WD_REPEATS_REGION domain-containing protein

Overview
NameWD_REPEATS_REGION domain-containing protein
Smed IDSMED30026430
Length (bp)347
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 WD_REPEATS_REGION domain-containing protein (SMED30026430) t-SNE clustered cells

Violin plots show distribution of expression levels for WD_REPEATS_REGION domain-containing protein (SMED30026430) in cells (dots) of each of the 12 neoblast clusters.

 

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




SMED30026430

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30026430h1SMcG0003267 SmedASXL_012755SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30026430h1SMcG0003267 SmedASXL_004094SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30026430h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026430h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026430h1SMcG0003267 dd_Smed_v4_74366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026430h1SMcG0003267 dd_Smed_v4_74366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30026430h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30026430h1SMcG0003267 dd_Smed_v4_21908_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
BLAST of WD_REPEATS_REGION domain-containing protein vs. Ensembl Celegans
Match: T05C3.2 (pep chromosome:WBcel235:V:5493747:5503010:1 gene:WBGene00020254.1 transcript:T05C3.2.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:T05C3.2)

HSP 1 Score: 64.6994 bits (156), Expect = 3.057e-13
Identity = 53/110 (48.18%), Postives = 73/110 (66.36%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQP 332
            ++QYHLPP+RRIPPLLWSRI++D+  Y++ER +D   V+ W HQ F  +  ERY  N N     H  M+++F G W G+PKP+ Y E+ K RFG+T  +  +DR V  QP
Sbjct:  736 IFQYHLPPVRRIPPLLWSRIRSDLPGYLSERAADGVIVLNWYHQQFRQVAIERYFKNVNHLETCHSAMAEYFLGVWGGVPKPYQYTEMQKQRFGVTENEGLADRKVPKQP 845          
BLAST of WD_REPEATS_REGION domain-containing protein vs. Ensembl Fly
Match: CG10185 (gene:FBgn0038397 transcript:FBtr0083235)

HSP 1 Score: 79.7221 bits (195), Expect = 2.108e-18
Identity = 56/114 (49.12%), Postives = 80/114 (70.18%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKW-AGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLW 341
            VYQYHLPP RRIPPLLW+RI+ND+ +Y++ERE+D   V+ W H+ F +   ERY  N N  +Y H +++D++ G W  G+PKPF + EI + RFGL + +  +DR V  QPL++
Sbjct:  665 VYQYHLPPTRRIPPLLWTRIRNDLPNYLSEREADGVNVMNWYHRQFRDTAKERYFKNMNMAIYFHSMIADYYLGIWGGGVPKPFKFTEIQRHRFGLADKEGSADRKVPIQPLVF 778          
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Match: A0A267GGQ3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig005707g1 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 3.280e-19
Identity = 61/111 (54.95%), Postives = 81/111 (72.97%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPL 335
            VYQYHLPP RRIPPLLW+RI+N++  ++ E+E+D + VV W H+ F  +  +RY  N NFK  IH  ++D++ GKWAG+PKPF Y E+ K RFGL ++ SESDR V  QPL
Sbjct: 1367 VYQYHLPPSRRIPPLLWTRIRNELPGFLVEKEADGASVVYWYHRQFFQVCEKRYFKNLNFKSSIHSNLADYYLGKWAGVPKPFAYSELQKQRFGLKDVNSESDRMVPPQPL 1477          
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Match: A0A267GDZ8 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026001g1 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 3.615e-19
Identity = 61/111 (54.95%), Postives = 81/111 (72.97%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPL 335
            VYQYHLPP RRIPPLLW+RI+N++  ++ E+E+D + VV W H+ F  +  +RY  N NFK  IH  ++D++ GKWAG+PKPF Y E+ K RFGL ++ SESDR V  QPL
Sbjct: 1379 VYQYHLPPSRRIPPLLWTRIRNELPGFLVEKEADGASVVYWYHRQFFQVCEKRYFKNLNFKSSIHSNLADYYLGKWAGVPKPFAYSELQKQRFGLKDVNSESDRMVPPQPL 1489          
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Match: A0A267FFL7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig027966g1 PE=4 SV=1)

HSP 1 Score: 91.6633 bits (226), Expect = 5.124e-19
Identity = 61/111 (54.95%), Postives = 81/111 (72.97%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPL 335
            VYQYHLPP RRIPPLLW+RI+N++  ++ E+E+D + VV W H+ F  +  +RY  N NFK  IH  ++D++ GKWAG+PKPF Y E+ K RFGL ++ SESDR V  QPL
Sbjct: 1469 VYQYHLPPSRRIPPLLWTRIRNELPGFLVEKEADGASVVYWYHRQFFQVCEKRYFKNLNFKSSIHSNLADYYLGKWAGVPKPFAYSELQKQRFGLKDVNSESDRMVPPQPL 1579          
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Match: A0A267FH80 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015065g1 PE=4 SV=1)

HSP 1 Score: 88.1965 bits (217), Expect = 5.549e-18
Identity = 62/111 (55.86%), Postives = 80/111 (72.07%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPL 335
            VYQYHLPP RRIPPLLW+RI+N++  ++ E+E+D   VV W H+ F  +  +RY  N NFK  IH  ++D+F GKWAG+PKPF Y E+ K RFGL ++ SESDR V  QPL
Sbjct:   49 VYQYHLPPTRRIPPLLWTRIRNELPGFLVEKEADGVDVVYWYHRQFFQVCEKRYFKNLNFKSGIHSNLADYFLGKWAGVPKPFVYSELQKQRFGLKDVNSESDRKVPPQPL 159          
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Match: A0A182VE12 (WD_REPEATS_REGION domain-containing protein OS=Anopheles merus OX=30066 PE=4 SV=1)

HSP 1 Score: 85.5001 bits (210), Expect = 5.864e-17
Identity = 58/113 (51.33%), Postives = 81/113 (71.68%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLW 341
            VYQYHLPP+RRIPPLLW+RI+ND+ +Y++ERE+D   V+ W H+ F +   ERY  N N  +Y H +++D++ G W G PKPF Y EI + RFGLT+ +  +DR V  QPL++
Sbjct:  665 VYQYHLPPVRRIPPLLWTRIRNDLPNYLSEREADGVNVMNWYHRQFRDTAKERYFKNMNMAIYFHSMIADYYLGIWGGKPKPFKYTEIQRHRFGLTDKEGIADRKVPMQPLVF 777          
BLAST of WD_REPEATS_REGION domain-containing protein vs. Planmine SMEST
Match: SMESG000018097.1 (SMESG000018097.1)

HSP 1 Score: 180.644 bits (457), Expect = 9.432e-54
Identity = 115/115 (100.00%), Postives = 115/115 (100.00%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE 347
            VYQYHLPPIRRIPPLLWSRIKNDILDYITERESDFSQVVCWRHQPFINIINERYLNNNNFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE
Sbjct:  340 VYQYHLPPIRRIPPLLWSRIKNDILDYITERESDFSQVVCWRHQPFINIINERYLNNNNFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE 454          
BLAST of WD_REPEATS_REGION domain-containing protein vs. Planmine SMEST
Match: SMESG000018097.1 (SMESG000018097.1)

HSP 1 Score: 180.259 bits (456), Expect = 1.319e-53
Identity = 115/115 (100.00%), Postives = 115/115 (100.00%), Query Frame = 3
Query:    3 VYQYHXXXXXXXXXXXXXXXKNDILDYITERESDFSQVVCWRHQPFXXXXXXXXXXXXXFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE 347
            VYQYHLPPIRRIPPLLWSRIKNDILDYITERESDFSQVVCWRHQPFINIINERYLNNNNFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE
Sbjct:  593 VYQYHLPPIRRIPPLLWSRIKNDILDYITERESDFSQVVCWRHQPFINIINERYLNNNNFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKSESDRFVCYQPLLWKE 707          
The following BLAST results are available for this feature:
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION domain-containing protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
T05C3.23.057e-1348.18pep chromosome:WBcel235:V:5493747:5503010:1 gene:W... [more]
back to top
BLAST of WD_REPEATS_REGION domain-containing protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG101852.108e-1849.12gene:FBgn0038397 transcript:FBtr0083235[more]
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267GGQ33.280e-1954.95Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GDZ83.615e-1954.95Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FFL75.124e-1954.95Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FH805.549e-1855.86Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A182VE125.864e-1751.33WD_REPEATS_REGION domain-containing protein OS=Ano... [more]
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION 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
back to top
BLAST of WD_REPEATS_REGION domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000018097.19.432e-54100.00SMESG000018097.1[more]
SMESG000018097.11.319e-53100.00SMESG000018097.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026430 ID=SMED30026430|Name=WD_REPEATS_REGION domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=347bp
ATGTTTACCAATATCATTTACCCCCTATACGTAGAATCCCGCCTCTTTTA
TGGAGTCGAATCAAGAACGATATTTTAGACTATATAACTGAAAGAGAATC
AGATTTTTCTCAAGTTGTTTGCTGGCGTCACCAGCCATTCATAAATATAA
TAAATGAACGTTATTTGAATAATAACAATTTTAAACTATATATCCATGGT
GTTATGTCAGATTTCTTTTCTGGAAAATGGGCAGGGCTTCCTAAGCCATT
TCATTATGATGAAATTCACAAAATAAGATTTGGACTGACAAATCTCAAGT
CAGAAAGTGATCGCTTTGTATGTTATCAGCCATTATTGTGGAAAGAA
back to top

protein sequence of SMED30026430-orf-1

>SMED30026430-orf-1 ID=SMED30026430-orf-1|Name=SMED30026430-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
VYQYHLPPIRRIPPLLWSRIKNDILDYITERESDFSQVVCWRHQPFINII
NERYLNNNNFKLYIHGVMSDFFSGKWAGLPKPFHYDEIHKIRFGLTNLKS
ESDRFVCYQPLLWKE
back to top
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR19871BETA TRANSDUCIN-RELATED PROTEINcoord: 1..113