Sh3bp2

Overview
NameSh3bp2
Smed IDSMED30025766
Length (bp)1153
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 Sh3bp2 (SMED30025766) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Sh3bp2 (SMED30025766) 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




SMED30025766

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
epidermisSMED30025766 dd_Smed_v4_11152_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025766 dd_Smed_v4_11152_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025766 dd_Smed_v4_11152_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30025766 dd_Smed_v4_11152_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
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072368.1 (SMESG000072368.1)

HSP 1 Score: 558.91 bits (1439), Expect = 0.000e+0
Identity = 311/311 (100.00%), Postives = 311/311 (100.00%), Query Frame = 3
Query:   60 MEDYSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHXXXXXXXXXXXXXXXXXXXXVAEETFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHXXXXXXXXXXXXXVFNSLQNLLNYYQKNDIPGRQCKLVIPYKLRMKN 992
            MEDYSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHNYNPDYYSNYNSSDESSNYDVAEETFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHQNNNCIQIKNNNIVFNSLQNLLNYYQKNDIPGRQCKLVIPYKLRMKN
Sbjct:    1 MEDYSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHNYNPDYYSNYNSSDESSNYDVAEETFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHQNNNCIQIKNNNIVFNSLQNLLNYYQKNDIPGRQCKLVIPYKLRMKN 311          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072391.1 (SMESG000072391.1)

HSP 1 Score: 189.889 bits (481), Expect = 2.383e-57
Identity = 123/307 (40.07%), Postives = 174/307 (56.68%), Query Frame = 3
Query:   69 YSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHXXXXXXXXXXXXXXXXXXXXVAEETFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHXXXXXXXXXXXXXVFNSLQNLLNYYQKNDIPGRQCKLVIPYKLRMK 989
            ++G LF ++ + G K W+KV+  L KGS Y+YS+  A +PKMV IL   S +EI + RK   +   ++  NS  NS+  L FGT ++  +  ++K F  +I++   N+F +    +  +S N+  S   FE   + EL  ++        + +     +           SE  S + IY                 LSI  +   INLD +I +GTS EAYQEL+ N+C+GAYLVR++   K LTVQ  +EVLKY LIT+ NNN +QI+N  + FNSLQ+LL YY KNDIPGR+CKLVIPYKLR K
Sbjct:   19 FAGDLFHKVSHLGSKTWVKVYTILFKGSFYVYSNVDAKQPKMVVILTASSKVEITSNRKNRYMLSFTVFSNSNDNSIRQLKFGTYSQEILSTLMKSFNESINRGANNYFTSNEPNDFKMSLNRVNSNTHFENNVNEELFIYDMPERPVIGFKNGMPDFDL----------SETSSQNSIY-----------------LSIDSETYNINLDDVIFKGTSYEAYQELEKNVCYGAYLVREENNAKRLTVQTRDEVLKYVLITNTNNNFVQIQNQEMKFNSLQDLLAYYHKNDIPGRKCKLVIPYKLRKK 298          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072396.1 (SMESG000072396.1)

HSP 1 Score: 120.939 bits (302), Expect = 3.000e-31
Identity = 97/315 (30.79%), Postives = 153/315 (48.57%), Query Frame = 3
Query:   48 ANRLMED----YSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHXXXXXXXXXXXXXXXXXXXXVAEETFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHXXXXXXXXXXXXXVFNSLQNLLNYYQKNDIPGRQCKLVIPYKL 980
            A  L++D    +SGYL ++I     K WIK ++ +  G+IYIYS   + KP +V IL  +  I+I+  R + P  V ++ P    +SV  L F   +E EM F +  F+  I  SK      K   E I S      +N+ E   +S + + N   D   + +                E  +   F          PL    T  ++LS+  D    N++++I  GT  EA+ EL      G+YLVRQD GR+ILTV+C + ++KY L++    + I I      F ++ +LL+YY ++ +P + CKL+IP+K 
Sbjct:   12 AQILLQDSSVTFSGYLERKITMLSFKHWIKCYVVISNGNIYIYSSSTSPKPVLVCILGAFHQIQIIKNRIQPPFWVFTLKPLI--DSVPELKFAAASEREMNFWISEFKLGIILSKNTQL--KDDSERISSQ---SCKNNMEGSIYSTVSERNEIVDTLLHSDKI-----------NIYEEPDDLIFQINPVNPTAPPLYPTLTQFDNLSLKSDTSDENVEYVIFYGTREEAFSELLKRPYLGSYLVRQDNGRQILTVKCESNIVKYCLLSDPKTDRIHIAGQKESFENVYHLLSYYHEHYLPNQNCKLLIPFKF 308          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072376.1 (SMESG000072376.1)

