PH domain-containing protein

Overview
NamePH domain-containing protein
Smed IDSMED30027564
Length (bp)1018
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 PH domain-containing protein (SMED30027564) t-SNE clustered cells

Violin plots show distribution of expression levels for PH domain-containing protein (SMED30027564) 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 PH domain-containing protein (SMED30027564) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for PH domain-containing protein (SMED30027564) 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



SMED30027564

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30027564SMESG000023120.1 dd_Smed_v4_12160_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30027564SMESG000023120.1 dd_Smed_v4_12160_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30027564SMESG000023120.1 dd_Smed_v4_12160_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
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BLAST of PH domain-containing protein vs. Ensembl Fly
Match: CG31342 (gene:FBgn0051342 transcript:FBtr0113403)

HSP 1 Score: 49.6766 bits (117), Expect = 2.656e-6
Identity = 31/101 (30.69%), Postives = 57/101 (56.44%), Query Frame = 1 
Query:  454 IAKLREESKHPGGVVINVRIADIVG-LRIVVSQNKIWVARCPKINK--IKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFAL 747
            + +LR E  HPGGV +N+R  D VG +  V +   +W+A   +     +   LH+GDQ++S+  V ++   +    +R+T  +  +++ L R+P GR +A+
Sbjct:  787 VMQLRREIMHPGGVRLNLRRKDCVGSIAWVEAFGGVWIAGWKQKEHPVLYNALHIGDQLLSIAGVSISSAAEANKIIRNT-NTLFVEVLLRRIPFGRAYAI 886
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BLAST of PH domain-containing protein vs. TrEMBL
Match: A0A210PYA8 (PH domain-containing protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT17353 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.239e-6
Identity = 53/195 (27.18%), Postives = 95/195 (48.72%), Query Frame = 1 
Query:  463 LREESKHPG-GVVINVRIADIVGLRIVVSQNKIWVA-----RCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYN-------------SVIFINPINQLV----------SFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIRE 960
            L EE K  G G+ ++ + A+ V L  V   N +W+A     RCP++ +    +H+GDQ++S+ DV VT  +     ++ T +S+ + L + RLP   + A+   N++              + +++P N LV          S   TG  NWM+TEI+  S+    + E +E   +  + + I I++    F+R+
Sbjct:  912 LNEEQKEHGVGLDVSPKSANAVAL--VEMYNGVWIAGWDGRRCPRLAE---KIHIGDQLLSVEDVRVTSSSHASKLLKQT-QSKRVTLVVKRLPYATILAIR-RNHDGENLGITREGGTAEITYVDP-NGLVARCGLQKRAKSVEGTGECNWMLTEINCRSLNFSYKGEEIER-LLNAVGRDISIVIQPADFVRQ 1097
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BLAST of PH domain-containing protein vs. Planmine SMEST
Match: SMESG000023120.1 (SMESG000023120.1)

HSP 1 Score: 641.343 bits (1653), Expect = 0.000e+0
Identity = 317/320 (99.06%), Postives = 319/320 (99.69%), Query Frame = 1 
Query:   16 MSNVECRKKSTSVLRAEKIESVKKLILENGFYDVQDEFNEDLIAIPTGVVINSEENENEDYKNYTCYLEMSEESGIDCGAYNAVDSRDADLVEKEMISDIINECQVVNYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIREFFEIK 975
            MSNVECRKKSTSVLRAEKIESVKKLILENGFYDVQDEFNEDLIAIPTGVVINSEENENEDYKNYTCYLEMSEESGIDCGAYNAVDSRDADLVEKEMISDIINECQVVNYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIREF ++K
Sbjct:    1 MSNVECRKKSTSVLRAEKIESVKKLILENGFYDVQDEFNEDLIAIPTGVVINSEENENEDYKNYTCYLEMSEESGIDCGAYNAVDSRDADLVEKEMISDIINECQVVNYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIREFLKLK 320
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BLAST of PH domain-containing protein vs. Planmine SMEST
Match: SMESG000025381.1 (SMESG000025381.1)

