DUF4817 domain-containing protein

Overview
NameDUF4817 domain-containing protein
Smed IDSMED30005349
Length (bp)2212
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 DUF4817 domain-containing protein (SMED30005349) t-SNE clustered cells

Violin plots show distribution of expression levels for DUF4817 domain-containing protein (SMED30005349) 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 DUF4817 domain-containing protein (SMED30005349) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DUF4817 domain-containing protein (SMED30005349) 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



SMED30005349

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
intestinal phagocyteSMED30005349SMESG000065415.1 Contig3049newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005349SMESG000065415.1 Contig3049uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005349SMESG000037599.1 Contig3049newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005349SMESG000037599.1 Contig3049uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30005349SMESG000065415.1 dd_Smed_v4_10251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30005349SMESG000065415.1 dd_Smed_v4_10251_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
[Close]
BLAST of DUF4817 domain-containing protein vs. TrEMBL
Match: A0A154PSY0 (Uncharacterized protein OS=Dufourea novaeangliae OX=178035 GN=WN55_08618 PE=4 SV=1)

HSP 1 Score: 102.834 bits (255), Expect = 6.043e-20
Identity = 49/97 (50.52%), Postives = 65/97 (67.01%), Query Frame = 3 
Query: 1389 LDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEIGNMAGYWWKQDGATAHTSRATI 1679
            L+G V+ QN R W TEN   VH  QLHP K TV CG++SERIIGP+FFEN     + + A ++R +L NF+ P + N    W++Q GATAHT+R T+
Sbjct:   51 LNGFVNKQNCRIWATENPRAVHQQQLHPLKCTVWCGISSERIIGPYFFENEAGNAITINAAQYRAMLENFLRPAVENHPQLWFQQGGATAHTARETM 147

HSP 2 Score: 25.7942 bits (55), Expect = 6.043e-20
Identity = 10/14 (71.43%), Postives = 12/14 (85.71%), Query Frame = 2 
Query: 1340 NINFIHNLIMGDEA 1381
            + +FIHNLIM DEA
Sbjct:   34 STDFIHNLIMSDEA 47

HSP 3 Score: 77.7962 bits (190), Expect = 5.258e-11
Identity = 41/96 (42.71%), Postives = 58/96 (60.42%), Query Frame = 3 
Query: 1389 LDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEI--GNMAGYWWKQDGATAHTSR 1670
            L G V+ QN R WG+EN   +    +HP++VTV CG  S  IIGP FFEN     V V  +R+R +L +F+ P+I   ++   W++QDGAT   S+
Sbjct:  258 LGGYVNKQNCRIWGSENPHVIVEKPMHPQRVTVWCGFWSGGIIGPFFFENEQGNAVTVNGDRYRAMLSDFLFPKIEEDDIDDIWFQQDGATNQDSK 353
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BLAST of DUF4817 domain-containing protein vs. TrEMBL
Match: V5G1X8 (DUF4817 domain-containing protein OS=Anoplophora glabripennis OX=217634 PE=4 SV=1)

HSP 1 Score: 95.1301 bits (235), Expect = 7.417e-18
Identity = 45/95 (47.37%), Postives = 64/95 (67.37%), Query Frame = 3 
Query: 1386 FLDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEI--GNMAGYWWKQDGATAHT 1664
             L G+V+ QN+RFWGT+N   +H + LHP K TV CG+ +  IIGP+FFEN     V V AER+++++ NF+ PE+    +   W +QDGATAH+
Sbjct:  164 LLSGHVNKQNSRFWGTQNPQLIHETSLHPLKTTVWCGIHAGNIIGPYFFENDQGVGVTVTAERYQDVIRNFLMPEMEEQGLEDMWIQQDGATAHS 258
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BLAST of DUF4817 domain-containing protein vs. TrEMBL
Match: J9KF38 (DUF4817 domain-containing protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 94.3597 bits (233), Expect = 2.400e-17
Identity = 44/101 (43.56%), Postives = 67/101 (66.34%), Query Frame = 3 
Query: 1389 LDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEIG--NMAGYWWKQDGATAHTSRATIWI 1685
            + G V+ QN R WGTEN+  +   Q+HP +VTV CG  S  +IGP+FF++ +E  V V  ER+R+ +  F+ P +   ++   W++QDGAT+HT+RATI +
Sbjct:  165 MSGFVNKQNCRLWGTENSQQIEQRQMHPERVTVWCGFWSGGVIGPYFFQDEYENTVTVNGERYRDNITEFLWPALNDFDITNKWFQQDGATSHTARATIML 265
[Close]
BLAST of DUF4817 domain-containing protein vs. TrEMBL
Match: E2BXQ8 (Uncharacterized protein (Fragment) OS=Harpegnathos saltator OX=610380 GN=EAI_06736 PE=4 SV=1)

