Retinoblastoma binding protein-1

Overview
NameRetinoblastoma binding protein-1
Smed IDSMED30027781
Length (bp)733
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 Retinoblastoma binding protein-1 (SMED30027781) t-SNE clustered cells

Violin plots show distribution of expression levels for Retinoblastoma binding protein-1 (SMED30027781) 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 Retinoblastoma binding protein-1 (SMED30027781) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Retinoblastoma binding protein-1 (SMED30027781) 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



SMED30027781

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30027781SMESG000007931.1 SmedASXL_015885SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30027781SMESG000007931.1 SmedASXL_015885SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30027781SMESG000007931.1 dd_Smed_v4_7612_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000046819.1 SMESG000046815.1 SMESG000046812.1 SMESG000046804.1 Contig43615uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000046819.1 SMESG000046815.1 SMESG000046812.1 SMESG000046804.1 Contig43615newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000046819.1 SMESG000046816.1 SMESG000046815.1 SMESG000046812.1 SMESG000046810.1 SMESG000046804.1 SMESG000046803.1 SMESG000035550.1 Contig11396uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000046819.1 SMESG000046816.1 SMESG000046815.1 SMESG000046812.1 SMESG000046810.1 SMESG000046804.1 SMESG000046803.1 SMESG000035550.1 Contig11396newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000025362.1 Contig14926uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027781SMESG000025362.1 Contig14926newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parapharyngeal regionSMED30027781SMESG000007931.1 dd_Smed_v6_7612_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30027781SMESG000016364.1 SMESG000016363.1 SMESG000009117.1 SMESG000007719.1 Contig20474uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30027781SMESG000016364.1 SMESG000016363.1 SMESG000009117.1 SMESG000007719.1 Contig20474newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
zeta neoblastSMED30027781SMESG000007931.1 dd_Smed_v4_7612_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027781SMESG000060842.1 SMESG000055161.1 SMESG000029096.1 SMESG000025362.1 SMESG000023638.1 SMESG000019154.1 SMESG000003920.1 SMED_02978_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Human
Match: RBBP7 (RB binding protein 7, chromatin remodeling factor [Source:HGNC Symbol;Acc:HGNC:9890])

HSP 1 Score: 48.9062 bits (115), Expect = 3.045e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:   92 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 135
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Human
Match: RBBP7 (RB binding protein 7, chromatin remodeling factor [Source:HGNC Symbol;Acc:HGNC:9890])

HSP 1 Score: 48.521 bits (114), Expect = 5.287e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  163 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 206
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Human
Match: RBBP7 (RB binding protein 7, chromatin remodeling factor [Source:HGNC Symbol;Acc:HGNC:9890])

HSP 1 Score: 48.521 bits (114), Expect = 5.341e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  172 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Human
Match: RBBP7 (RB binding protein 7, chromatin remodeling factor [Source:HGNC Symbol;Acc:HGNC:9890])

HSP 1 Score: 48.521 bits (114), Expect = 5.785e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  216 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 259
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Fly
Match: Caf1-55 (gene:FBgn0263979 transcript:FBtr0301845)

HSP 1 Score: 50.0618 bits (118), Expect = 7.457e-7
Identity = 22/40 (55.00%), Postives = 29/40 (72.50%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPE 205
            L+GH +EG+G SWN    G LLS++ + TI LWDIN TP+
Sbjct:  176 LRGHQKEGYGLSWNPNLNGYLLSASDDHTICLWDINATPK 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Fly
Match: Caf1-55 (gene:FBgn0263979 transcript:FBtr0083052)

HSP 1 Score: 50.0618 bits (118), Expect = 7.604e-7
Identity = 22/40 (55.00%), Postives = 29/40 (72.50%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPE 205
            L+GH +EG+G SWN    G LLS++ + TI LWDIN TP+
Sbjct:  177 LRGHQKEGYGLSWNPNLNGYLLSASDDHTICLWDINATPK 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Zebrafish
Match: rbbp4 (retinoblastoma binding protein 4 [Source:NCBI gene;Acc:321726])

HSP 1 Score: 47.7506 bits (112), Expect = 6.265e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + TI LWDI+  P E KI
Sbjct:  173 LRGHQKEGYGLSWNPNLSGCLLSASDDHTICLWDISTVPKEGKI 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Mouse
Match: Rbbp7 (retinoblastoma binding protein 7, chromatin remodeling factor [Source:MGI Symbol;Acc:MGI:1194910])