HSP 1 Score: 103.219 bits (256), Expect = 7.115e-25
Identity = 94/310 (30.32%), Postives = 155/310 (50.00%), Query Frame = 3
Query:   69 YSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILAGYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLFESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHXXXXXXXXXXXXXXXXXXXXVAEETFKENSEGCSFDEIYFISE-NTPLQDNETVDNDLSIYVD-----DCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHXXXXXXXXXXXXXVFNSLQNLLNYYQKNDIPGRQCKLVIPYKL 980
            + G  +Q+I     K+W+K  + + KG+IY Y + K+  P M+A L    +IEI+   KK  L V  +  +S  N +  + FG  +  +++ +V+  E ++  ++Q       +  N  SN+ +G  +         LP+                  +  +   T  +N E CS + + +I+E NTP  DN       +IY D     D  +NL++II +GTS EA +EL  +   GA+L+R  +  KILTVQC   ++KY L     +N + IK  ++ F+++ +LL YY K  +P + CKL  PYKL
Sbjct:   20 FIGNFYQKISRFWIKQWLKRLVIISKGTIYTYPNSKSKLPTMMAHLNISCSIEIV---KKFTLFVCVLKSDS-SNPLSSIKFGAKSRSKLDELVRAVEESMKFNEQEIHLVGVSQRN--SNSTSGYLSI-------PLPE-----------------ISKSLTSSTMLKN-EFCSDNNVIYINEKNTPKNDNRC---SFTIYYDYSELCDPQLNLENIIFKGTSDEASKELFRSFHLGAFLIRLREDVKILTVQCPECIIKYVLEVDPESNRVNIKGESVTFDNIMDLLAYYHKFCLPRQNCKLTTPYKL 295          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072377.1 (SMESG000072377.1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.810e-13
Identity = 50/142 (35.21%), Postives = 77/142 (54.23%), Query Frame = 3
Query:  564 TFKENSEGCSFDEIYFISENTPLQDNETVDNDLSIYVDDC---PINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTVQCANEVLKYELITHXXXXXXXXXXXXXVFNSLQNLLNYYQKNDIPGRQCKLVIPYKL 980
            T   N++G S   ++ I    P +   T+++ +  Y D     P+NL +II  GTS              ++LVRQ+  R++LTVQ  ++VLKY L T+     I +    + F++LQ LL+YYQ+ D+P  + KL IPYKL
Sbjct:   85 TLTANNKGSSQRALFQI----PPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTS--------------SFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKL 208          
The following BLAST results are available for this feature:
BLAST of Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 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 Sh3bp2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072368.10.000e+0100.00SMESG000072368.1[more]
SMESG000072391.12.383e-5740.07SMESG000072391.1[more]
SMESG000072396.13.000e-3130.79SMESG000072396.1[more]
SMESG000072376.17.115e-2530.32SMESG000072376.1[more]
SMESG000072377.11.810e-1335.21SMESG000072377.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025766 ID=SMED30025766|Name=Sh3bp2|organism=Schmidtea mediterranea sexual|type=transcript|length=1153bp
TTAAATTAGAATTTTGTTTAAACGAATTAACAATAAAATAATTATAAGCT
AATAGATTAATGGAAGATTATTCTGGATATTTGTTTCAGCAAATCTTAAA
TTCGGGTAAGAAAAAATGGATCAAAGTTTTCATTAAACTGCACAAAGGAT
CCATTTATATATATTCTGACGACAAAGCGATAAAACCAAAAATGGTAGCC
ATTTTAGCAGGATATTCAACAATTGAAATTTTAACTGGCCGAAAAAAACA
TCCCCTTCATGTGATTTCCATTTGTCCCAATTCACCAAGGAATTCAGTGG
TCCCATTAGTATTCGGAACTACCACAGAACCGGAAATGGAGTTTATTGTC
AAACTGTTCGAAAGTAATATCAGTAAAAGCAAACAAAATTTTTTTTTCAA
TAAATCAACTGGTGAAAATATCATTTCAAACAATAAAACAGGATCTAGAA
ATTCTTTTGAAAAAGAATCGCATAGCGAGCTACCGCAACATAATTACAAT
CCAGACTATTATTCGAATTACAATTCCAGCGATGAGTCTTCGAACTACGA
TGTTGCCGAAGAAACCTTTAAAGAAAACTCTGAAGGTTGTAGTTTTGATG
AGATATACTTTATTTCCGAAAATACACCACTTCAAGATAACGAAACAGTT
GACAATGATTTAAGCATCTATGTTGATGACTGTCCAATCAATTTGGATCA
TATTATACTCGAAGGAACAAGTATTGAAGCCTACCAAGAACTGAAAAATA
ACATCTGTCATGGTGCTTACCTTGTTAGACAAGACAAAGGTCGAAAAATA
TTAACAGTTCAATGCGCAAATGAAGTTCTAAAATACGAACTTATCACTCA
TCAAAACAATAATTGCATCCAAATTAAAAACAACAATATTGTGTTCAATT
CTTTACAAAATTTATTAAATTATTATCAAAAAAATGACATCCCCGGAAGG
CAGTGCAAACTGGTTATTCCTTACAAACTGCGAATGAAAAATTAAAGTTT
TTTTTTCATACTCAATTTTACTTTTATTGTTTGTATTCAGTGGCAAAAAT
CTTTTCCAAACGAAAGTTTCATAAAACCTTTCATAATAACGTGAAATTCT
TCATTCATTATCAACAATGTCATCTTTGTTTTAATGTTAATTAAATGATA
TTT
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protein sequence of SMED30025766-orf-1

