SMED30019559

Overview
NameSMED30019559
Smed IDSMED30019559
Length (bp)1675
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 SMED30019559 (SMED30019559) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30019559 (SMED30019559) 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 SMED30019559 (SMED30019559) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019559 (SMED30019559) 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




SMED30019559

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
X1 cellSMED30019559h1SMcG0022605 SmedASXL_007107SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30019559h1SMcG0022605 SmedASXL_007107SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30019559h1SMcG0022605 SmedASXL_007544SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30019559h1SMcG0022605 dd_Smed_v4_5972_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30019559h1SMcG0022605 Contig3379GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30019559 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005068:6129..7932 +8084
Homology
BLAST of SMED30019559 vs. Ensembl Fly
Match: CG14805 (gene:FBgn0023514 transcript:FBtr0070312)

HSP 1 Score: 53.1434 bits (126), Expect = 4.713e-7
Identity = 49/198 (24.75%), Postives = 86/198 (43.43%), Query Frame = 1
Query:   61 CLVTSGSFANNNNISVWDGSTGVNLMNLPGNKCS-NNSITIIK-DTVIACVENKALFEVWRLNSEGKKKIIPLPVPAK--AIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIEN--NVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKIIVSFYWLLSGV 636
             L  S S  +N   SV D  TG +LM   G  C+ ++S+ +I  + V+A    K L  VW +N + +   +   VP K  A+      N L   +  ++Y+W   +G++L  LS  H    + + F +N  + ++  + G V  W        +L +   P D+G       D    L+  ++ G  +   Y  + G+
Sbjct:    7 ALFISTSSEDNTTCSVQDLRTGTDLMRYKGGGCAQHHSLNMIHLNYVMAANSAKPLLHVWPINKQEQMAGLRFVVPGKVNALALTPDGNFLVAGIQENIYLWHMSSGRMLNTLSK-HYQAITCLRFTDNGEHFISGGKDGAVLVW--------DLTFSAAPLDTG----GGKDSTEPLYSFNDHGLAVTDLYSGIGGI 191          
BLAST of SMED30019559 vs. Planmine SMEST
Match: SMESG000016230.1 (SMESG000016230.1)

HSP 1 Score: 389.037 bits (998), Expect = 2.020e-131
Identity = 188/189 (99.47%), Postives = 188/189 (99.47%), Query Frame = 1
Query:   40 MNFSSNYCLVTSGSFANNNNISVWDGSTGVNLMNLPGNKCSNNSITIIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII 606
            MNFSSNYCLVTSGSFANNNNISVWDGSTGVNLMNLPGNKCSNNSI IIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII
Sbjct:    1 MNFSSNYCLVTSGSFANNNNISVWDGSTGVNLMNLPGNKCSNNSIAIIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII 189          

HSP 2 Score: 263.077 bits (671), Expect = 1.705e-104
Identity = 141/142 (99.30%), Postives = 141/142 (99.30%), Query Frame = 2
Query: 1232 SSPPDHIVTQVTLSPDNKHLXXXXXXXXXXXXXSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK 1657
             SPPDHIVTQVTLSPDNKHLIIAIDGRDIFIIDSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK
Sbjct:  252 GSPPDHIVTQVTLSPDNKHLIIAIDGRDIFIIDSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK 393          

HSP 3 Score: 137.117 bits (344), Expect = 1.705e-104
Identity = 62/63 (98.41%), Postives = 63/63 (100.00%), Query Frame = 3
Query:  981 CLSLTDGTPTAPMQELGGLTAHCIARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG 1169
            CLSLTDGTPTAPMQELGGLTAHC+ARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG
Sbjct:  190 CLSLTDGTPTAPMQELGGLTAHCMARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG 252          
BLAST of SMED30019559 vs. Planmine SMEST
Match: SMESG000016230.1 (SMESG000016230.1)

