Alpha-and gamma-adaptin-binding protein p34-like protein

Overview
NameAlpha-and gamma-adaptin-binding protein p34-like protein
Smed IDSMED30014068
Length (bp)783
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 Alpha-and gamma-adaptin-binding protein p34-like protein (SMED30014068) t-SNE clustered cells

Violin plots show distribution of expression levels for Alpha-and gamma-adaptin-binding protein p34-like protein (SMED30014068) 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 Alpha-and gamma-adaptin-binding protein p34-like protein (SMED30014068) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Alpha-and gamma-adaptin-binding protein p34-like protein (SMED30014068) 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



SMED30014068

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30014068h1SMcG0005633 dd_Smed_v4_2426_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Match: E0VF03 (Uncharacterized protein OS=Pediculus humanus subsp. corporis OX=121224 GN=8239505 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.372e-8
Identity = 60/241 (24.90%), Postives = 102/241 (42.32%), Query Frame = 1 
Query:   85 ILFCDCRSERSDEIVIQIIRNITGNSELIFQANV-DYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDINSEIRLLVTCDSELGNHVHDWCXXXXXXXXXXXXKASDSDIEDI-----------NNEVTGWRRIKSALEANDWCNLISDSASD------EELQV-----------DQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 720
            +LF  C +   DE++  +++      ++I + N+  + W I  KYY   V +     + +       +  AVVL  D                + EI+LLVT      N  ++ C + +     + +     ++E I             E+TG  RI  AL A+ W NL+ +S         E+L++           + F  L  QL D+K RV + +  ++++ AEEV   FW+AMGG
Sbjct:    7 VLFMSCSNTHPDELIKSVLKVDELPQKIIIEENIYAFSWLIDNKYYSAEVYLCSFPEKKLMSKQFAERVQAVVLHFDSSQ-----------KYDPEIKLLVT-----NNFPNETCTKKDALEWCVNKNFELIELEPIIDDEESELEDDFPEITGIPRIIQALNAHVWPNLVMNSFHQDNNLGREKLELVRSLEEILENDNDFSMLFSQLSDLKERVSSYSGAEKKKAAEEVVKAFWKAMGG 231
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Match: A0A1E1XHT9 (Uncharacterized protein OS=Amblyomma aureolatum OX=187763 PE=2 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.487e-8
Identity = 68/256 (26.56%), Postives = 109/256 (42.58%), Query Frame = 1 
Query:   76 LKKILFCDCRSERSDEIVIQIIRNITGNSELIFQANVDYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDG--KDMNNVDKLWNLLDINSEIRLLVT--CDSELG------NHVHDWCXXXXXXXXXXXXKASDSDIEDINNEVTGWRRIKSALEANDWCNL----------ISD-----SASD------------EELQVD----QFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 720
            L   L   C  + +D +V +I+  ++     + +    + W I TKYY   V +   +   +  ++       +++L D   KD   +   W +   + ++ LLV   C S           V +WC+E + ELIE     +  D ED   + TG +RI  AL A+ W  L          I+D     SA D            E +  D     FE+L  +  DMK   +  + E+R++ AE+V +QFWRA GG
Sbjct:    5 LDGCLIVSCCDDSTDVLVKEIVHPVSVAPVRVSEGGQAFPWAIETKYYTATVYLHTTSASVVDYDDSAENIHGLIVLFDPNQKDTLEIAAKW-IEKCHCDVVLLVCGRCPSAAEPQGLSRQQVLEWCIERSCELIE-----TRPDQEDDEEDATGVKRIVEALHAHPWPQLEMKEAPGPSRITDQCSRLSAGDSGEADKDLKLFTEAMATDGEDVSFEELFAKFKDMKVEADKLSGEERKKFAEKVAIQFWRAFGG 254
