DUF862 domain-containing protein

Overview
NameDUF862 domain-containing protein
Smed IDSMED30002215
Length (bp)590
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 DUF862 domain-containing protein (SMED30002215) t-SNE clustered cells

Violin plots show distribution of expression levels for DUF862 domain-containing protein (SMED30002215) 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 DUF862 domain-containing protein (SMED30002215) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DUF862 domain-containing protein (SMED30002215) 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



SMED30002215

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
epidermisSMED30002215SMESG000024669.1 dd_Smed_v4_3583_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002215SMESG000024669.1 dd_Smed_v4_3583_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30002215SMESG000024669.1 SMED30002215smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30002215SMESG000024669.1 SMED30002215smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 4 cellSMED30002215SMESG000024669.1 dd_Smed_v4_3583_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 DUF862 domain-containing protein vs. TrEMBL
Match: E9GQZ7 (Uncharacterized protein OS=Daphnia pulex OX=6669 GN=DAPPUDRAFT_305262 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 3.582e-6
Identity = 38/133 (28.57%), Postives = 64/133 (48.12%), Query Frame = 3 
Query:  162 DLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEER--------NLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDF---NSKGFGDKVYDNII 527
            D S+ I  V  Y  P++W Q++ +  +H FIV+ET+ ++WS+EK+  GI IQ+ +   +V+ +     R        NL +  E          ++V+ +   E        DY F   N K F + +YDN +
Sbjct:   48 DSSEKINEVRYYTHPLNWWQMSKYVLHHAFIVLETESWWWSIEKDEGGITIQRSKHLENVLDQCRRHGRITGLATWINLGVTCEKKGPSHASVIDVVNRMWREECLHS----DYHFLQNNCKHFANTIYDNFV 176
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BLAST of DUF862 domain-containing protein vs. TrEMBL
Match: E9GQ32 (Uncharacterized protein OS=Daphnia pulex OX=6669 GN=DAPPUDRAFT_320721 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 5.989e-6
Identity = 45/160 (28.12%), Postives = 71/160 (44.38%), Query Frame = 3 
Query:   69 ESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGD--------FGQFRNLVDWIEINELQKGYSCNDYDF---NSKGFGDKVY 515
            E+D   GR FFI   +    + + G+       S  IL V  Y  P++ +Q+T    +H FIV  T+  +WS+E+N LG+ IQ+ +    V  K   ++R       DL G         FG     +  +  +  ++ Y   DYD    N K F + +Y
Sbjct:   25 EADSSTGRDFFITAADLRKGVESLGK-------SDNILEVRYYTNPLYGVQVTQLVLHHAFIVFLTERAWWSIERNELGVTIQRSKKIEFVRDKFRRQDRTT-----DLFGSGIHWEKRCFGITNVTLKELLTHICREDYLNEDYDLLENNCKHFAENIY 172
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024669.1 (SMESG000024669.1)

HSP 1 Score: 330.102 bits (845), Expect = 3.004e-117
Identity = 160/160 (100.00%), Postives = 160/160 (100.00%), Query Frame = 3 
Query:   60 MCFESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNIINKQF 539
            MCFESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNIINKQF
Sbjct:    1 MCFESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNIINKQF 160
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024663.1 (SMESG000024663.1)

HSP 1 Score: 155.606 bits (392), Expect = 2.640e-48
Identity = 68/150 (45.33%), Postives = 105/150 (70.00%), Query Frame = 3 
Query:   78 DWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNII 527
            +WE RI FI +T+ PNE++NG EM++  D S+ I+ VWKYK  + W Q+TSFY YH F++ ET++++WS+EKN  GIWIQK + K+++++K+ G ERN    L+  QG F   +N+++WIE  EL+  Y   + D N +GF D+ Y++I+
Sbjct:   13 NWESRIHFINNTSAPNEVFNGSEMRKLIDTSETIVKVWKYKEKLVWWQITSFYLYHAFVIFETNDWYWSMEKNGSGIWIQKSKSKDNLVAKIGGNERNSTTLLDSCQGRFVTIKNIIEWIEKEELKSAYWYMNSDDNCQGFADRGYNHIV 162
[Close]
BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024661.1 (SMESG000024661.1)

HSP 1 Score: 143.665 bits (361), Expect = 1.219e-43
Identity = 65/150 (43.33%), Postives = 98/150 (65.33%), Query Frame = 3 
Query:   78 DWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNII 527
            +W  RIFFI +T+ PN+++ G EM++  D S+ I+  WKYK  + W Q+TSF+ YH F++ ET +++WS+EKN  GIWIQK + KN++++K  G ERN    L+   G+F     L++W+E NEL   Y   +  FN +GF D+ Y +II
Sbjct:   13 NWLSRIFFINNTSAPNDVFKGSEMRKLIDTSETIIQAWKYKQKLVWFQITSFFLYHAFVIFETKDWYWSIEKNGSGIWIQKSKSKNELVTKNGGNERNSTTLLDSEFGNFITIGELIEWVENNELINRYFYIETYFNCQGFADRAYQHII 162
[Close]
BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024649.1 (SMESG000024649.1)

HSP 1 Score: 129.798 bits (325), Expect = 2.667e-38
Identity = 66/159 (41.51%), Postives = 97/159 (61.01%), Query Frame = 3 
Query:   54 LAMCFESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNIIN 530
            +++  +   WE ++F I D   PN LY G +MK+  +LS+ I  VW+YK P+   QLTS  FYHIF+V++TD++ WS+EKN  GIW+QK    N+++ K  G ER  V  L    G+F + ++L DWI  NEL+  Y   D  +N KGF ++ +  I N
Sbjct:    1 MSLDIKGGKWESQLFLINDIRHPNNLYYGSQMKQMGNLSERIQQVWRYKEPLKSWQLTSVIFYHIFLVLQTDKWNWSIEKNGTGIWVQKSENHNELLKKKGGVERKSVSLLGHRIGNFVRIKSLFDWIIKNELKIKYYWLDSYYNCKGFVERAFKFITN 159
[Close]
BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000070711.1 (SMESG000070711.1)

HSP 1 Score: 92.8189 bits (229), Expect = 7.416e-24
Identity = 48/154 (31.17%), Postives = 86/154 (55.84%), Query Frame = 3 
Query:   78 DWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTSFYFY-----HIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNI 524
            +WEG+IF+I D   P E+YN  E+ ++    + I+ +  YKTP+  +       Y     H F+V++T  F++S +KN  GI+IQK   K+DV+  + G++R+  + L+        F  ++ WI  +EL++GY   +++ N +GF   +Y  +
Sbjct:    6 NWEGKIFYIDDLERPEEIYNQHEILQKIGSKETIVEIDVYKTPLQGLDFVEEKVYEKIVHHAFVVVKTTNFYFSFDKNGRGIYIQKSENKDDVLKSVFGDQRSRPVKLKSNTNVRVDFDTIIKWIIRDELKRGYHILNFETNCQGFSASLYTKV 159
The following BLAST results are available for this feature:
BLAST of DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
E9GQZ73.582e-628.57Uncharacterized protein OS=Daphnia pulex OX=6669 G... [more]
E9GQ325.989e-628.13Uncharacterized protein OS=Daphnia pulex OX=6669 G... [more]
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BLAST of DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein 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 DUF862 domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of DUF862 domain-containing protein 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 DUF862 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024669.13.004e-117100.00SMESG000024669.1[more]
SMESG000024663.12.640e-4845.33SMESG000024663.1[more]
SMESG000024661.11.219e-4343.33SMESG000024661.1[more]
SMESG000024649.12.667e-3841.51SMESG000024649.1[more]
SMESG000070711.17.416e-2431.17SMESG000070711.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002215 ID=SMED30002215|Name=DUF862 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=590bp
TCCGATCTTAAATTCCAAGTGCAATTTGAATTAAGCTATTCAACTAAGAA
TTATTAGCAATGTGTTTCGAATCAGATGATTGGGAGGGTCGAATATTTTT
CATCAGAGACACGAATTGTCCCAATGAGCTTTACAATGGCGGAGAAATGA
AGAGGCAATTCGACCTTTCAAAGCCGATTTTGCACGTATGGAAATACAAA
ACCCCAATGCATTGGATCCAGTTGACTTCGTTTTATTTTTATCACATTTT
CATTGTTATAGAAACTGATGAGTTTTTTTGGTCGGTGGAAAAGAACAATC
TCGGTATTTGGATTCAGAAAGGCAGATTCAAGAATGATGTAATCAGCAAA
ATGGCGGGTGAAGAAAGAAATTTGGTGATTTGTCTAGAAGACTTGCAAGG
TGATTTTGGACAATTTAGAAATCTTGTTGACTGGATTGAGATAAATGAAT
TGCAAAAGGGTTATTCGTGCAACGATTACGATTTCAACAGCAAAGGGTTT
GGGGATAAAGTTTACGATAACATTATTAATAAACAATTTTAATATTCATA
ACTGTGCTTCAATTTTTATTGAATTCACATCTTATCCAAC
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protein sequence of SMED30002215-orf-1

>SMED30002215-orf-1 ID=SMED30002215-orf-1|Name=SMED30002215-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MCFESDDWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPM
HWIQLTSFYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAG
EERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDK
VYDNIINKQF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000026gut
PLANA:0002142parenchyma