HSP 1 Score: 324.709 bits (831), Expect = 1.032e-106
Identity = 156/157 (99.36%), Postives = 156/157 (99.36%), Query Frame = 1
Query:  136 MNLPGNKCSNNSITIIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII 606
            MNLPGNKCSNNSI IIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII
Sbjct:    1 MNLPGNKCSNNSIAIIKDTVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGFDVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDLCDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKII 157          

HSP 2 Score: 262.307 bits (669), Expect = 3.916e-104
Identity = 141/142 (99.30%), Postives = 141/142 (99.30%), Query Frame = 2
Query: 1232 SSPPDHIVTQVTLSPDNKHLXXXXXXXXXXXXXSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK 1657
             SPPDHIVTQVTLSPDNKHLIIAIDGRDIFIIDSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK
Sbjct:  220 GSPPDHIVTQVTLSPDNKHLIIAIDGRDIFIIDSYGSAFIPRAMFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTDCRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK 361          

HSP 3 Score: 136.732 bits (343), Expect = 3.916e-104
Identity = 62/63 (98.41%), Postives = 63/63 (100.00%), Query Frame = 3
Query:  981 CLSLTDGTPTAPMQELGGLTAHCIARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG 1169
            CLSLTDGTPTAPMQELGGLTAHC+ARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG
Sbjct:  158 CLSLTDGTPTAPMQELGGLTAHCMARYADRIFIGCNKGRLVIYSFLQHAIDRLHQIYDCNTEG 220          
The following BLAST results are available for this feature:
BLAST of SMED30019559 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 SMED30019559 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 SMED30019559 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG148054.713e-724.75gene:FBgn0023514 transcript:FBtr0070312[more]
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BLAST of SMED30019559 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 SMED30019559 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 SMED30019559 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 SMED30019559 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 SMED30019559 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30019559 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 SMED30019559 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 SMED30019559 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 SMED30019559 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 SMED30019559 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 SMED30019559 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000016230.12.020e-13199.47SMESG000016230.1[more]
SMESG000016230.11.032e-10699.36SMESG000016230.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019559 ID=SMED30019559|Name=SMED30019559|organism=Schmidtea mediterranea sexual|type=transcript|length=1675bp
TTCAAAAATTGTTTAAATATTCATATCCAGCCTGATTAAATGAATTTCTC
ATCAAATTATTGTTTGGTCACCTCAGGATCATTTGCAAACAATAATAATA
TTTCAGTTTGGGATGGTTCTACTGGCGTTAACTTAATGAATTTACCTGGA
AATAAGTGCTCGAATAATTCTATTACAATAATCAAAGACACAGTGATAGC
ATGTGTTGAAAACAAAGCTTTATTCGAAGTTTGGAGGTTAAATAGTGAAG
GTAAGAAAAAAATTATCCCGCTACCCGTTCCCGCTAAGGCCATTGTTTAT
TATGAAAAAATGAATGTTTTATGTTGCTTCCTTGGATTTGATGTTTACGT
GTGGCAGCCACAAACAGGTCAATTACTGACAATCCTATCCAATATACATT
CTCATCCCGGTTCGCAAATTCTGTTCATTGAAAATAACGTGCTAACAATT
GATGAATCGGGATTAGTGGCTTTCTGGCGCGTGGATTTGTGCGATGGAAC
GGAACTCATTTGGAAAGGTCGACCATTCGATAGCGGTAAACTTTTCGCAT
CTATCATTGACATTCATTACGAGTTGTTTCTCGTTTCGGAATTCGGGAAA
ATTATCGTGAGTTTTTATTGGTTATTATCTGGTGTATTTTGGTTGGTTGA
TTGGAAATCGGAGTAATGTTTGCTAGTTTGTAATGATCGATAAATTGTGA
TGGAAATGGGATAATATTGGGGCCATCGTGAGGATGGGAGGGAATGTGCT
GTAATGCACGCTTGATGCTGAGGGCCATTGGCACTGTCCCCCCCCCCCAC
CCCAACTGCTGCCACTGGCCCACGACTCCCCCATTCTCTATATGAGCCAT
GTCACTGCTAATATTTGTCCTGTGGGGGGAGGCGGTGTGCCGGGCCTGCA
TGCTCGTATTGACCGCCAATTGCCATGGATACCGCCATATTTCACTATCT
GTATTAATCAATATATCCATCACACCGCAGTGCCTATCCCTGACAGACGG
AACCCCTACAGCACCAATGCAGGAACTAGGGGGCCTCACTGCTCATTGCA
TCGCTCGATATGCCGACAGGATATTTATCGGCTGCAACAAAGGCCGCTTG
GTGATCTACTCGTTCCTGCAGCACGCCATTGACAGGCTCCACCAAATCTA
TGACTGCAATACCGAGGGGTAACTATTGATTGATTGCCGTTACCAGCGGC
CGCCGGTTACTACTGCGTCACTGTTGCCTTCAGCTCCCCGCCCGATCACA
TCGTCACTCAGGTTACCCTCAGCCCTGACAACAAGCACTTGATCATTGCC
ATTGACGGCCGCGACATTTTCATCATTGATTCATACGGCAGCGCATTCAT
ACCGAGGGCCATGTTCAAGCTGGGGCTCACTGTCAACGGCCTGTTGGCGG
CAGGGAGAATCGAGGATTTATTTGAGGACTCTGTCGAGATCATTCAGCGG
CTGAATTTCTCTGTGGACGATCCTCACAGATGTCGCATGGAGATCCGCAT
GAAAACGGACTGCAGATCACACGCACAAGTCATTGCCAGCCTTGACAACG
GTTGCTATGAGGCATTTGATCGAATGCTTGCTGAACATCCCAAACAGGTC
CAACCGAAGCCAATCAAAAATATTCAGAAAATCCTATTTGATATTTTAGG
CAGTAAATAAATTTGGACTTGTCAA
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protein sequence of SMED30019559-orf-1

