RabBD domain-containing protein

Overview
NameRabBD domain-containing protein
Smed IDSMED30014552
Length (bp)1220
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 RabBD domain-containing protein (SMED30014552) t-SNE clustered cells

Violin plots show distribution of expression levels for RabBD domain-containing protein (SMED30014552) 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 RabBD domain-containing protein (SMED30014552) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for RabBD domain-containing protein (SMED30014552) 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



SMED30014552

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30014552h1SMcG0005152 SmedASXL_017660SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30014552h1SMcG0005152 SmedASXL_012646SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30014552h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014552h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30014552h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30014552h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014552h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30014552h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30014552h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30014552h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014552h1SMcG0005152 Contig40700uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014552h1SMcG0005152 Contig40700newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30014552h1SMcG0005152 dd_Smed_v6_9615_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30014552h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30014552h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30014552h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30014552h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30014552h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30014552h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of RabBD domain-containing protein vs. TrEMBL
Match: A0A1I8IP29 (RabBD domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 6.053e-6
Identity = 29/44 (65.91%), Postives = 34/44 (77.27%), Query Frame = 2 
Query:  584 PVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLRIHSCD 715
            PVTPP PDLSHL+D ER  IA+V+ARA+  E +EDERLR H  D
Sbjct:  454 PVTPPEPDLSHLTDEERLQIARVLARARQTELEEDERLR-HFAD 496
[Close]
BLAST of RabBD domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 218.009 bits (554), Expect = 2.300e-63
Identity = 121/122 (99.18%), Postives = 121/122 (99.18%), Query Frame = 2 
Query:  335 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLLENCXXXXXXXXXXXXPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 700
            MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDL ENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR
Sbjct:    1 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLSENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 122
[Close]
BLAST of RabBD domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 217.238 bits (552), Expect = 4.749e-62
Identity = 121/122 (99.18%), Postives = 121/122 (99.18%), Query Frame = 2 
Query:  335 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLLENCXXXXXXXXXXXXPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 700
            MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDL ENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR
Sbjct:    1 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLSENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 122
[Close]
BLAST of RabBD domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 217.238 bits (552), Expect = 4.984e-62
Identity = 121/122 (99.18%), Postives = 121/122 (99.18%), Query Frame = 2 
Query:  335 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLLENCXXXXXXXXXXXXPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 700
            MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDL ENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR
Sbjct:    1 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLSENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 122
[Close]
BLAST of RabBD domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 216.853 bits (551), Expect = 7.211e-62
Identity = 121/122 (99.18%), Postives = 121/122 (99.18%), Query Frame = 2 
Query:  335 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLLENCXXXXXXXXXXXXPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 700
            MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDL ENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR
Sbjct:    1 MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQKLPIFAYSSDGAAEKKDLSENCSVSSDELVSEDSPVTPPGPDLSHLSDSEREHIAKVIARAKNIERDEDERLR 122
The following BLAST results are available for this feature:
BLAST of RabBD 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 RabBD 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 RabBD domain-containing 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 RabBD 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 RabBD 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 RabBD 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 RabBD 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 RabBD domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1I8IP296.053e-665.91RabBD domain-containing protein OS=Macrostomum lig... [more]
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BLAST of RabBD 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 RabBD 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 RabBD 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 RabBD 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 RabBD 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 RabBD domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000050479.12.300e-6399.18SMESG000050479.1[more]
SMESG000050479.14.749e-6299.18SMESG000050479.1[more]
SMESG000050479.14.984e-6299.18SMESG000050479.1[more]
SMESG000050479.17.211e-6299.18SMESG000050479.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014552 ID=SMED30014552|Name=RabBD domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1220bp
GAGAACTATTCAGGAGGCCATTCATCCCTCTCTGTTCTTTCTTCTGAAAT
TGTTGTTTAGTCTGTTAGGAAGTGTGTGTTGTATGCAAACTCTCTCCGAA
TATATGAAAACAAAGTCAGATTTAAATTCTGAAAGAAAAGAAATAAAAAA
TGTGATACTGGTTGGATTTAGACTCATGTAAATCATTTCTTTCAGCCAAT
AAATTTATCGGATACATGTTCTTCAACACATGTTGAACAACAAATAGGAT
CTATACTGCACGAAAACATGGGGAAAATTAATTATATCAACTGAAAACCG
TTCTTTCTCTCATACTGCGTTTGTATGGTGCTTCATGGGCAATGAGGAAA
GCCTGCCAACAGATAATCGTTCTATAAATCCAAGCATCATTTATACCAGT
AAATTAAAAACTGATATAATTAAAGAAAAACCACCGAAAACTCTTGATAG
CAAACGAAAAATGTCCATTAGCTTGTTGCAAAAACTGCCCATTTTTGCTT
ATTCCTCGGATGGAGCTGCTGAGAAAAAGGATTTATTAGAAAATTGCTCA
GTATCCAGCGACGAATTGGTATCGGAAGATTCTCCAGTCACTCCACCGGG
TCCCGATCTTTCTCATTTGTCCGATTCCGAAAGAGAACACATCGCAAAAG
TCATTGCGCGAGCAAAAAATATTGAAAGAGACGAAGATGAAAGACTCAGG
ATCCATTCCTGCGATCCCGGAGATCAATATTGTCAGAATATGGGGATTTC
ATCGCTCTTTCCAATTGTTCTCACTTACATTTGCACAAAATACATACAGA
ATCCTCTACTACGTCAATTCAATACGCTTTCATTGCTTGTTATGATGAAT
GTAAATACCCGTTTCAGCTCAGAACATTTGAGCGGATGAAGATCAAGATG
CCAGAATTGATTGATGAGCTGTATCCATTGATAAGTAAAGTACCAAAATT
TATTAACCTGTTTTGCCGAGAACCAACAAAGAACGACGAAATTTTCCAGA
ATGACATCAAAGAAGAGTTTGGAAACTGAATCAGTATATAATTTATGTAA
AAACAAGATGAAATATTCTTTACGTTATGGTGGAACGTTTTTAGAAAGTC
AAAAACTGCATTTAAAAATCATTTACTGATCTTAACTAGTCTTTTTTATT
TGAGGTAGAATTAGTGATAATTACTAATTTGATCTAATGTTTCTCGTTTG
CTACAATACCAGCAAAAGCG
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protein sequence of SMED30014552-orf-1

>SMED30014552-orf-1 ID=SMED30014552-orf-1|Name=SMED30014552-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=185bp
MGNEESLPTDNRSINPSIIYTSKLKTDIIKEKPPKTLDSKRKMSISLLQK
LPIFAYSSDGAAEKKDLLENCSVSSDELVSEDSPVTPPGPDLSHLSDSER
EHIAKVIARAKNIERDEDERLRIHSCDPGDQYCQNMGISSLFPIVLTYIC
TKYIQNPLLRQFNTLSLLVMMNVNTRFSSEHLSG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0006886intracellular protein transport
Vocabulary: molecular function
TermDefinition
GO:0017137Rab GTPase binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD