Retinoblastoma binding protein-1

Overview
NameRetinoblastoma binding protein-1
Smed IDSMED30024509
Length (bp)1056
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 Retinoblastoma binding protein-1 (SMED30024509) t-SNE clustered cells

Violin plots show distribution of expression levels for Retinoblastoma binding protein-1 (SMED30024509) 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



SMED30024509

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30024509SMESG000011014.1 Contig979newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30024509SMESG000011014.1 Contig979uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30024509SMESG000024325.1 SMESG000020480.1 Contig979newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30024509SMESG000024325.1 SMESG000020480.1 Contig979uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Retinoblastoma binding protein-1 vs. TrEMBL
Match: I1ZIK2 (Retinoblastoma binding protein-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 74.3294 bits (181), Expect = 6.685e-11
Identity = 40/79 (50.63%), Postives = 51/79 (64.56%), Query Frame = 1 
Query:   25 DLVLQRYSQEAFGFS*NIKNPGVLLSSGVNGTIQLQDINCTPKNKMEFIIGSRAWFPSGGHAQILNTKSQVRGRQTIIQ 261
            DLVL+ +SQE FG S NIKN GVLLSS V+GTIQL DINCTP+NK +F              ++LN+ SQ  G +  ++
Sbjct:  165 DLVLKGHSQEGFGLSWNIKNAGVLLSSAVDGTIQLWDINCTPENKNDF--------------KVLNSLSQYLGHEGSVE 229
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000069545.1 (SMESG000069545.1)

HSP 1 Score: 117.857 bits (294), Expect = 5.319e-30
Identity = 66/92 (71.74%), Postives = 73/92 (79.35%), Query Frame = 1 
Query:  151 KNKMEFIIGSRAWFPSGGHAQILNTKSQVRGRQTIIQPHHKTGHFMFXXXXXXXXXXXXERGQGHQTEEQQPSRDQMMDSRASRNACCFYWV 426
            +NKMEF IGSRAW PSGG AQILNTK+QV+G QTIIQP HKTGHF F  QLISIR IQRER QGHQTE QQPSR Q+MD RA R     +++
Sbjct:   90 ENKMEFTIGSRAWLPSGGLAQILNTKAQVKGHQTIIQPQHKTGHFSF-SQLISIRTIQRERSQGHQTEGQQPSRGQLMDPRAPRQELFLFFI 180
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000003895.1 (SMESG000003895.1)

HSP 1 Score: 75.8702 bits (185), Expect = 2.972e-20
Identity = 32/49 (65.31%), Postives = 42/49 (85.71%), Query Frame = -2 
Query:  753 GQEPAREARKRVEFSLYRLEGLERKFHWRTNMARRHLARVNADIASGLK 899
            G+ P+R+ R++ +F+LYRLE L++KF WR NMARR LAR+NADIASGLK
Sbjct:  198 GRNPSRQIRQKAKFTLYRLENLKKKFRWRANMARRKLARINADIASGLK 246

HSP 2 Score: 41.5874 bits (96), Expect = 2.972e-20
Identity = 27/55 (49.09%), Postives = 32/55 (58.18%), Query Frame = -3 
Query:  890 LQVPAYSAARYHQAL*DHGYSLATKG--EKDCQSQPEDRNNEI--IDIKKGPDRN 1042
            L+V A  AARY QAL D  YSLAT G  E  C+S   D   E+  + IK+ P RN
Sbjct:  146 LRVTAQFAARYRQALWDRQYSLATCGNDEWPCRSISRDNETELPSVAIKREPGRN 200
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000025362.1 (SMESG000025362.1)

HSP 1 Score: 88.5817 bits (218), Expect = 6.814e-19
Identity = 41/48 (85.42%), Postives = 43/48 (89.58%), Query Frame = 1 
Query:   25 DLVLQRYSQEAFGFS*NIKNPGVLLSSGVNGTIQLQDINCTPKNKMEF 168
            DLVLQR+SQE FGFS NIKN GVLLSS VNGTIQL DINCTP+NKMEF
Sbjct:  717 DLVLQRHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKMEF 764
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000016363.1 (SMESG000016363.1)

HSP 1 Score: 80.4925 bits (197), Expect = 4.088e-18
Identity = 38/48 (79.17%), Postives = 41/48 (85.42%), Query Frame = 1 
Query:   25 DLVLQRYSQEAFGFS*NIKNPGVLLSSGVNGTIQLQDINCTPKNKMEF 168
            DLVLQ +SQE FGFS NIKN G+LL S VNGTIQL DINCTP+NKMEF
Sbjct:   85 DLVLQEHSQEGFGFSWNIKNAGILLCSAVNGTIQLWDINCTPENKMEF 132
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000021373.1 (SMESG000021373.1)