HSP 1 Score: 88.5817 bits (218), Expect = 3.500e-17
Identity = 43/99 (43.43%), Postives = 65/99 (65.66%), Query Frame = 3 
Query: 1389 LDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEIGNM--AGYWWKQDGATAHTSRATI 1679
            LDG V+ QN R WG+EN   +   Q+HP++VTV CG  +  IIGP FF+N+  + + V   R+R++++ F  P++ +M     W++QDGAT HT+R TI
Sbjct:   12 LDGLVNRQNCRIWGSENPRVIVEKQMHPQRVTVWCGFWAGGIIGPFFFKNAAGQAITVNGARYRDMIIQFFVPKLQDMDVDDMWFQQDGATCHTARETI 110
[Close]
BLAST of DUF4817 domain-containing protein vs. TrEMBL
Match: V5GQ71 (Transposase (Fragment) OS=Anoplophora glabripennis OX=217634 GN=TC3A PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.314e-16
Identity = 46/99 (46.46%), Postives = 66/99 (66.67%), Query Frame = 3 
Query: 1389 LDGNVD*QNTRFWGTENTCNVHASQLHPRKVTV*CGVTSERIIGPHFFENSHEKVVIVIAERFREILLNFV*PEIG--NMAGYWWKQDGATAHTSRATI 1679
            L+G V+ QN R+W   N   V   QL+P+KVTV CG+ +  IIGP+FFEN + + V V  ER+R +L NF+ P++   ++ G W++QDGAT HT+  TI
Sbjct:   12 LNGYVNKQNMRYWEENNPRQVLEKQLYPQKVTVWCGLWTGGIIGPYFFENDNGERVTVNGERYRLMLTNFLWPQLDDLDLDGMWFQQDGATCHTAAETI 110
[Close]
BLAST of DUF4817 domain-containing protein vs. Planmine SMEST
Match: SMESG000065415.1 (SMESG000065415.1)

HSP 1 Score: 265.003 bits (676), Expect = 2.274e-83
Identity = 127/130 (97.69%), Postives = 127/130 (97.69%), Query Frame = 1 
Query:  385 MEWQMTYKPDRYFKDICCSNDQETSIKTKDKHFYFFEYFPSDPIPNKENFEAFIRNFQLCLSEIRQNPRFICGLLLKDAFDSGKFPFLNFVCLKYDEDNFISPSKKWISLSSDCSKGLCTKFHNSLIGEF 774
            MEWQMTYKPDRYFKDICCSNDQETSIKTKDKHFYFFEYFPSDPIPNKEN EAFIRNFQLCLSEIRQNPRFICGLLLKDAFDSGKFPFLNFVCLKYDEDNFISPSKKWISLSSDCSKGLCTKFHNSLI  F
Sbjct:    1 MEWQMTYKPDRYFKDICCSNDQETSIKTKDKHFYFFEYFPSDPIPNKENVEAFIRNFQLCLSEIRQNPRFICGLLLKDAFDSGKFPFLNFVCLKYDEDNFISPSKKWISLSSDCSKGLCTKFHNSLIAGF 130

HSP 2 Score: 250.751 bits (639), Expect = 6.579e-78
Identity = 120/122 (98.36%), Postives = 122/122 (100.00%), Query Frame = 1 
Query: 1672 LLSGFEEYESLALCSDTNQPKLNSVFFISSFKASGNLDWLEKNWRQWTGVVCILKNLSHSLRRDLQKISFYRRVVPTGEFMFVLICEFTCENTELYRLKDLMERMNERYSGYSQVYVVHSMY 2037
            L++GFEEYESLALCSDTNQPKLNSVFFISSFKASGNLDWLEKNWRQWTGVVCILKNLSHSLRRDLQKISFYRRVVPTGEFMFVLICEFTCENTELYRLKDLMERMNERYSGYSQVYVVHSMY
Sbjct:  126 LIAGFEEYESLALCSDTNQPKLNSVFFISSFKASGNLDWLEKNWRQWTGVVCILKNLSHSLRRDLQKISFYRRVVPTGEFMFVLICEFTCENTELYRLKDLMERMNERYSGYSQVYVVHSMY 247
The following BLAST results are available for this feature:
BLAST of DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A154PSY06.043e-2050.52Uncharacterized protein OS=Dufourea novaeangliae O... [more]
V5G1X87.417e-1847.37DUF4817 domain-containing protein OS=Anoplophora g... [more]
J9KF382.400e-1743.56DUF4817 domain-containing protein OS=Acyrthosiphon... [more]
E2BXQ83.500e-1743.43Uncharacterized protein (Fragment) OS=Harpegnathos... [more]
V5GQ711.314e-1646.46Transposase (Fragment) OS=Anoplophora glabripennis... [more]
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BLAST of DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 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 DUF4817 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000065415.12.274e-8397.69SMESG000065415.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005349 ID=SMED30005349|Name=DUF4817 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=2212bp
TGCTTTGCATTTTTATTCAACATCTGTTTCGAATCTAACAGTTTTTAATT
GAAATTATTCATTGCCTGTCACAGCATGAAGCTCCCAGACTTGTCTCACG
AACAGTCATCTCCCAAATATTTGGATTCCCAGCCGACTGATTGCCCACGA
TCAAACCATCGAATCCAACCAATGCATTTGTGTTGTCACACTACAACACA
AATTTTATCACATATGGAAAACTTTTCTCTCCGTCTATTTCTCTATCTCT
CTCTTCTCTCAACCTCCCTTTCTCTAGCTGTCGGTTATTTAGGATGCTAA
GCTATTGGTGGAAAGTAATTTTAATTTAATATTATTAATAATATCTTTTT
CGACTTATTATTAAAACACTTTCAACAAATTCCCATGGAATGGCAAATGA
CCTACAAGCCTGACCGTTATTTCAAAGATATCTGTTGCAGTAACGATCAA
GAAACGTCTATAAAAACAAAAGATAAACATTTTTATTTTTTCGAATATTT
CCCATCAGATCCGATTCCAAATAAAGAAAATTTTGAAGCATTTATTCGAA
ACTTTCAGCTCTGTTTGTCAGAAATTCGTCAAAATCCGAGATTTATCTGT
GGTCTTCTTTTAAAGGACGCCTTTGATTCAGGAAAGTTTCCGTTTTTAAA
TTTCGTTTGTCTGAAATATGATGAAGACAATTTTATCAGTCCAAGCAAAA
AATGGATATCCTTATCTTCAGACTGCTCCAAAGGTCTTTGTACCAAGTTT
CACAATTCACTAATAGGTGAGTTCATTTCATTGTCTTTTATATTGACATT