HSP 1 Score: 48.521 bits (114), Expect = 3.043e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  172 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Mouse
Match: Rbbp7 (retinoblastoma binding protein 7, chromatin remodeling factor [Source:MGI Symbol;Acc:MGI:1194910])

HSP 1 Score: 48.521 bits (114), Expect = 3.630e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  163 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 206
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Mouse
Match: Rbbp7 (retinoblastoma binding protein 7, chromatin remodeling factor [Source:MGI Symbol;Acc:MGI:1194910])

HSP 1 Score: 48.521 bits (114), Expect = 3.667e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDIN  P E KI
Sbjct:  172 LRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. UniProt/SwissProt
Match: sp|O22467|MSI1_ARATH (Histone-binding protein MSI1 OS=Arabidopsis thaliana OX=3702 GN=MSI1 PE=1 SV=1)

HSP 1 Score: 51.2174 bits (121), Expect = 3.163e-6
Identity = 23/42 (54.76%), Postives = 29/42 (69.05%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENK 211
            L+GHS EG+G SW+    G LLS + +  I LWDIN TP+NK
Sbjct:  174 LRGHSSEGYGLSWSKFKQGHLLSGSDDAQICLWDINATPKNK 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. UniProt/SwissProt
Match: sp|O22466|MSI1_SOLLC (WD-40 repeat-containing protein MSI1 OS=Solanum lycopersicum OX=4081 GN=MSI1 PE=2 SV=1)

HSP 1 Score: 50.0618 bits (118), Expect = 6.359e-6
Identity = 23/42 (54.76%), Postives = 29/42 (69.05%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENK 211
            L+GHS EG+G SW+    G LLS + +  I LWDIN TP+NK
Sbjct:  174 LRGHSTEGYGLSWSQFKQGHLLSGSDDSHICLWDINATPKNK 215
[Close]
BLAST of Retinoblastoma binding protein-1 vs. UniProt/SwissProt
Match: sp|Q24572|CAF1_DROME (Probable histone-binding protein Caf1 OS=Drosophila melanogaster OX=7227 GN=Caf1 PE=1 SV=1)

HSP 1 Score: 50.0618 bits (118), Expect = 7.622e-6
Identity = 22/40 (55.00%), Postives = 29/40 (72.50%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPE 205
            L+GH +EG+G SWN    G LLS++ + TI LWDIN TP+
Sbjct:  177 LRGHQKEGYGLSWNPNLNGYLLSASDDHTICLWDINATPK 216
[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: 90.8929 bits (224), Expect = 2.227e-17
Identity = 41/47 (87.23%), Postives = 44/47 (93.62%), Query Frame = 2 
Query:   80 FVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKIEF 220
             VL+GHSQEGFG SWNIKNAGVLLSSAV+GTIQLWDINCTPENK +F
Sbjct:  166 LVLKGHSQEGFGLSWNIKNAGVLLSSAVDGTIQLWDINCTPENKNDF 212
[Close]
BLAST of Retinoblastoma binding protein-1 vs. TrEMBL
Match: A0A226DJ27 (Putative histone-binding protein rbbD OS=Folsomia candida OX=158441 GN=Fcan01_21356 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 5.478e-6
Identity = 26/51 (50.98%), Postives = 32/51 (62.75%), Query Frame = 2 
Query:   80 FVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKIEFTRYF 232
             VL+GHSQ GFG +WNIK  G+L S + +G I LWDI   P+   E T Y 
Sbjct:  529 LVLRGHSQGGFGLAWNIKERGILASGSNDGVICLWDICANPDTTPEPTIYL 579
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Cavefish
Match: rbbp4 (RB binding protein 4, chromatin remodeling factor [Source:NCBI gene;Acc:103039809])

HSP 1 Score: 47.3654 bits (111), Expect = 5.457e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + TI LWDI+  P E KI
Sbjct:  173 LRGHQKEGYGLSWNPNLSGCLLSASDDHTICLWDISTVPKEGKI 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Cavefish
Match: rbb4l (histone-binding protein RBBP7 [Source:NCBI gene;Acc:103023991])