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Match: A0A0K2TSP3 (Alpha and gammaadaptinbinding protein p34like [Amphimedon queenslandica] OS=Lepeophtheirus salmonis OX=72036 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.535e-7
Identity = 52/191 (27.23%), Postives = 88/191 (46.07%), Query Frame = 1 
Query:  196 WNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDI-NSEIRLLV------TCDSELGNHVHDWCXXXXXXXXXXXXKASDSDIEDINNEVTGWRRIKSALEANDW--CNLISDSAS-------DEELQVDQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 720
            W I  KYY   V + ++  ++   N+     PAV++  D K ++N D+   L D  N+E+RL+V      +C SE    +   C       +   E       E++   V G  R+  AL+   W    +  D+ S       ++E +++ FE+L  Q   +K+   + +  +R+R  E+V   FWRAMGG
Sbjct:   40 WRISNKYYSASVKLTLQPKEESSPNDP----PAVLVYID-KSISNFDETQVLKDFPNAEVRLIVAQEPNSSCSSEFIAAIP--CSGWELVDLSEKE-------EELGGSV-GLPRVAEALQTVAWDPGEITKDTKSNKEESIREQEKEMESFEKLFNQFAALKSHSNSLSGHERKRYTEKVVTSFWRAMGG 215
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Match: A0A482W5J2 (Adaptin binding domain containing protein OS=Asbolus verrucosus OX=1661398 GN=BDFB_002636 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.620e-6
Identity = 62/208 (29.81%), Postives = 100/208 (48.08%), Query Frame = 1 
Query:  184 VDYKWNIVTKYYKTLVSIE--IKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKL--WNLL--DINSEIRLLV----TCDSELGNHVH-DWCXXXXXXXXXXXXKASDSDIEDINNEVTGWRRIKSALEANDWCNLI---SDSASDEELQ---------------VDQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 720
            V + W I TKYY   V I    ++YQ   + N      A+++  D      ++ L  W++L  D   E++LL+    T D+++      +WCL++ FELIEL      +D +DI  E  G  R+  AL+A+ W NL+      + D E++                D F  L  QL  MK  +++  +  R++ AE+V   FW+A+GG
Sbjct:   40 VSHVWTIDTKYYTAEVDIIGISEHYQRGQEFN--ETVEALIIHMDTNKETGLEDLSKWSVLEEDCAPEVKLLIANYCTNDTKITKSTATEWCLKHGFELIELYPAQQTTD-QDIIEEKIGVDRVVEALQAHTWSNLVMKNEKKSGDSEVKNDLTEICEEFLTSEGADDFSDLFAQLSMMKESLQSLPMNQRKQCAEQVVTAFWKAIGG 244
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Match: A0A2T7NFK4 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_20453 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 2.321e-6
Identity = 54/168 (32.14%), Postives = 87/168 (51.79%), Query Frame = 1 
Query:   88 LFCDCRSERSDEIVIQIIRNIT--GNSELIFQANVDYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVD--KLW--NLLDINSEIRLLVTCDSELGNHV-----HDWCXXXXXXXXXXXXKASDSDIEDINNEVTGWRRIKSALEANDWCNL 558
            LF  C + + +E+V QI+ N+T       + ++ + Y W+I TKYY   V +   + + I D N  +   A V+  D +++++ D  K W   L  IN  +++LV   S   + V       WC+E+ FEL+EL  +A+  D +D   E  G +RI  AL A+ W NL
Sbjct:    7 LFASCAAFQPEELVKQIL-NVTDLPAGRPVIESVLAYDWHIDTKYYTADVHLCTASTRTIGDENFAQSVQAFVVYFDSREVSSFDSVKSWMSYLRHINPAVQILVCQTSHQDDPVSRLTAQQWCIEHGFELVELEPEANSDDEDDDFVESNGVKRIIQALHAHTWPNL 173
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like protein vs. Planmine SMEST
Match: SMESG000024634.1 (SMESG000024634.1)

HSP 1 Score: 410.994 bits (1055), Expect = 3.278e-147
Identity = 216/216 (100.00%), Postives = 216/216 (100.00%), Query Frame = 1 
Query:   73 MLKKILFCDCRSERSDEIVIQIIRNITGNSELIFQANVDYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDINSEIRLLVTCDSELGNHVHDWCXXXXXXXXXXXXKASDSDIEDINNEVTGWRRIKSALEANDWCNLISDSASDEELQVDQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 720
            MLKKILFCDCRSERSDEIVIQIIRNITGNSELIFQANVDYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDINSEIRLLVTCDSELGNHVHDWCLENNFELIELLEKASDSDIEDINNEVTGWRRIKSALEANDWCNLISDSASDEELQVDQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG
Sbjct:    1 MLKKILFCDCRSERSDEIVIQIIRNITGNSELIFQANVDYKWNIVTKYYKTLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDINSEIRLLVTCDSELGNHVHDWCLENNFELIELLEKASDSDIEDINNEVTGWRRIKSALEANDWCNLISDSASDEELQVDQFEQLLGQLGDMKNRVETANLEDRRRIAEEVTVQFWRAMGG 216
The following BLAST results are available for this feature:
BLAST of Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like protein 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
E0VF031.372e-824.90Uncharacterized protein OS=Pediculus humanus subsp... [more]
A0A1E1XHT91.487e-826.56Uncharacterized protein OS=Amblyomma aureolatum OX... [more]
A0A0K2TSP33.535e-727.23Alpha and gammaadaptinbinding protein p34like [Amp... [more]
A0A482W5J21.620e-629.81Adaptin binding domain containing protein OS=Asbol... [more]
A0A2T7NFK42.321e-632.14Uncharacterized protein OS=Pomacea canaliculata OX... [more]
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BLAST of Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like 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 Alpha-and gamma-adaptin-binding protein p34-like protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000024634.13.278e-147100.00SMESG000024634.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014068 ID=SMED30014068|Name=Alpha-and gamma-adaptin-binding protein p34-like protein|organism=Schmidtea mediterranea sexual|type=transcript|length=783bp
CTTTAAAAACATTTGAAAATCCATTCTTTAAATACATTACTTTGCAAATA
AAGCGAAAACTTAATATTTAAAATGTTGAAAAAAATTTTATTTTGTGACT
GTCGAAGTGAACGCTCTGATGAAATTGTTATTCAGATAATAAGAAATATA
ACTGGTAATTCAGAATTAATCTTTCAAGCAAATGTTGATTATAAGTGGAA
TATTGTGACTAAGTATTATAAAACATTAGTTTCAATTGAGATAAAAAATT
ATCAAGATATTCATGATAATAATTGCGTTCGTAAATATCCAGCAGTTGTG
TTGTTAACTGATGGAAAGGACATGAATAATGTCGACAAATTGTGGAACTT
GTTAGATATAAATTCTGAGATACGTTTATTAGTAACTTGTGACTCGGAAT
TAGGCAATCATGTGCACGATTGGTGCTTGGAAAACAATTTTGAATTGATA
GAATTGTTAGAAAAAGCATCAGATAGTGATATAGAAGATATAAACAATGA
AGTTACCGGCTGGCGTCGGATTAAATCAGCTTTAGAAGCCAATGATTGGT
GCAATTTGATTTCAGATTCCGCAAGCGACGAAGAGTTACAAGTTGATCAA
TTTGAGCAGTTGCTGGGCCAATTAGGCGATATGAAGAATCGAGTTGAAAC
TGCGAATCTGGAAGATCGCAGGCGAATCGCAGAGGAAGTTACGGTGCAGT
TTTGGCGAGCAATGGGCGGATCAGAGAGCGAATTGAATGATTTGTGATTG
TTGTGAAATAAATCAATTTCTTTATTATCATTG
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protein sequence of SMED30014068-orf-1

>SMED30014068-orf-1 ID=SMED30014068-orf-1|Name=SMED30014068-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=225bp
MLKKILFCDCRSERSDEIVIQIIRNITGNSELIFQANVDYKWNIVTKYYK
TLVSIEIKNYQDIHDNNCVRKYPAVVLLTDGKDMNNVDKLWNLLDINSEI
RLLVTCDSELGNHVHDWCLENNFELIELLEKASDSDIEDINNEVTGWRRI
KSALEANDWCNLISDSASDEELQVDQFEQLLGQLGDMKNRVETANLEDRR
RIAEEVTVQFWRAMGGSESELNDL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR019341Alpha/Gamma-adaptin-bd_p34
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019341Alpha/gamma-adaptin-binding protein p34PANTHERPTHR14659FAMILY NOT NAMEDcoord: 170..220
coord: 39..169