bambi

Overview
Namebambi (ADX42731.1)
Smed IDSMED30005819
Length (bp)1212
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 bambi (SMED30005819) t-SNE clustered cells

Violin plots show distribution of expression levels for bambi (SMED30005819) 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 bambi (SMED30005819) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for bambi (SMED30005819) 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



SMED30005819

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30005819h1SMcG0006765 Contig29032uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005819h1SMcG0006765 Contig29032newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30005819h1SMcG0006765 dd_Smed_v4_11062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005819h1SMcG0006765 dd_Smed_v4_11062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30005819h1SMcG0006765 dd_Smed_v4_11062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30005819h1SMcG0006765 dd_Smed_v6_11062_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
dorsal midlineSMED30005819h1SMcG0006765 bambismed_ncbi_20240424PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
dorsal region of the whole animalSMED30005819h1SMcG0006765 bambismed_ncbi_20240424PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30005819h1SMcG0006765 dd_Smed_v4_11062_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the whole animalSMED30005819h1SMcG0006765 dd_Smed_v4_11062_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of bambi vs. TrEMBL
Match: F1DT96 (Bambi (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 381.719 bits (979), Expect = 7.390e-130
Identity = 219/221 (99.10%), Postives = 220/221 (99.55%), Query Frame = 3 
Query:  483 TDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENXXXXXXXXXXXXXXXHRESKIYSLKQNFRYPLSLIIIIASFCGXXXXXXXXXXXXXXXXXYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSR 1145
            TDDCLAQDKTTCIAPTTCFVEYLQESTENP+KFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMI NQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSR
Sbjct:    1 TDDCLAQDKTTCIAPTTCFVEYLQESTENPVKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIRNQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSR 221
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BLAST of bambi vs. TrEMBL
Match: A0A1S3JFI4 (uncharacterized protein LOC106172815 OS=Lingula unguis OX=7574 GN=LOC106172815 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 2.287e-7
Identity = 33/85 (38.82%), Postives = 46/85 (54.12%), Query Frame = 3 
Query:  465 ITCHCTTDDCLAQDKTTCIAPTTCFVEYLQ-ESTENPIKFHAKGCISESYPLMCNQNLLSPSG-NGPKLYLECCYKNYCNSNTRP 713
            I C CTT DC  + KTTC+A  +C+V++L  +  + P     +GCI++  PL+C      P G  GP   L CC+ N CN    P
Sbjct:   23 IQCECTTADCSREQKTTCLAEHSCYVQHLPVDKDDGPTPPILRGCINDPTPLLCENR--RPLGYKGPWPVLHCCFTNGCNKEVLP 105
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BLAST of bambi vs. Planmine SMEST
Match: SMESG000054829.1 (SMESG000054829.1)

HSP 1 Score: 452.981 bits (1164), Expect = 6.835e-161
Identity = 255/255 (100.00%), Postives = 255/255 (100.00%), Query Frame = 3 
Query:  393 MIFKLFVNFIMIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENXXXXXXXXXXXXXXXHRESKIYSLKQNFRYPLSLIIIIASFCGXXXXXXXXXXXXXXXXXYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT 1157
            MIFKLFVNFIMIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT
Sbjct:    1 MIFKLFVNFIMIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT 255
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BLAST of bambi vs. Planmine SMEST
Match: SMESG000054829.1 (SMESG000054829.1)

HSP 1 Score: 433.721 bits (1114), Expect = 1.883e-153
Identity = 245/245 (100.00%), Postives = 245/245 (100.00%), Query Frame = 3 
Query:  423 MIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENXXXXXXXXXXXXXXXHRESKIYSLKQNFRYPLSLIIIIASFCGXXXXXXXXXXXXXXXXXYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT 1157
            MIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT
Sbjct:    1 MIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKRLANFFNMIHNQIKPENISKSQQEVSSKSQIIHRESKIYSLKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIYSVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQSRVILT 245
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BLAST of bambi vs. Planmine SMEST
Match: SMESG000021049.1 (SMESG000021049.1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.938e-10
Identity = 31/112 (27.68%), Postives = 55/112 (49.11%), Query Frame = 3 
Query:  393 MIFKLFVNFIMIILIYFPKSYFCKIT-----CHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRP 713
            M+F  F       L++  +  +C++      CHC   +C       CIA T C+ E +Q+   + +   + GC++E+ PL+C  ++      GP ++ +CC  N+CN   RP
Sbjct:    1 MLFAWF-------LLFLIQQNYCRLIKKQLLCHCNNTECKINHSEYCIATTFCYDELIQKHINDSLNHVSSGCLNEATPLVCGIDIRRQYEEGPWIFHKCCADNFCNQ--RP 103
[Close]
BLAST of bambi vs. Planmine SMEST
Match: SMESG000021049.1 (SMESG000021049.1)