HSP 1 Score: 117.472 bits (293), Expect = 2.136e-30
Identity = 58/206 (28.16%), Postives = 113/206 (54.85%), Query Frame = 1 
Query:  337 NYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFI 954
            +Y +    L  QP+  NR  L   P++  +  L+  +F   KL+EES H GGV I+V++ D+  +R V S   IWV+R       +    +GD++IS+++ ++ ++      + S    + +K RL RLP  ++FA+   +Y S    +   Q     ++ ++  +IT IDG++++ +  +E L++YF++  D+++ +I+  L F+
Sbjct:   90 DYTVPPLNLKFQPIQENRTQLITTPLVTISRALNFRLFACMKLKEESVHSGGVEISVKLPDLFNMRFVRSGESIWVSRVGHRKGDRDIFFIGDRVISVDNKIILNMPTLQHIMASASHDQTLKFRLCRLPYAKIFAIKSTSYKSYFSFDKECQEFILNNSDTTKLVITGIDGVNVDGISTEEQLKSYFVETRDRYVTVIMQPLKFL 295
[Close]
BLAST of PH domain-containing protein vs. Planmine SMEST
Match: SMESG000023122.1 (SMESG000023122.1)

HSP 1 Score: 85.1149 bits (209), Expect = 3.076e-18
Identity = 65/212 (30.66%), Postives = 105/212 (49.53%), Query Frame = 1 
Query:  337 NYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSS--NWMITEID---GISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIR 957
            +Y I  ++   Q ++G    L  FP     +  DS+IF   K+REE  + GGV I V    I  +++ V   K+W++     N++  +LHVGD+IIS+N+  V DL  F +    TK  ED  L + RLPK RVF    +  +        N     + T     +W ITEI+    ++I D +   N+++     I +++ +I+H   FI+
Sbjct:  166 DYEIPEYQPEAQTMNGGYITLETFPFRNKNTFNDSNIFVAMKIREEVCNFGGVTITVGKHLIENIQVKVMNKKLWISDIQNWNEMNASLHVGDRIISVNERPVNDLQTFRE---CTKNREDYILIVQRLPKARVFVFDKNKLDVKTIKLEKNNFFLTKPTKPKDLDWAITEINRTKTVNINDQNIISNIQSVISSYI-RYLAVIIHPARFIK 373
[Close]
BLAST of PH domain-containing protein vs. Planmine SMEST
Match: SMESG000023122.1 (SMESG000023122.1)

HSP 1 Score: 84.7297 bits (208), Expect = 3.121e-18
Identity = 65/212 (30.66%), Postives = 105/212 (49.53%), Query Frame = 1 
Query:  337 NYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSS--NWMITEID---GISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIR 957
            +Y I  ++   Q ++G    L  FP     +  DS+IF   K+REE  + GGV I V    I  +++ V   K+W++     N++  +LHVGD+IIS+N+  V DL  F +    TK  ED  L + RLPK RVF    +  +        N     + T     +W ITEI+    ++I D +   N+++     I +++ +I+H   FI+
Sbjct:  139 DYEIPEYQPEAQTMNGGYITLETFPFRNKNTFNDSNIFVAMKIREEVCNFGGVTITVGKHLIENIQVKVMNKKLWISDIQNWNEMNASLHVGDRIISVNERPVNDLQTFRE---CTKNREDYILIVQRLPKARVFVFDKNKLDVKTIKLEKNNFFLTKPTKPKDLDWAITEINRTKTVNINDQNIISNIQSVISSYI-RYLAVIIHPARFIK 346
[Close]
BLAST of PH domain-containing protein vs. Planmine SMEST
Match: SMESG000023122.1 (SMESG000023122.1)

