e-6
Identity = 21/54 (38.89%), Postives = 38/54 (70.37%), Query Frame = 2 
Query:  173 TSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVP 334
            ++V S++G +L KP K  F L+R+ +V +  + +G+ IS+  AALL ++++FVP
Sbjct:   34 SAVSSSSGAILPKPKKTPFGLMRIALVVVPFLYVGTQISKNFAALLEEHDIFVP 87
[Close]
BLAST of UPF0466 protein-like vs. Planmine SMEST
Match: SMESG000075952.1 (SMESG000075952.1)

HSP 1 Score: 45.8246 bits (107), Expect = 2.765e-7
Identity = 18/62 (29.03%), Postives = 38/62 (61.29%), Query Frame = 2 
Query:  158 HKNNFTSVYSNTGQVLEKPFKIRFPLIRVTIVSLVCITLGSMISEKSAALLAKYNVFVPSDE 343
            +++ + S Y ++G +  +P   +F  ++  ++ L  + LG  IS + AA + +Y++FVPSD+
Sbjct:   22 YRDEYYSAYKDSGCLRNRPTYEKFGWLKSFLMVLPFLYLGGCISREGAAYMEEYDIFVPSDD 83
The following BLAST results are available for this feature:
BLAST of UPF0466 protein-like 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 UPF0466 protein-like 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 UPF0466 protein-like 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 UPF0466 protein-like vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
smdt1b1.313e-848.15single-pass membrane protein with aspartate-rich t... [more]
smdt1a5.441e-638.60single-pass membrane protein with aspartate-rich t... [more]
back to top
BLAST of UPF0466 protein-like vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 2
Match NameE-valueIdentityDescription
steap19.537e-740.74six transmembrane epithelial antigen of the prosta... [more]
steap11.082e-640.74six transmembrane epithelial antigen of the prosta... [more]
back to top
BLAST of UPF0466 protein-like 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 UPF0466 protein-like vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q28ED6|EMRE_XENTR5.382e-640.74Essential MCU regulator, mitochondrial OS=Xenopus ... [more]
back to top
BLAST of UPF0466 protein-like 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 UPF0466 protein-like vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
smdt1a8.906e-741.51single-pass membrane protein with aspartate rich t... [more]
back to top
BLAST of UPF0466 protein-like 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 UPF0466 protein-like 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 UPF0466 protein-like 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 UPF0466 protein-like vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 2
Match NameE-valueIdentityDescription
smdt1b8.804e-742.31essential MCU regulator, mitochondrial [Source:NCB... [more]
smdt1a2.269e-638.89single-pass membrane protein with aspartate rich t... [more]
back to top
BLAST of UPF0466 protein-like vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000075952.12.765e-729.03SMESG000075952.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016918 ID=SMED30016918|Name=UPF0466 protein-like|organism=Schmidtea mediterranea sexual|type=transcript|length=405bp
GATATTAGACAAATTTTGAAAATTTAAAGTCAAGTTTAACTACATATCAC
TTTTAAGATTTATTAACTAAATTTTAAGCTTTTTGAGTATAAATTTTTAA
ATAAAATTGGTATTTTGGCAGTAAACTTCAGAAATGTCTATTCCGCACAT
GAGAGAACATAAAAATAATTTTACAAGTGTATATTCAAATACTGGACAAG
TGTTAGAAAAGCCTTTCAAAATTCGTTTCCCACTGATCAGAGTCACAATC
GTAAGTTTAGTTTGCATTACTCTCGGGTCAATGATCAGTGAAAAATCAGC
GGCGTTGCTTGCGAAATACAACGTTTTTGTGCCTTCAGACGAGTGAATTA
AAATGAATTTTACTTTTATTTTATTTATTTATGAATATATCAAATTTAGT
TTTTA
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR018782MCU_reg
Vocabulary: biological process
TermDefinition
GO:0036444mitochondrial calcium uptake
GO:0051560mitochondrial calcium ion homeostasis
Vocabulary: cellular component
TermDefinition
GO:1990246uniplex complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018782Essential MCU regulator, mitochondrialPFAMPF10161DDDDcoord: 11..69
e-value: 8.8E-13
score: 47.8
IPR018782Essential MCU regulator, mitochondrialPANTHERPTHR33904FAMILY NOT NAMEDcoord: 7..70
NoneNo IPR availableTMHMMTMhelixcoord: 32..51