>SMED30019559-orf-1 ID=SMED30019559-orf-1|Name=SMED30019559-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MFKLGLTVNGLLAAGRIEDLFEDSVEIIQRLNFSVDDPHRCRMEIRMKTD
CRSHAQVIASLDNGCYEAFDRMLAEHPKQVQPKPIKNIQKILFDILGSK*
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protein sequence of SMED30019559-orf-2

>SMED30019559-orf-2 ID=SMED30019559-orf-2|Name=SMED30019559-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=209bp
MNFSSNYCLVTSGSFANNNNISVWDGSTGVNLMNLPGNKCSNNSITIIKD
TVIACVENKALFEVWRLNSEGKKKIIPLPVPAKAIVYYEKMNVLCCFLGF
DVYVWQPQTGQLLTILSNIHSHPGSQILFIENNVLTIDESGLVAFWRVDL
CDGTELIWKGRPFDSGKLFASIIDIHYELFLVSEFGKIIVSFYWLLSGVF
WLVDWKSE*
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protein sequence of SMED30019559-orf-3

>SMED30019559-orf-3 ID=SMED30019559-orf-3|Name=SMED30019559-orf-3|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MDILINTDSEIWRYPWQLAVNTSMQARHTASPHRTNISSDMAHIENGGVV
GQWQQLGWGGGTVPMALSIKRALQHIPSHPHDGPNIIPFPSQFIDHYKLA
NITPISNQPTKIHQIITNKNSR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR036322WD40_repeat_dom_sf
IPR015943WD40/YVTN_repeat-like_dom_sf
IPR017986WD40_repeat_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR015943WD40/YVTN repeat-like-containing domain superfamilyGENE3DG3DSA:2.130.10.10coord: 1..161
e-value: 1.0E-7
score: 32.9
IPR036322WD40-repeat-containing domain superfamilySUPERFAMILYSSF50978WD40 repeat-likecoord: 3..166