plexin B-2

Overview
Nameplexin B-2 (AJA72713.1)
Smed IDSMED30010585
Length (bp)695
Neoblast Clusters

Zeng et. al., 2018




 



 

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




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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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




SMED30010585

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30010585SMESG000070796.1 SmedASXL_023427SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of plexin B-2 vs. TrEMBL
Match: A0A0K0LJ30 (Plexin B-2 (Fragment) OS=Schmidtea mediterranea OX=79327 GN=plxnB-2 PE=2 SV=1)

HSP 1 Score: 360.533 bits (924), Expect = 7.055e-125
Identity = 178/183 (97.27%), Postives = 178/183 (97.27%), Query Frame = 1
Query:   46 DGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMECDPNCPSSCGKVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERFFIDTDGNIKTNRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQ 594
            DGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMEC PNC SSCG VSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERF IDTDGNIK NRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQ
Sbjct:    1 DGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMECYPNCSSSCGYVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERFLIDTDGNIKRNRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQ 183          
BLAST of plexin B-2 vs. Planmine SMEST
Match: SMESG000070796.1 (SMESG000070796.1)

HSP 1 Score: 463.766 bits (1192), Expect = 7.026e-166
Identity = 226/231 (97.84%), Postives = 228/231 (98.70%), Query Frame = 1
Query:    1 ILCGILIQIVNSSGNDGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMECDPNCPSSCGKVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERFFIDTDGNIKTNRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQLLRENLSGLQLKTTSDFSIKFHKVFEFTTRTSE 693
            ILCGILIQIVNSSGNDGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMECDPNCPSSCGKVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERF IDTDGNI  NRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQLLRENLSGLQLKTTS+FS+KFHKVFEFTTRTSE
Sbjct:    5 ILCGILIQIVNSSGNDGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIVSDSFTYQILNTITTGPVNDSLYCINSMECDPNCPSSCGKVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERFLIDTDGNINPNRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQLLRENLSGLQLKTTSEFSLKFHKVFEFTTRTSE 235          
BLAST of plexin B-2 vs. Planmine SMEST
Match: SMESG000006542.1 (SMESG000006542.1)

HSP 1 Score: 58.5362 bits (140), Expect = 8.243e-10
Identity = 54/174 (31.03%), Postives = 82/174 (47.13%), Query Frame = 1
Query:  109 HKRIIVAIKNFII-VSDSFTYQILNTITTGPVNDSLYCINSMECDPN-CPSS------CGKVSTDVSVKSWIVDRNQQYLIVCYNIYQGYCERFFIDTDGNIKTNRSIDKTTTPVVNADPRGASTLFVFDNILIVCSQ--RNISYDPLKLN-LPVISFRNIDDFHIIQPK-PFQ 594
            HK I+V+ KN+I+  S++   + L    TGPVN S+ C    +C  + CP        C    TDV VK W       YL+VCY+++QG+CE   ID      +  S       +V  D +  ST+   D  L   ++     +Y  +  N + ++SF N+  F   +P  PFQ
Sbjct:   46 HKSILVSGKNYILQFSENNLKEPLAIRKTGPVNHSVMCTEPYQCQTSLCPKELISRDQCRIKLTDVFVKLWTFA--DSYLVVCYDVFQGFCE--IIDLYNQFSS--SYKNKVYSIVTNDRKFHSTVLYHDQRLFFANEVYHPSNYREIDFNTMSILSFPNMTYF---KPDYPFQ 210          
The following BLAST results are available for this feature:
BLAST of plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0K0LJ307.055e-12597.27Plexin B-2 (Fragment) OS=Schmidtea mediterranea OX... [more]
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BLAST of plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 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 plexin B-2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000070796.17.026e-16697.84SMESG000070796.1[more]
SMESG000006542.18.243e-1031.03SMESG000006542.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30010585
GenBankAJA72713.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010585 ID=SMED30010585|Name=plexin B-2|organism=Schmidtea mediterranea sexual|type=transcript|length=695bp
ATTTTATGTGGAATTTTGATCCAAATAGTGAATAGTTCCGGTAACGACGG
GATGAAAGGAAGCCAAAAAATAAGTTTTCCATCCGTCATTGATCATGTAG
TTTTTATCCACAAAAGGATAATAGTAGCAATTAAGAATTTCATAATCGTT
TCCGATAGTTTTACTTATCAAATTCTGAATACAATTACCACAGGACCTGT
CAATGATTCTTTATACTGTATTAATTCGATGGAATGCGATCCTAACTGTC
CCAGTTCTTGTGGAAAGGTTTCAACTGACGTCAGTGTTAAATCTTGGATA
GTAGACAGAAATCAACAGTATTTAATTGTTTGTTATAATATATATCAAGG
TTATTGCGAAAGGTTTTTTATTGATACTGACGGTAACATAAAGACAAATA
GGTCAATTGACAAAACTACTACACCTGTTGTAAATGCAGACCCACGAGGC
GCATCCACCCTGTTCGTATTTGATAACATTTTGATAGTATGCTCTCAGCG
AAATATTTCCTATGATCCACTGAAATTAAATCTTCCGGTAATTTCCTTCC
GTAACATTGATGATTTTCATATTATCCAACCAAAGCCATTTCAATTACTG
AGAGAAAATCTTTCCGGCTTACAATTGAAAACTACAAGTGACTTTTCTAT
AAAGTTTCACAAGGTTTTCGAATTCACTACAAGAACATCAGAAGC
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protein sequence of SMED30010585-orf-1

>SMED30010585-orf-1 ID=SMED30010585-orf-1|Name=SMED30010585-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=231bp
ILCGILIQIVNSSGNDGMKGSQKISFPSVIDHVVFIHKRIIVAIKNFIIV
SDSFTYQILNTITTGPVNDSLYCINSMECDPNCPSSCGKVSTDVSVKSWI
VDRNQQYLIVCYNIYQGYCERFFIDTDGNIKTNRSIDKTTTPVVNADPRG
ASTLFVFDNILIVCSQRNISYDPLKLNLPVISFRNIDDFHIIQPKPFQLL
RENLSGLQLKTTSDFSIKFHKVFEFTTRTSE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR036352Semap_dom_sf
IPR015943WD40/YVTN_repeat-like_dom_sf
IPR001627Semap_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: 22..228
e-value: 3.3E-19
score: 71.2
IPR036352Sema domain superfamilySUPERFAMILYSSF101912Sema domaincoord: 26..148