XendoU domain-containing protein

Overview
NameXendoU domain-containing protein
Smed IDSMED30001357
Length (bp)677
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 XendoU domain-containing protein (SMED30001357) t-SNE clustered cells

Violin plots show distribution of expression levels for XendoU domain-containing protein (SMED30001357) 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 XendoU domain-containing protein (SMED30001357) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for XendoU domain-containing protein (SMED30001357) 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




SMED30001357

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
headSMED30001357SMESG000008612.1 SmedASXL_000499SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30001357SMESG000008612.1 dd_Smed_v4_25168_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30001357SMESG000008612.1 dd_Smed_v4_25168_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
headSMED30001357SMESG000008612.1 dd_Smed_v6_25168_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30001357SMESG000008612.1 OX_Smed_1.0.16036ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of XendoU domain-containing protein vs. TrEMBL
Match: A0A267FPC5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015604g2 PE=4 SV=1)

HSP 1 Score: 100.138 bits (248), Expect = 2.862e-22
Identity = 63/188 (33.51%), Postives = 97/188 (51.60%), Query Frame = 3
Query:   27 MSLFNS-----NLPFLVLIRFQHNDAAAYHNSVIRQKPLLR---TIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDEN-TIVEILEIVKYRSPSRFSSECLDKIDSAKEN--NIVAVPRYATEVLRGSWNPLYIIINVWS 557
            M+LF       N+ +  +IRF  + A  YHNSV R   +++      E   L  + R+E  E           R+ YG G++ FP+    + W E + EVRQ++WL+  DIVIVP+R    + D+   ++EI +   +R  + F  E L  +++  E   NIVA P Y    +R SW+P Y++IN WS
Sbjct:    1 MALFRGLEEPENVGYYAVIRFTQDIAYNYHNSVKRTASIIQRSHGGHECAFLPDVQRIEGDE-----------RRLYGYGVLYFPNFDAAKYWYECTNEVRQQDWLWSADIVIVPAR---GAFDKGMAVLEINDWSAFRDQTAFEDEYLKGLNNTTEGRWNIVACPDYLQYRMRSSWSPKYLVINQWS 174          
BLAST of XendoU domain-containing protein vs. TrEMBL
Match: A0A267DNX7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015604g1 PE=4 SV=1)