HSP 1 Score: 59.3066 bits (142), Expect = 6.278e-10
Identity = 32/116 (27.59%), Postives = 57/116 (49.14%), Query Frame = 3 
Query:  393 MIFKLFVNFIMIILIYFPKSYFCKIT-----CHCTTDDCLAQDKTTCIAPTTCFVEYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNYCNSNTRPNMKR 725
            M+F  F+ F++       +  +C++      CHC   +C       CIA T C+ E +Q+   + +   + GC++E+ PL+C  ++      GP ++ +CC  N+CN   RP  K 
Sbjct:    1 MLFAWFLLFLI-------QQNYCRLIKKQLLCHCNNTECKINHSEYCIATTFCYDELIQKHINDSLNHVSSGCLNEATPLVCGIDIRRQYEEGPWIFHKCCADNFCNQ--RPIYKE 107
The following BLAST results are available for this feature:
BLAST of bambi 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 bambi 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 bambi 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 bambi 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 bambi 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 bambi 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 bambi 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 bambi vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
F1DT967.390e-13099.10Bambi (Fragment) OS=Schmidtea mediterranea OX=7932... [more]
A0A1S3JFI42.287e-738.82uncharacterized protein LOC106172815 OS=Lingula un... [more]
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BLAST of bambi 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 bambi 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 bambi 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 bambi 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 bambi 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 bambi vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000054829.16.835e-161100.00SMESG000054829.1[more]
SMESG000054829.11.883e-153100.00SMESG000054829.1[more]
SMESG000021049.14.938e-1027.68SMESG000021049.1[more]
SMESG000021049.16.278e-1027.59SMESG000021049.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30005819
GenBankADX42731.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005819 ID=SMED30005819|Name=bambi|organism=Schmidtea mediterranea sexual|type=transcript|length=1212bp
TATTATTATTATTAATTATTAATTATTATTATTACTATTATTATTTTTTG
ATTCTGTATGGCGCTGTATTTCAATCTATCTCTCGATTGCCCACTCTCAA
AATGACAGTAGCTGGCCACAAATTGATTTCTAATCATCAGACATCATCTC
TGCTTTCATAATGACGTCTGCAGAAATGGCGCTATTTCTTAATTAATATT
CATACAGCCAATTGATGATAAAGAATCCTTTCAAAATCAACCAATAGCAA
TCGGACTTTGTAGACTAGTTAAATTTCGCTATCTCTACCGTATTATTTTT
AAGATTAACTGGCTCAGCATCAGATATAAATATATAATAATAAATATTGC
CCGACCGAAAATAGTTCATCAATTCTTTCAGTTTGGAGAACAATGATTTT
TAAATTGTTTGTCAATTTTATCATGATTATCCTGATTTATTTTCCAAAAT
CCTATTTCTGCAAAATTACTTGTCATTGTACTACTGATGATTGTTTAGCA
CAGGATAAAACGACTTGTATCGCTCCAACGACATGTTTCGTTGAATATCT
CCAAGAATCCACGGAAAATCCAATAAAATTTCATGCAAAAGGCTGCATAA
GTGAATCATACCCTTTAATGTGTAACCAGAACTTATTAAGTCCAAGCGGA
AATGGACCGAAATTGTATTTAGAATGTTGCTATAAAAACTATTGCAATTC
AAACACAAGGCCAAATATGAAGCGGCTTGCAAACTTTTTCAATATGATAC
ACAACCAAATCAAACCAGAAAACATATCAAAATCACAGCAAGAAGTTTCA
TCGAAATCTCAAATAATTCATCGAGAATCCAAAATTTACTCATTAAAACA
AAATTTTCGTTATCCGCTGTCTCTCATTATTATTATTGCTTCATTTTGTG
GAATATTGCTCATGATCATATTGATAGTCGCCATTATCAAATTGATATTA
ATTTATACACATCCAGATTACATTGACAACGATCAAATATATAGTGTCAG
TTTATCAGGATCATCAAATGATCCAGAAAATAGTATCATTGCCACAGTCG
ACTCTCGGAAAGCAATGATCTACTCTCCCAATTATGATGTCAACACATTT
TATAGGAAATTATTAAAATATCTCAAGTTTAACCATCAATCTCGAGTTAT
TTTGACGTAATTTTTCAGTTTCTTTTTGTGTTTTTCATATGATTTCTAAA
CGCATTTTCAGA
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protein sequence of SMED30005819-orf-1

>SMED30005819-orf-1 ID=SMED30005819-orf-1|Name=SMED30005819-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=256bp
MIFKLFVNFIMIILIYFPKSYFCKITCHCTTDDCLAQDKTTCIAPTTCFV
EYLQESTENPIKFHAKGCISESYPLMCNQNLLSPSGNGPKLYLECCYKNY
CNSNTRPNMKRLANFFNMIHNQIKPENISKSQQEVSSKSQIIHRESKIYS
LKQNFRYPLSLIIIIASFCGILLMIILIVAIIKLILIYTHPDYIDNDQIY
SVSLSGSSNDPENSIIATVDSRKAMIYSPNYDVNTFYRKLLKYLKFNHQS
RVILT*
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Aliases
The feature 'bambi' has the following synonyms
Synonym
bambi
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000032dorsal midline
PLANA:0000034epidermis
PLANA:0000141dorsal region of the whole animal
PLANA:0000418head
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR000472Activin_recp
Vocabulary: molecular function
TermDefinition
GO:0004675transmembrane receptor protein serine/threonine kinase activity
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000472Activin types I and II receptor domainPFAMPF01064Activin_recpcoord: 26..104
e-value: 3.9E-5
score: 24.6
NoneNo IPR availableGENE3DG3DSA:2.10.60.10coord: 24..124
e-value: 2.3E-8
score: 36.2
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.729
NoneNo IPR availableTMHMMTMhelixcoord: 5..22
NoneNo IPR availableTMHMMTMhelixcoord: 159..181