TTGTTTGAAGTCTGTCAAGGATGAAGCGTAGTTGAACTTAGATCACGAAT
ACTCTGATGAGTTTAATGTTAAATTTTGATGATCTGTACTATAAATACGT
TATTTTCCCGGCCCTAATTTAAATGAAAACATTCTCGTTAGTAGATGGAC
GGTGATTAAGGAAATATAATGTCTAATAGATTACAACCAAAATAAGTATA
GGAAATTTGATTACAGAAAGGACATGTTAATATCGTTTTAAATTAAACGT
TATGATGGTATTGACTTTATTAAAACACATATATCTCAATTTTAGAGTCC
CTTCAACCCAAAAATATATAATCATGTTAGTATGTTTTTTATTTATAAAG
TTTAATAAAATCTACAGAATACACAAATTAAATGATGAAAACTAGTTGTC
AAAAATTAACAAACATTTCATAATTAAAATTTAACTTTCCCAACTTTTTA
ATGTAAATTCAATATTATTATCTTTTACTATTTTAGTATACTACTATTTA
ATAAATGATGCTGTCAGATTTCAGGAAATTGCAAGAATTAACATCAACTT
TATTCACAACTTGATTATGGGAGATGAGGCTGATGTTTTTGGACGGAAAT
GTGGATTAACAGAATACGAGATTTTGGGGTACCGAAAATACATGTAACGT
TCATGCAAGTCAATTGCACCCACGTAAGGTTACAGTATGATGTGGAGTAA
CCTCAGAAAGAATTATTGGGCCTCACTTCTTTGAGAATTCTCATGAGAAG
GTCGTTATTGTAATTGCTGAGCGATTTAGAGAAATTCTGTTAAATTTTGT
TTAGCCTGAGATAGGAAATATGGCAGGGTATTGGTGGAAGCAAGATGGTG
CAACTGCACATACGTCTAGAGCTACTATCTGGATTCGAGGAATATGAATC
TTTGGCCCTTTGTAGTGACACCAACCAACCCAAACTGAATTCAGTATTTT
TCATCTCCTCTTTCAAAGCGTCTGGAAATTTGGATTGGTTGGAGAAAAAT
TGGAGACAATGGACGGGGGTAGTATGTATTTTGAAAAATCTTTCTCATTC
ATTGCGGCGAGATTTGCAAAAGATATCTTTCTATCGCCGAGTTGTTCCGA
CGGGAGAGTTTATGTTCGTGTTGATCTGCGAATTTACTTGTGAAAATACA
GAGCTGTACCGGCTTAAAGATTTAATGGAACGCATGAATGAAAGATATTC
GGGATACAGCCAAGTTTATGTCGTTCATTCTATGTATTAAATCTGTAAAT
ACTCCATTTCTAATCAACAAGATTCGTATTTTTTTTAAAACTTTGTCCTA
ATTCAATCGCGAATAAAAAAGAATTTTTAAAAATATTTTGAAATACATTT
TTTATTTACTTTTGTGCAATAAAAATGTTTAAACTGTTATTTATAATTTT
CCTGTTTCTGGC
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protein sequence of SMED30005349-orf-1

>SMED30005349-orf-1 ID=SMED30005349-orf-1|Name=SMED30005349-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=149bp
MEWQMTYKPDRYFKDICCSNDQETSIKTKDKHFYFFEYFPSDPIPNKENF
EAFIRNFQLCLSEIRQNPRFICGLLLKDAFDSGKFPFLNFVCLKYDEDNF
ISPSKKWISLSSDCSKGLCTKFHNSLIGEFISLSFILTFCLKSVKDEA*
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protein sequence of SMED30005349-orf-2

>SMED30005349-orf-2 ID=SMED30005349-orf-2|Name=SMED30005349-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
MVQLHIRLELLSGFEEYESLALCSDTNQPKLNSVFFISSFKASGNLDWLE
KNWRQWTGVVCILKNLSHSLRRDLQKISFYRRVVPTGEFMFVLICEFTCE
NTELYRLKDLMERMNERYSGYSQVYVVHSMY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
Vocabulary: molecular function
TermDefinition
GO:0005524ATP binding
GO:0016887ATPase activity