slc31a-3

Overview
Nameslc31a-3 (AKN21633.1)
Smed IDSMED30021535
Length (bp)782
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 slc31a-3 (SMED30021535) t-SNE clustered cells

Violin plots show distribution of expression levels for slc31a-3 (SMED30021535) in cells (dots) of each of the 12 neoblast clusters.

 

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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 slc31a-3 (SMED30021535) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for slc31a-3 (SMED30021535) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30021535

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30021535h1SMcG0013096 Contig5836GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30021535h1SMcG0013096 dd_Smed_v4_6792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30021535h1SMcG0013096 dd_Smed_v4_6792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021535h1SMcG0013096 dd_Smed_v4_6792_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
Homology
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BLAST of slc31a-3 vs. Ensembl Xenopus
Match: tax1bp1 (Tax1 binding protein 1 [Source:Xenbase;Acc:XB-GENE-492305])

HSP 1 Score: 46.9802 bits (110), Expect = 5.181e-6
Identity = 21/52 (40.38%), Postives = 34/52 (65.38%), Query Frame = 2 
Query:  416 SGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKL 571
            S  ++ QV++ ++LML VM +N AIFI++V G+G GYF+      +Y K  +
Sbjct:  123 SLLHMSQVVLGYMLMLCVMSYNAAIFIAVVLGSGLGYFLAFPLLSKYPKPHI 174
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BLAST of slc31a-3 vs. TrEMBL
Match: A0A0H3YKE8 (Slc31a-3 OS=Schmidtea mediterranea OX=79327 GN=slc31a-3 PE=2 SV=1)

HSP 1 Score: 308.531 bits (789), Expect = 7.340e-104
Identity = 181/181 (100.00%), Postives = 181/181 (100.00%), Query Frame = 2 
Query:   80 MENYFKLDNSFVFLMENLQIDSKWKLSCTCIGFFILASLYEIVXXXXXXXXXXWLSRNEFENSRNKIKLIPXXXXXXXXXXXXXXXXFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 622
            MENYFKLDNSFVFLMENLQIDSKWKLSCTCIGFFILASLYEIVKIFNNNIFKNWLSRNEFENSRNKIKLIPKQKSKYEESSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV
Sbjct:    1 MENYFKLDNSFVFLMENLQIDSKWKLSCTCIGFFILASLYEIVKIFNNNIFKNWLSRNEFENSRNKIKLIPKQKSKYEESSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 181
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BLAST of slc31a-3 vs. Ensembl Nematostella
Match: EDO27532 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T904])

HSP 1 Score: 46.9802 bits (110), Expect = 9.194e-7
Identity = 37/141 (26.24%), Postives = 62/141 (43.97%), Query Frame = 2 
Query:  113 VFLMENLQIDSKWKLSCTCIGFFILASLYEIVXXXXXXXXXXWLSRNEFENSRNKIKLIPXXXXXXXXXXXXXXXXFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIF 535
            V L E   +D+   +  +CI  FILA LYE +K          +SR   +     +  +      Y  +        E R    + +     + +  +   S  +++QV +S+ LML  M +NG + I++  G GFGYF+F
Sbjct:   10 VILFEGWSVDTVGGMIGSCIAVFILAVLYEGLK----------VSREMLKRKYGYVMSVDMDTKVYGSNQNQTVTVTETRGHIPRSK-----ICNLHHFIQSLLHIVQVTLSYFLMLIFMTYNGWLCIAVALGAGFGYFLF 135
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BLAST of slc31a-3 vs. Planmine SMEST
Match: SMESG000020554.1 (SMESG000020554.1)

HSP 1 Score: 231.876 bits (590), Expect = 9.463e-77
Identity = 128/128 (100.00%), Postives = 128/128 (100.00%), Query Frame = 2 
Query:  239 WLSRNEFENSRNKIKLIPXXXXXXXXXXXXXXXXFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 622
            WLSRNEFENSRNKIKLIPKQKSKYEESSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV
Sbjct:   86 WLSRNEFENSRNKIKLIPKQKSKYEESSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 213
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BLAST of slc31a-3 vs. Planmine SMEST
Match: SMESG000020554.1 (SMESG000020554.1)