>SMED30025766-orf-1 ID=SMED30025766-orf-1|Name=SMED30025766-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=312bp
MEDYSGYLFQQILNSGKKKWIKVFIKLHKGSIYIYSDDKAIKPKMVAILA
GYSTIEILTGRKKHPLHVISICPNSPRNSVVPLVFGTTTEPEMEFIVKLF
ESNISKSKQNFFFNKSTGENIISNNKTGSRNSFEKESHSELPQHNYNPDY
YSNYNSSDESSNYDVAEETFKENSEGCSFDEIYFISENTPLQDNETVDND
LSIYVDDCPINLDHIILEGTSIEAYQELKNNICHGAYLVRQDKGRKILTV
QCANEVLKYELITHQNNNCIQIKNNNIVFNSLQNLLNYYQKNDIPGRQCK
LVIPYKLRMKN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0005070SH3/SH2 adaptor activity
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
GO:0009967positive regulation of signal transduction
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR036860SH2_dom_sf
IPR035848SH3BP2
IPR011993PH-like_dom_sf
IPR000980SH2
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR011993PH-like domain superfamilyGENE3DG3DSA:2.30.29.30coord: 2..111
e-value: 1.1E-6
score: 30.6
IPR036860SH2 domain superfamilyGENE3DG3DSA:3.30.505.10coord: 219..311
e-value: 8.4E-10
score: 40.3
IPR036860SH2 domain superfamilySUPERFAMILYSSF55550SH2 domaincoord: 221..305
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 126..145
NoneNo IPR availableCDDcd00173SH2coord: 220..289
e-value: 1.8625E-5
score: 40.1315
NoneNo IPR availableSUPERFAMILYSSF50729PH domain-likecoord: 4..94
IPR035848SH3 domain-binding protein 2PANTHERPTHR15126SH3-BINDINGcoord: 4..167
coord: 232..306