HSP 1 Score: 98.9821 bits (245), Expect = 6.674e-22
Identity = 60/177 (33.90%), Postives = 93/177 (52.54%), Query Frame = 3
Query:   45 NLPFLVLIRFQHNDAAAYHNSVIRQKPLLR---TIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDEN-TIVEILEIVKYRSPSRFSSECLDKIDSAKEN--NIVAVPRYATEVLRGSWNPLYIIINVWS 557
            N+ +  +IRF  + A  YHNSV R   +++      E   L  + R+E  E           R+ YG G++ FP+    + W E + EVRQ++WL+  DIVIVP+R    + D+   ++EI +   +R  + F  E L  +++  E   NIVA P Y    +R SW+P Y++IN WS
Sbjct:   12 NVGYYAVIRFTQDIAYNYHNSVKRTASIIQRSHGGHECAFLPDVQRIEGDE-----------RRLYGYGVLYFPNFDAAKYWYECTNEVRQQDWLWSADIVIVPAR---GAFDKGMAVLEINDWSAFRDQTAFEDEYLKGLNNTTEGRWNIVACPDYLQYRMRSSWSPKYLVINQWS 174          
BLAST of XendoU domain-containing protein vs. TrEMBL
Match: A0A267G5A5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig002947g3 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 8.677e-20
Identity = 55/173 (31.79%), Postives = 95/173 (54.91%), Query Frame = 3
Query:   45 NLPFLVLIRFQHNDAAAYHNSVIRQKPLLRTIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDEN-TIVEILEIVKYRSPSRFSSECLDKIDSAKEN--NIVAVPRYATEVLRGSWNPLYIIINVW 554
            N+ +  +IRF  + A  YHNS+ R   +++          +  ++LIE  G+       R++YG G++ FPS    + W E + EVRQ++WL+   I++VP+R    + D+  ++VEI +   +R  + F +E L +++   +   N+VA P Y    LR SW+P Y++IN W
Sbjct:   12 NVGYYAVIRFGKDIAYNYHNSIKRIASIIQRSHNGQDCAFLPDVQLIE--GED------RRQYGYGLLYFPSFEAAKYWYECTNEVRQQDWLWSAAILLVPAR---GAFDKAMSVVEINDWSDFRDQTAFENEYLAELNDPSDGRWNVVACPDYLQYRLRSSWSPKYLVINQW 173          
BLAST of XendoU domain-containing protein vs. TrEMBL
Match: A0A267DBP7 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig002947g1 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 9.488e-20
Identity = 55/173 (31.79%), Postives = 95/173 (54.91%), Query Frame = 3
Query:   45 NLPFLVLIRFQHNDAAAYHNSVIRQKPLLRTIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDEN-TIVEILEIVKYRSPSRFSSECLDKIDSAKEN--NIVAVPRYATEVLRGSWNPLYIIINVW 554
            N+ +  +IRF  + A  YHNS+ R   +++          +  ++LIE  G+       R++YG G++ FPS    + W E + EVRQ++WL+   I++VP+R    + D+  ++VEI +   +R  + F +E L +++   +   N+VA P Y    LR SW+P Y++IN W
Sbjct:   21 NVGYYAVIRFGKDIAYNYHNSIKRIASIIQRSHNGQDCAFLPDVQLIE--GED------RRQYGYGLLYFPSFEAAKYWYECTNEVRQQDWLWSAAILLVPAR---GAFDKAMSVVEINDWSDFRDQTAFENEYLAELNDPSDGRWNVVACPDYLQYRLRSSWSPKYLVINQW 182          
BLAST of XendoU domain-containing protein vs. TrEMBL
Match: A0A1I8FH46 (XendoU domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.177e-10
Identity = 45/147 (30.61%), Postives = 74/147 (50.34%), Query Frame = 3
Query:   45 NLPFLVLIRFQHNDAAAYHNSVIRQKPLLR---TIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDEN-TIVEILEIVKYRSPSRFSSECLDKIDSAKEN 473
            N+ +  +IRF  + A  YHNSV R   +++      E   L  + R+E  E           R+ YG G++ FP+    + W E + EVRQ++WL+  DIVIVP+R    + D+   ++EI +   +R  + F  E L  +++  E 
Sbjct:  432 NVGYYAVIRFTQDIAYNYHNSVKRTASIIQRSHGGHECAFLPDVQRIEGDE-----------RRLYGYGVLYFPNFDAAKYWYECTNEVRQQDWLWSADIVIVPAR---GAFDKGMAVLEINDWSAFRDQTAFEDEYLKGLNNTTEG 564          
BLAST of XendoU domain-containing protein vs. Planmine SMEST
Match: SMESG000008612.1 (SMESG000008612.1)

HSP 1 Score: 244.973 bits (624), Expect = 9.196e-84
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 3
Query:  288 MSYEVRQKEWLFPVDIVIVPSRWRIKSIDENTIVEILEIVKYRSPSRFSSECLDKIDSAKENNIVAVPRYATEVLRGSWNPLYIIINVWSSDTEYNSNSHFALNDISDLVVGYSYIGHCY 647
            MSYEVRQKEWLFPVDIVIVPSRWRIKSIDENTIVEILEIVKYRSPSRFSSECLDKIDSAKENNIVAVPRYATEVLRGSWNPLYIIINVWSSDTEYNSNSHFALNDISDLVVGYSYIGHCY
Sbjct:    1 MSYEVRQKEWLFPVDIVIVPSRWRIKSIDENTIVEILEIVKYRSPSRFSSECLDKIDSAKENNIVAVPRYATEVLRGSWNPLYIIINVWSSDTEYNSNSHFALNDISDLVVGYSYIGHCY 120          
BLAST of XendoU domain-containing protein vs. Planmine SMEST
Match: SMESG000069776.1 (SMESG000069776.1)

HSP 1 Score: 97.4413 bits (241), Expect = 7.793e-25
Identity = 55/170 (32.35%), Postives = 92/170 (54.12%), Query Frame = 3
Query:   60 VLIRFQHNDAAAYHNSVIRQKPLLRTIFEALPLLTISRLELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFPVDIVIVPSRWRIKSIDENT-IVEILEIVKYRSPSRFSSECLDKIDSAK--ENNIVAVPRYATEVLRGSWNPLYIIINVWSS 560
            ++  F+ +DA +Y NS++RQ  +L   F    +    +++ IE        T    ++G+GII FP     ++W E S+E+RQ +WL  V +++VP+R     +D    IVE  E   +R   +F +E L  +++A   +NNI+A P Y    LRG+W P Y+ +  W+S
Sbjct:   14 LISHFKESDAYSYRNSIVRQITILERNFCGREVAFCQKMQPIE--------TNTENKFGIGIIHFPDFQIAKNWYESSHEIRQPDWLNNVTLILVPAR---NDVDFTMPIVEFAEWNFFRDVQKFQNEYLSHLNTADKGQNNIIAAPEYTYVKLRGNWCPKYLAVTQWAS 172          
The following BLAST results are available for this feature:
BLAST of XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267FPC52.862e-2233.51Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DNX76.674e-2233.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267G5A58.677e-2031.79Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DBP79.488e-2031.79Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8FH462.177e-1030.61XendoU domain-containing protein OS=Macrostomum li... [more]
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BLAST of XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU 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 XendoU domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000008612.19.196e-84100.00SMESG000008612.1[more]
SMESG000069776.17.793e-2532.35SMESG000069776.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001357 ID=SMED30001357|Name=XendoU domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=677bp
TTTCAAACAAAAGAAGATAATCTGTAATGTCTTTATTCAATTCGAATTTG
CCATTTCTTGTATTGATACGTTTTCAACACAATGATGCAGCGGCCTATCA
TAATAGCGTCATCAGACAGAAACCCTTATTAAGAACAATATTTGAAGCTT
TACCTTTGCTGACGATCTCACGCCTTGAATTAATTGAAGAAATAGGAAAA
AAATCCGAATTCACAATCCCTAGGCAAAGATATGGGCTTGGAATTATTGC
GTTCCCGTCTATTGGTAAAATTCGAGATTGGCTGGAAATGAGCTATGAAG
TCCGACAGAAAGAATGGCTATTTCCAGTTGATATTGTCATTGTGCCATCG
AGATGGAGAATCAAAAGTATCGATGAAAATACTATTGTTGAAATTCTGGA
AATTGTAAAATATCGCAGTCCATCAAGATTTAGTTCAGAGTGTTTGGATA
AAATTGACTCTGCAAAAGAAAATAATATTGTTGCTGTTCCTCGATACGCT
ACTGAAGTTCTTAGAGGAAGTTGGAATCCATTATATATAATAATTAATGT
TTGGTCTTCGGACACGGAATATAATTCGAACTCACATTTTGCATTAAATG
ATATAAGTGACTTAGTCGTAGGTTACTCTTATATTGGGCATTGTTATTAA
ATGGCTGACAATATAACTCAAACATTA
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protein sequence of SMED30001357-orf-1

>SMED30001357-orf-1 ID=SMED30001357-orf-1|Name=SMED30001357-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=208bp
MSLFNSNLPFLVLIRFQHNDAAAYHNSVIRQKPLLRTIFEALPLLTISRL
ELIEEIGKKSEFTIPRQRYGLGIIAFPSIGKIRDWLEMSYEVRQKEWLFP
VDIVIVPSRWRIKSIDENTIVEILEIVKYRSPSRFSSECLDKIDSAKENN
IVAVPRYATEVLRGSWNPLYIIINVWSSDTEYNSNSHFALNDISDLVVGY
SYIGHCY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004521endoribonuclease activity
Vocabulary: biological process
TermDefinition
GO:0090502RNA phosphodiester bond hydrolysis, endonucleolytic
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head