Cytoplasmic polyadenylation element-binding protein 2

Overview
NameCytoplasmic polyadenylation element-binding protein 2
Smed IDSMED30035755
Length (bp)322
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 Cytoplasmic polyadenylation element-binding protein 2 (SMED30035755) t-SNE clustered cells

Violin plots show distribution of expression levels for Cytoplasmic polyadenylation element-binding protein 2 (SMED30035755) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 Cytoplasmic polyadenylation element-binding protein 2 (SMED30035755) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Cytoplasmic polyadenylation element-binding protein 2 (SMED30035755) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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




SMED30035755

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035755h1SMcG0007589 SmedASXL_016021SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30035755h1SMcG0007589 SmedASXL_010054SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30035755h1SMcG0007589 SmedASXL_001683SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30035755h1SMcG0007589 dd_Smed_v4_8889_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035755h1SMcG0007589 dd_Smed_v6_8889_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30035755h1SMcG0007589 OX_Smed_1.0.06748ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
neuronSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite fluorescence in situ hybridization evidence
testisSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite fluorescence in situ hybridization evidence
testisSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
spermatogoniumSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite fluorescence in situ hybridization evidence
spermatocyteSMED30035755h1SMcG0007589 KX074204smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite fluorescence in situ hybridization evidence
reproductive organSMED30035755h1SMcG0007589 Contig45882uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig45882newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig35135newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig35135uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig39085uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig39085newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035755h1SMcG0007589 Contig29000newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Cytoplasmic polyadenylation element-binding protein 2 vs. TrEMBL
Match: A0A1W6I181 (Cytoplasmic polyadenylation element-binding protein 2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 3.458e-14
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 2
Query:   56 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQXXXXXXXXXXXXXXXXXXKKIIQQRNLV 232
            PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV
Sbjct:  370 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV 428          
BLAST of Cytoplasmic polyadenylation element-binding protein 2 vs. TrEMBL
Match: A0A219TTV5 (Cytoplasmic polyadenylation element binding protein 2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 3.770e-14
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 2
Query:   56 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQXXXXXXXXXXXXXXXXXXKKIIQQRNLV 232
            PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV
Sbjct:  358 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV 416          
BLAST of Cytoplasmic polyadenylation element-binding protein 2 vs. Planmine SMEST
Match: SMESG000055629.1 (SMESG000055629.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.048e-17
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 2
Query:   56 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQXXXXXXXXXXXXXXXXXXKKIIQQRNLV 232
            PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV
Sbjct:  358 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV 416          
BLAST of Cytoplasmic polyadenylation element-binding protein 2 vs. Planmine SMEST
Match: SMESG000055629.1 (SMESG000055629.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.049e-17
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 2
Query:   56 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQXXXXXXXXXXXXXXXXXXKKIIQQRNLV 232
            PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV
Sbjct:  370 PNNPWNQALVNQKLGLAPAPVNAMNLGGFPQMNNKLINNMNMMPMSNTNKKIIQQRNLV 428          
The following BLAST results are available for this feature:
BLAST of Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Cytoplasmic polyadenylation element-binding protein 2 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A1W6I1813.458e-14100.00Cytoplasmic polyadenylation element-binding protei... [more]
A0A219TTV53.770e-14100.00Cytoplasmic polyadenylation element binding protei... [more]
back to top
BLAST of Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 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
back to top
BLAST of Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 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 Cytoplasmic polyadenylation element-binding protein 2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000055629.11.048e-17100.00SMESG000055629.1[more]
SMESG000055629.11.049e-17100.00SMESG000055629.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035755 ID=SMED30035755|Name=Cytoplasmic polyadenylation element-binding protein 2|organism=Schmidtea mediterranea sexual|type=transcript|length=322bp
ACAACAGCAACAGCAACAACAGCGACAGCAACAACAGCAACAACAACAGC
AGCAACCTAATAATCCATGGAATCAAGCTCTCGTCAATCAAAAACTCGGA
TTAGCACCAGCTCCAGTTAACGCAATGAATCTAGGTGGATTCCCACAAAT
GAATAACAAATTAATCAACAACATGAACATGATGCCAATGTCAAATACGA
ATAAGAAAATTATTCAACAACGCAATCTCGTCAATAGTCCACAATCGAAT
CCAATAACATCAAACAATACCAACTCATCGGCTCTTAATAATAACAATAA
CAATAACAATAACAACAACAAC
back to top

protein sequence of SMED30035755-orf-1

>SMED30035755-orf-1 ID=SMED30035755-orf-1|Name=SMED30035755-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
QQQQQQQRQQQQQQQQQQPNNPWNQALVNQKLGLAPAPVNAMNLGGFPQM
NNKLINNMNMMPMSNTNKKIIQQRNLVNSPQSNPITSNNTNSSALNNNNN
NNNNNNN
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0003723RNA binding
GO:0003730mRNA 3'-UTR binding
GO:0045182translation regulator activity
Vocabulary: biological process
TermDefinition
GO:0006417regulation of translation
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000044cephalic ganglia
PLANA:0000208testis
PLANA:0000220spermatogonium
PLANA:0000221spermatocyte
PLANA:0000418head
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 90..104
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 63..104
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..28
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..26