HSP 1 Score: 84.7297 bits (208), Expect = 3.147e-18
Identity = 65/212 (30.66%), Postives = 105/212 (49.53%), Query Frame = 1 
Query:  337 NYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKLREESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGDQIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYNSVIFINPINQLVSFRSTGSS--NWMITEID---GISIEDLDEKENLENYFMKEIDQFIPIIVHKLSFIR 957
            +Y I  ++   Q ++G    L  FP     +  DS+IF   K+REE  + GGV I V    I  +++ V   K+W++     N++  +LHVGD+IIS+N+  V DL  F +    TK  ED  L + RLPK RVF    +  +        N     + T     +W ITEI+    ++I D +   N+++     I +++ +I+H   FI+
Sbjct:  142 DYEIPEYQPEAQTMNGGYITLETFPFRNKNTFNDSNIFVAMKIREEVCNFGGVTITVGKHLIENIQVKVMNKKLWISDIQNWNEMNASLHVGDRIISVNERPVNDLQTFRE---CTKNREDYILIVQRLPKARVFVFDKNKLDVKTIKLEKNNFFLTKPTKPKDLDWAITEINRTKTVNINDQNIISNIQSVISSYI-RYLAVIIHPARFIK 349
The following BLAST results are available for this feature:
BLAST of PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG313422.656e-630.69gene:FBgn0051342 transcript:FBtr0113403[more]
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BLAST of PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A210PYA83.239e-627.18PH domain-containing protein OS=Mizuhopecten yesso... [more]
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BLAST of PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein 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 PH domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000023120.10.000e+099.06SMESG000023120.1[more]
SMESG000025381.12.136e-3028.16SMESG000025381.1[more]
SMESG000023122.13.076e-1830.66SMESG000023122.1[more]
SMESG000023122.13.121e-1830.66SMESG000023122.1[more]
SMESG000023122.13.147e-1830.66SMESG000023122.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027564 ID=SMED30027564|Name=PH domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1018bp
TTTAAATAGAAATTAATGTCAAATGTTGAATGTAGAAAGAAATCCACGAG
TGTTTTACGGGCAGAAAAAATAGAAAGCGTGAAGAAATTGATTTTAGAAA
ATGGTTTTTATGACGTTCAGGATGAATTTAATGAAGATCTCATAGCTATA
CCAACAGGAGTTGTTATCAATTCCGAGGAAAATGAAAACGAAGACTATAA
AAATTATACGTGCTACTTGGAAATGTCCGAAGAATCTGGGATTGATTGTG
GCGCATATAATGCAGTGGATTCTAGAGATGCTGATCTTGTGGAAAAAGAA
ATGATTTCAGATATCATAAACGAATGTCAAGTGGTCAATTATAATATTGA
CAGCTTCCGACTTAATGTGCAACCTTTAGATGGCAATCGAAATAATTTAT
TTCATTTCCCAATAATTGAAAATACATCAAACTTAGATTCTGATATTTTT
TATATAGCCAAATTAAGAGAAGAATCAAAACATCCTGGAGGAGTCGTAAT
AAATGTACGGATAGCCGATATAGTTGGTTTACGGATTGTCGTTTCACAAA
ATAAAATCTGGGTTGCTAGATGTCCAAAAATAAATAAAATAAAAGGAAAT
CTTCATGTTGGTGACCAAATAATAAGCTTGAATGACGTTTTGGTCACGGA
TCTAAATCAGTTTATCGATTTCGTGCGTTCCACGAAAAAGTCTGAAGATA
TTAAATTAAGGCTTTTAAGGCTTCCAAAAGGTCGCGTATTTGCTTTGACA
CCTCATAATTATAATTCAGTTATCTTTATTAATCCCATCAATCAATTAGT
GTCGTTCCGTAGTACCGGTAGTAGCAATTGGATGATTACTGAAATTGATG
GAATCAGTATAGAAGATCTTGATGAAAAGGAAAATTTAGAAAACTATTTC
ATGAAAGAAATAGACCAGTTTATTCCAATTATTGTCCACAAATTATCTTT
TATTCGGGAATTTTTTGAAATTAAAAAATCTTTAATTTGTTTTTATTATT
AAACATCATTAAACATCC
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protein sequence of SMED30027564-orf-1

>SMED30027564-orf-1 ID=SMED30027564-orf-1|Name=SMED30027564-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=329bp
MSNVECRKKSTSVLRAEKIESVKKLILENGFYDVQDEFNEDLIAIPTGVV
INSEENENEDYKNYTCYLEMSEESGIDCGAYNAVDSRDADLVEKEMISDI
INECQVVNYNIDSFRLNVQPLDGNRNNLFHFPIIENTSNLDSDIFYIAKL
REESKHPGGVVINVRIADIVGLRIVVSQNKIWVARCPKINKIKGNLHVGD
QIISLNDVLVTDLNQFIDFVRSTKKSEDIKLRLLRLPKGRVFALTPHNYN
SVIFINPINQLVSFRSTGSSNWMITEIDGISIEDLDEKENLENYFMKEID
QFIPIIVHKLSFIREFFEIKKSLICFYY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
Vocabulary: INTERPRO
TermDefinition
IPR001478PDZ
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding