GRB2 associated binding protein-1

Overview
NameGRB2 associated binding protein-1 (AFJ24813.1)
Smed IDSMED30023388
Length (bp)807
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 GRB2 associated binding protein-1 (SMED30023388) t-SNE clustered cells

Violin plots show distribution of expression levels for GRB2 associated binding protein-1 (SMED30023388) 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 GRB2 associated binding protein-1 (SMED30023388) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GRB2 associated binding protein-1 (SMED30023388) 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.
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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



SMED30023388

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30023388 SmedASXL_071173SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30023388 dd_Smed_v4_5117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023388 dd_Smed_v4_5117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023388 dd_Smed_v4_5117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023388 dd_Smed_v4_5117_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023388 dd_Smed_v6_5117_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30023388 dd_Smed_v4_5117_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of GRB2 associated binding protein-1 vs. TrEMBL
Match: I1ZIF9 (GRB2 associated binding protein-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 299.286 bits (765), Expect = 1.495e-100
Identity = 146/149 (97.99%), Postives = 146/149 (97.99%), Query Frame = 1 
Query:   67 MISPRRRSTTKQKLPVDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFIIHTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE 513
            MIS RR STTKQKL VDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFIIHTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE
Sbjct:    1 MISIRRSSTTKQKLSVDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFIIHTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE 149
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BLAST of GRB2 associated binding protein-1 vs. TrEMBL
Match: E9FU37 (PH domain-containing protein (Fragment) OS=Daphnia pulex OX=6669 GN=DAPPUDRAFT_27812 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 3.366e-7
Identity = 37/127 (29.13%), Postives = 68/127 (53.54%), Query Frame = 1 
Query:  139 ADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFII-HTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIED-QNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE 513
            A+ EI  +G+L+KSPP K+       I++AK+R+R+F++ H+     + + +Y+      +  KG IDL+Q  ++   + IE  + R     D  + +R Y+L +  + E +M SW+  I     L+
Sbjct:    4 ANTEIVHEGWLVKSPPTKR-------IWRAKWRRRWFVLKHSGELPGQYFLEYY-TDRTCRKLKGKIDLDQCEQVDSGLTIESRKQRYAHMFDIRTPKRVYFLAA--DSESDMNSWVGCICHVCGLK 120
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BLAST of GRB2 associated binding protein-1 vs. TrEMBL
Match: A0A0R3T437 (PH domain-containing protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS1813 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 5.661e-7
Identity = 42/144 (29.17%), Postives = 73/144 (50.69%), Query Frame = 1 
Query:  136 PADYEIHKQGYLIKSPP-LKKVRRSSLPIF--------QAKYRKRYFIIHT--NNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKI-SHPVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE*KKISN 531
            P   E+   GYL K+P  L+  ++  L IF        + +++KR+ I +   N T  +I+F+Y+ K  D K P+GS+DLN    I    V  +  N  +++T     RR+Y  ++  N  +EM  WI  + + + +   ++SN
Sbjct:    6 PIGREVLVNGYLRKAPSSLQSTKKQGLNIFCTGCNVLLEPRWKKRFCIFYKVRNATETQIFFEYYNKASD-KNPRGSVDLNSCDCIYEQKVGNQLPNVFVVQTTYRGKRRDYLFSA--NTPEEMNEWISQLTKVLHMVPDQVSN 146
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BLAST of GRB2 associated binding protein-1 vs. Planmine SMEST
Match: SMESG000074673.1 (SMESG000074673.1)

HSP 1 Score: 271.552 bits (693), Expect = 4.282e-93
Identity = 130/148 (87.84%), Postives = 141/148 (95.27%), Query Frame = 1 
Query:   67 MISPRRRSTTKQKLPVDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFIIHTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQL 510
            MIS R+RSTTK+KL VDRIYPLDPADYEIHKQGYLIKSPPLK  RRS+  +FQ+KYRKRYFIIHTNNTN+KIYFDYFCKHEDLKYPKGSIDLNQITKIS+PVHIE +NRLLIET+NGSNRREYYLTSVNNDEDEMQSWI+H+KRFIQL
Sbjct:    1 MISIRKRSTTKKKLAVDRIYPLDPADYEIHKQGYLIKSPPLKNGRRSNYFVFQSKYRKRYFIIHTNNTNSKIYFDYFCKHEDLKYPKGSIDLNQITKISYPVHIEGKNRLLIETENGSNRREYYLTSVNNDEDEMQSWIHHVKRFIQL 148
[Close]
BLAST of GRB2 associated binding protein-1 vs. Planmine SMEST
Match: SMESG000035904.1 (SMESG000035904.1)

HSP 1 Score: 84.3445 bits (207), Expect = 6.504e-20
Identity = 56/144 (38.89%), Postives = 78/144 (54.17%), Query Frame = 1 
Query:   82 RRSTTKQKLPVDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLPIFQAKYRKRYFIIH-TNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISHPVHIEDQNRLLIETD----NGS-NRREYYLTSVNN-DEDEMQSWIYHI 492
            R+++ K K      YPL+   YEI K+GYL+KSPPL          F  K+++RYFI++      N+I+FDYF +H     P G+IDL Q T I   V IE  N + IET     NGS   R YYLT  +   +  +++W+  I
Sbjct:   13 RKNSQKIKPQSKICYPLNTDHYEIIKEGYLLKSPPLNNDEAEIKMGFLKKWKRRYFILYRAKEYENEIFFDYFKRHHLTHIPTGTIDLMQCTNIKMNVKIEKSNAMAIETKYVNFNGSLADRIYYLTPTDQCHQRTLEAWLTAI 156
The following BLAST results are available for this feature:
BLAST of GRB2 associated 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
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BLAST of GRB2 associated 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 GRB2 associated 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
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BLAST of GRB2 associated 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
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BLAST of GRB2 associated 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 GRB2 associated 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
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BLAST of GRB2 associated 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
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BLAST of GRB2 associated binding protein-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
I1ZIF91.495e-10097.99GRB2 associated binding protein-1 OS=Schmidtea med... [more]
E9FU373.366e-729.13PH domain-containing protein (Fragment) OS=Daphnia... [more]
A0A0R3T4375.661e-729.17PH domain-containing protein OS=Rodentolepis nana ... [more]
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BLAST of GRB2 associated 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
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BLAST of GRB2 associated 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
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BLAST of GRB2 associated 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 GRB2 associated 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 GRB2 associated 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
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BLAST of GRB2 associated binding protein-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000074673.14.282e-9387.84SMESG000074673.1[more]
SMESG000035904.16.504e-2038.89SMESG000035904.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30023388
GenBankAFJ24813.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023388 ID=SMED30023388|Name=GRB2 associated binding protein-1|organism=Schmidtea mediterranea sexual|type=transcript|length=807bp
TCAACAGTGAGCTTGCTTCATAATTTTTCATCAAAAATTATTTATTATTG
GAATTAATAGTCACTTATGATTAGCCCTAGGAGGCGCTCGACTACTAAAC
AAAAACTACCAGTAGATAGAATTTACCCATTGGATCCAGCAGATTATGAG
ATTCATAAACAAGGATATTTAATTAAATCACCGCCACTTAAAAAAGTCCG
AAGATCAAGTCTTCCCATATTTCAAGCAAAATATAGAAAAAGATACTTTA
TAATTCACACAAACAACACAAATAATAAAATATATTTCGATTATTTTTGC
AAACACGAAGATTTGAAGTACCCCAAAGGCTCAATAGACTTGAATCAAAT
TACTAAAATATCACATCCAGTACATATAGAGGATCAAAATAGACTTTTGA
TTGAAACAGACAACGGTAGTAATCGAAGAGAATACTATTTGACATCAGTA
AATAATGATGAAGATGAAATGCAAAGTTGGATCTATCATATTAAAAGATT
TATTCAATTAGAATAAAAAAAAATCTCAAATGTTGAAATGATGCAAAGCG
ACAAATATCAATTTATCGTGATTTTCATTTCGTTATTTTATCGAATTACT
TTATTTTCAAATAAAACTTGAAGTAGTGATTCGAAAAACCTTGACATTAT
TTACAAAAGGCTATGTACATAAATTTTCACAAAGTTACGTAATTATGTAT
ACGAATAGCATATTTAAACAAATTGTTTTGAAGTTGTGATATTTTTCAAA
TCAGCTGTATATCAAATCAAGTTGTCCTTAAAAGTTTTAAATCTATTTAA
ATTTAAG
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protein sequence of SMED30023388-orf-1

>SMED30023388-orf-1 ID=SMED30023388-orf-1|Name=SMED30023388-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
MISPRRRSTTKQKLPVDRIYPLDPADYEIHKQGYLIKSPPLKKVRRSSLP
IFQAKYRKRYFIIHTNNTNNKIYFDYFCKHEDLKYPKGSIDLNQITKISH
PVHIEDQNRLLIETDNGSNRREYYLTSVNNDEDEMQSWIYHIKRFIQLE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR001849PH_domain
IPR011993PH-like_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 148..148
NoneNo IPR availablePANTHERPTHR45960:SF2PROTEIN DAUGHTER OF SEVENLESScoord: 30..148
NoneNo IPR availablePANTHERPTHR45960FAMILY NOT NAMEDcoord: 30..148
NoneNo IPR availableSUPERFAMILYSSF50729PH domain-likecoord: 29..146
IPR001849Pleckstrin homology domainSMARTSM00233PH_updatecoord: 29..148
e-value: 6.7E-9
score: 45.6
IPR001849Pleckstrin homology domainPFAMPF00169PHcoord: 30..145
e-value: 1.3E-10
score: 41.7
IPR001849Pleckstrin homology domainPROSITEPS50003PH_DOMAINcoord: 28..146
score: 10.509
IPR011993PH-like domain superfamilyGENE3DG3DSA:2.30.29.30coord: 23..148
e-value: 3.7E-14
score: 54.3