HSP 1 Score: 228.024 bits (580), Expect = 4.205e-75
Identity = 126/129 (97.67%), Postives = 126/129 (97.67%), Query Frame = 2 
Query:  239 WLSRNEFENSRNKIKLIPXXXXX-XXXXXXXXXXXFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 622
            WLSRNEFENSRNKIKLIPKQKSK  E SSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV
Sbjct:   86 WLSRNEFENSRNKIKLIPKQKSKYEESSSKTKEVKFECRNETEKKRKWEGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYFIFRKSHYRYSKSKLTTSERPKMEVDKILPKV 214
The following BLAST results are available for this feature:
BLAST of slc31a-3 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
tax1bp15.181e-640.38Tax1 binding protein 1 [Source:Xenbase;Acc:XB-GENE... [more]
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BLAST of slc31a-3 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0H3YKE87.340e-104100.00Slc31a-3 OS=Schmidtea mediterranea OX=79327 GN=slc... [more]
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BLAST of slc31a-3 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO275329.194e-726.24Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of slc31a-3 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of slc31a-3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000020554.19.463e-77100.00SMESG000020554.1[more]
SMESG000020554.14.205e-7597.67SMESG000020554.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30021535
GenBankAKN21633.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021535 ID=SMED30021535|Name=slc31a-3|organism=Schmidtea mediterranea sexual|type=transcript|length=782bp
GGACAATTATCCATTTAATAGCGAATCCAAACCGCACAATTAAAATTTGA
TAGTATTAATTCGGCTTTCAAGTTATACAATGGAAAATTACTTCAAATTA
GATAACTCTTTCGTTTTTCTAATGGAAAATTTACAAATTGATTCAAAATG
GAAGTTGTCCTGCACTTGTATCGGGTTTTTCATCCTGGCCAGTCTTTATG
AAATTGTTAAAATATTCAATAATAATATTTTCAAAAATTGGCTTTCGAGA
AATGAATTTGAAAATTCTAGGAATAAAATTAAATTAATTCCCAAGCAAAA
ATCTAAGTACGAAGAAAGTTCAAAAACGAAAGAGGTAAAATTCGAATGTC
GGAATGAAACTGAAAAAAAACGGAAATGGGAAGGAATAATGCTGAGTTGG
CAAAACTGTTGCCACTCTGGGTTCTACCTGTTACAAGTGCTGATCAGCTT
CATATTGATGCTATCAGTTATGTATTTCAATGGCGCTATCTTCATATCAA
TTGTCTTTGGGAATGGATTTGGTTACTTTATTTTCAGGAAGTCTCACTAC
CGATATTCTAAGTCCAAGCTGACAACCTCTGAAAGGCCTAAAATGGAAGT
TGACAAAATCCTCCCAAAAGTCTAATTGTAGAAATAATTGACAATTGACT
TAATTTTTTTTACTTTTTGTATGCAGTTTAAATTATTTCGATTTCGGATA
TATTTACTTTGTCATTTGGAAAAATGACGTTAAGAAGCTATTCTTTGGCA
AATAAAATGTGACTCGTACCAATATAATGTAG
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protein sequence of SMED30021535-orf-1

>SMED30021535-orf-1 ID=SMED30021535-orf-1|Name=SMED30021535-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=182bp
MENYFKLDNSFVFLMENLQIDSKWKLSCTCIGFFILASLYEIVKIFNNNI
FKNWLSRNEFENSRNKIKLIPKQKSKYEESSKTKEVKFECRNETEKKRKW
EGIMLSWQNCCHSGFYLLQVLISFILMLSVMYFNGAIFISIVFGNGFGYF
IFRKSHYRYSKSKLTTSERPKMEVDKILPKV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
Vocabulary: INTERPRO
TermDefinition
IPR007274Cop_transporter
Vocabulary: biological process
TermDefinition
GO:0035434copper ion transmembrane transport
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: molecular function
TermDefinition
GO:0005375copper ion transmembrane transporter activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007274Ctr copper transporterPFAMPF04145Ctrcoord: 4..152
e-value: 3.3E-27
score: 95.9
IPR007274Ctr copper transporterPANTHERPTHR12483SOLUTE CARRIER FAMILY 31 COPPER TRANSPORTERScoord: 1..157
NoneNo IPR availablePANTHERPTHR12483:SF27COPPER TRANSPORTER 1A, ISOFORM C-RELATEDcoord: 1..157
NoneNo IPR availableTMHMMTMhelixcoord: 130..152