HSP 1 Score: 78.5666 bits (192), Expect = 3.555e-17
Identity = 37/48 (77.08%), Postives = 42/48 (87.50%), Query Frame = 1 
Query:   25 DLVLQRYSQEAFGFS*NIKNPGVLLSSGVNGTIQLQDINCTPKNKMEF 168
            DLVLQ +SQE FGFS NIKN GVL+SS +NGTIQL DINCTP+NK+EF
Sbjct:  122 DLVLQGHSQERFGFSWNIKNAGVLISSAMNGTIQLLDINCTPENKLEF 169
The following BLAST results are available for this feature:
BLAST of Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIK26.685e-1150.63Retinoblastoma binding protein-1 OS=Schmidtea medi... [more]
back to top
BLAST of Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 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 Retinoblastoma binding protein-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000069545.15.319e-3071.74SMESG000069545.1[more]
SMESG000003895.12.972e-2065.31SMESG000003895.1[more]
SMESG000025362.16.814e-1985.42SMESG000025362.1[more]
SMESG000016363.14.088e-1879.17SMESG000016363.1[more]
SMESG000021373.13.555e-1777.08SMESG000021373.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024509 ID=SMED30024509|Name=Retinoblastoma binding protein-1|organism=Schmidtea mediterranea sexual|type=transcript|length=1056bp
AGATCAAAATGGCAAATGTAAGCCGATCTCGTTCTTCAAAGATATTCTCA
GGAAGCTTTTGGATTTTCTTGAAACATCAAAAACCCTGGTGTATTACTTA
GTTCTGGAGTGAATGGAACCATTCAATTGCAGGATATTAATTGTACTCCA
AAAAATAAAATGGAATTCATCATTGGTAGCAGAGCGTGGTTCCCTTCGGG
GGGCCACGCACAGATTCTGAATACGAAATCACAGGTGAGGGGGCGTCAAA
CTATTATCCAGCCTCACCACAAAACAGGTCATTTTATGTTCAGTATTCAA
CTTATCAGTATTCGCATAATTCAGCGAGAACGCGGCCAGGGGCATCAAAC
TGAAGAACAGCAGCCAAGCCGAGATCAGATGATGGATTCCAGAGCCTCAA
GAAATGCCTGCTGCTTCTACTGGGTGATGGTGCTTGCCTCTTCGGATGCC
GGGTGCTGGTACTGGTCTACTGTTTTCCGATGTTTGCATGGAGATTCCCT
CTGCCTCCGCTGAATGATGATATATTGCCTGAGACTAAGTGACGGAATTC
CGATTATGAATGTTGTTCGCTGCTCCTGCTTTTGGCTGCCTGGTTGACCG
CTGATGACCAGGAATGTGTTTGCGAACTGATGCTCACTCAATTCGTCGGA
TGTACTAAGATGAATAAACAGAAATTCTAAGGAATGAGAAATTGATCTCT
CCTTATGCCTGTTATGGCAATGGCTTGTTATATTAATAAAACTTTGATTT
TTTTTTAATCCGCTGGCGATATCCGCGTTCACACGAGCTAGATGCCTTCG
GGCCATATTGGTTCGCCAATGAAACTTTCTTTCCAGGCCCTCCAAGCGAT
ATAAGCTGAATTCGACTCGTTTGCGGGCTTCTCGTGCCGGTTCCTGTCCG
GTCCCTTTTTGATGTCTATGATCTCGTTATTTCGATCTTCCGGTTGACTC
TGACAATCCTTCTCTCCTTTGGTTGCCAACGAGTATCCGTGGTCTCACAA
CGCCTGGTGGTATCTGGCAGCCGAGTACGCGGGTACTTGTAAGGTGATTC
GAGAGC
back to top

protein sequence of SMED30024509-orf-1

>SMED30024509-orf-1 ID=SMED30024509-orf-1|Name=SMED30024509-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
MARRHLARVNADIASGLKKNQSFINITSHCHNRHKERSISHSLEFLFIHL
STSDELSEHQFANTFLVISGQPGSQKQEQRTTFIIGIPSLSLRQYIIIQR
RQRESPCKHRKTVDQYQHPASEEASTITQ*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 84..106