HSP 1 Score: 46.9802 bits (110), Expect = 7.955e-6
Identity = 23/44 (52.27%), Postives = 32/44 (72.73%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + TI LWDI+ +P E KI
Sbjct:  173 LRGHQKEGYGLSWNPNLSGNLLSASDDHTICLWDISGSPKEGKI 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000008002.1 (pep scaffold:Pmarinus_7.0:GL477852:421:9512:1 gene:ENSPMAG00000007189.1 transcript:ENSPMAT00000008002.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 47.7506 bits (112), Expect = 1.011e-6
Identity = 22/44 (50.00%), Postives = 32/44 (72.73%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + T+ LWDI+ TP E K+
Sbjct:  173 LRGHQKEGYGLSWNPNLSGHLLSASDDHTVCLWDISGTPREGKV 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Ensembl Medaka
Match: rbbp4 (RB binding protein 4, chromatin remodeling factor [Source:NCBI gene;Acc:101155071])

HSP 1 Score: 47.7506 bits (112), Expect = 5.277e-6
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 2 
Query:   86 LQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTP-ENKI 214
            L+GH +EG+G SWN   +G LLS++ + TI LWDI+  P E KI
Sbjct:  173 LRGHQKEGYGLSWNPNLSGCLLSASDDHTICLWDISTVPKEGKI 216
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000043653.1 (SMESG000043653.1)

HSP 1 Score: 130.183 bits (326), Expect = 5.221e-35
Identity = 60/71 (84.51%), Postives = 67/71 (94.37%), Query Frame = 2 
Query:    2 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKI 214
            PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGV+L+SAVNGTI+LWD N   ++++
Sbjct:  192 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVILNSAVNGTIRLWDSNEVSDSEL 262
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000043653.1 (SMESG000043653.1)

HSP 1 Score: 130.183 bits (326), Expect = 1.027e-34
Identity = 60/71 (84.51%), Postives = 67/71 (94.37%), Query Frame = 2 
Query:    2 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKI 214
            PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGV+L+SAVNGTI+LWD N   ++++
Sbjct:  192 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVILNSAVNGTIRLWDSNEVSDSEL 262
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000043653.1 (SMESG000043653.1)

HSP 1 Score: 128.642 bits (322), Expect = 3.379e-34
Identity = 59/62 (95.16%), Postives = 62/62 (100.00%), Query Frame = 2 
Query:    2 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWD 187
            PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGV+L+SAVNGTI+LWD
Sbjct:  192 PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVILNSAVNGTIRLWD 253
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000016363.1 (SMESG000016363.1)

HSP 1 Score: 96.6709 bits (239), Expect = 6.195e-25
Identity = 43/50 (86.00%), Postives = 47/50 (94.00%), Query Frame = 2 
Query:   80 FVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKIEFTRY 229
             VLQ HSQEGFGFSWNIKNAG+LL SAVNGTIQLWDINCTPENK+EFT++
Sbjct:   86 LVLQEHSQEGFGFSWNIKNAGILLCSAVNGTIQLWDINCTPENKMEFTKH 135
[Close]
BLAST of Retinoblastoma binding protein-1 vs. Planmine SMEST
Match: SMESG000013977.1 (SMESG000013977.1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.165e-23
Identity = 43/48 (89.58%), Postives = 46/48 (95.83%), Query Frame = 2 
Query:   80 FVLQGHSQEGFGFSWNIKNAGVLLSSAVNGTIQLWDINCTPENKIEFT 223
             VLQGHSQEGFGFSWNIKN+GVLLSSAVNG IQLWDINCTPENK+EF+
Sbjct:  686 LVLQGHSQEGFGFSWNIKNSGVLLSSAVNGMIQLWDINCTPENKMEFS 733
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: 4
Match NameE-valueIdentityDescription
RBBP73.045e-652.27RB binding protein 7, chromatin remodeling factor ... [more]
RBBP75.287e-652.27RB binding protein 7, chromatin remodeling factor ... [more]
RBBP75.341e-652.27RB binding protein 7, chromatin remodeling factor ... [more]
RBBP75.785e-652.27RB binding protein 7, chromatin remodeling factor ... [more]
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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
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BLAST of Retinoblastoma binding protein-1 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Caf1-557.457e-755.00gene:FBgn0263979 transcript:FBtr0301845[more]
Caf1-557.604e-755.00gene:FBgn0263979 transcript:FBtr0083052[more]
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BLAST of Retinoblastoma binding protein-1 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rbbp46.265e-652.27retinoblastoma binding protein 4 [Source:NCBI gene... [more]
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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
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BLAST of Retinoblastoma binding protein-1 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 3
Match NameE-valueIdentityDescription
Rbbp73.043e-652.27retinoblastoma binding protein 7, chromatin remode... [more]
Rbbp73.630e-652.27retinoblastoma binding protein 7, chromatin remode... [more]
Rbbp73.667e-652.27retinoblastoma binding protein 7, chromatin remode... [more]
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BLAST of Retinoblastoma binding protein-1 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 3
Match NameE-valueIdentityDescription
sp|O22467|MSI1_ARATH3.163e-654.76Histone-binding protein MSI1 OS=Arabidopsis thalia... [more]
sp|O22466|MSI1_SOLLC6.359e-654.76WD-40 repeat-containing protein MSI1 OS=Solanum ly... [more]
sp|Q24572|CAF1_DROME7.622e-655.00Probable histone-binding protein Caf1 OS=Drosophil... [more]
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BLAST of Retinoblastoma binding protein-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
I1ZIK22.227e-1787.23Retinoblastoma binding protein-1 OS=Schmidtea medi... [more]
A0A226DJ275.478e-650.98Putative histone-binding protein rbbD OS=Folsomia ... [more]
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BLAST of Retinoblastoma binding protein-1 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
rbbp45.457e-652.27RB binding protein 4, chromatin remodeling factor ... [more]
rbb4l7.955e-652.27histone-binding protein RBBP7 [Source:NCBI gene;Ac... [more]
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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: 1
Match NameE-valueIdentityDescription
ENSPMAT00000008002.11.011e-650.00pep scaffold:Pmarinus_7.0:GL477852:421:9512:1 gene... [more]
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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
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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
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BLAST of Retinoblastoma binding protein-1 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rbbp45.277e-652.27RB binding protein 4, chromatin remodeling factor ... [more]
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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
SMESG000043653.15.221e-3584.51SMESG000043653.1[more]
SMESG000043653.11.027e-3484.51SMESG000043653.1[more]
SMESG000043653.13.379e-3495.16SMESG000043653.1[more]
SMESG000016363.16.195e-2586.00SMESG000016363.1[more]
SMESG000013977.11.165e-2389.58SMESG000013977.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027781 ID=SMED30027781|Name=Retinoblastoma binding protein-1|organism=Schmidtea mediterranea sexual|type=transcript|length=733bp
TCCACAACTACGATATTTTTGCATCCTCATGAGCTTTGTAGCAATCGATA
ATAAATTAACTTCAATTCAAACTAACTATTTCGTTCTTCAAGGACATTCT
CAGGAAGGTTTTGGATTTTCTTGGAACATCAAAAACGCTGGTGTATTACT
TAGTTCTGCAGTGAATGGAACAATTCAATTGTGGGATATTAATTGTACTC
CAGAAAATAAAATTGAATTCACCAGGTATTTTCCGTTAGAAAATAAGGGA
ATCAAATACAGATGTGCTAATATAAGATCAATTAGTGGTCCTCAGCAAAA
AGTATGTTTAATAAATAAAAATGAATGAGAAATATGAGAAACATGAGCCA
TATGGAGAGACCGAGCTATTGTAAAATCCAAGAAAATTGGATAAAGTCTC
ATAAAATCAATAAACGTAATTAGTTTCGTGTTACTAGAGACGGCAGAAGT
CGCTTAACAATTAGGGTAGCGAAAATAAAATAATTATTTTGTGGAAACTT
AATATGATTAGTTTGTTGAACAGCTACATAAACTAGGAAACAAATTCTGA
AGTGATAAGTGAGTCGAAGTAAAGAAAAAGCGTGTCCATATTTTGAATTT
TTAAGGTGAGTCGGAAAGCGAGTAAAACGTAATATTAGACAATTCAGTTT
AACGTGCATACAAGAAAGGCCGATCTACCATGGGTAGTCTTAATCCTATT
GCAAAAGTGTAGATCAAGAAATATTGTATCGAG
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protein sequence of SMED30027781-orf-1

>SMED30027781-orf-1 ID=SMED30027781-orf-1|Name=SMED30027781-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
PQLRYFCILMSFVAIDNKLTSIQTNYFVLQGHSQEGFGFSWNIKNAGVLL
SSAVNGTIQLWDINCTPENKIEFTRYFPLENKGIKYRCANIRSISGPQQK
VCLINKNE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000420parapharyngeal region
PLANA:0000429neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR017986WD40_repeat_dom
IPR015943WD40/YVTN_repeat-like_dom_sf
IPR019775WD40_repeat_CS
IPR001680WD40_repeat
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus