LITAF domain-containing protein

Overview
NameLITAF domain-containing protein
Smed IDSMED30028698
Length (bp)596
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 LITAF domain-containing protein (SMED30028698) t-SNE clustered cells

Violin plots show distribution of expression levels for LITAF domain-containing protein (SMED30028698) 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 LITAF domain-containing protein (SMED30028698) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for LITAF domain-containing protein (SMED30028698) 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



SMED30028698

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30028698SMESG000020869.1 SmedASXL_054807SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30028698SMESG000020869.1 dd_Smed_v4_5171_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028698SMESG000020869.1 dd_Smed_v4_5171_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30028698SMESG000020869.1 dd_Smed_v6_5171_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30028698SMESG000020869.1 dd_Smed_v4_5171_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30028698SMESG000020869.1 dd_Smed_v4_5171_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30028698SMESG000020869.1 dd_Smed_v4_5171_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
[Close]
BLAST of LITAF domain-containing protein vs. Ensembl Medaka
Match: si:ch211-157c3.4 (lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:NCBI gene;Acc:101165558])

HSP 1 Score: 45.4394 bits (106), Expect = 5.258e-6
Identity = 24/67 (35.82%), Postives = 37/67 (55.22%), Query Frame = 2 
Query:  287 TKCDKCENEVIPKLKYKIGSFTWCMCVVXXXXXXXXXXXXXX--SNNYKDIYHKCPVCDHTLYVTRR 481
            T C KCE +V   + YK G++ W MC++F     IL         N++KD+YH CP C   L++ ++
Sbjct:   87 TNCPKCERQVETVVDYKAGTYAWLMCLLFICCGLILLCCLIPFFMNSFKDVYHSCPNCHKILHIEKK 153
[Close]
BLAST of LITAF domain-containing protein vs. Ensembl Medaka
Match: si:ch211-157c3.4 (lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:NCBI gene;Acc:101165558])

HSP 1 Score: 45.0542 bits (105), Expect = 7.069e-6
Identity = 24/67 (35.82%), Postives = 37/67 (55.22%), Query Frame = 2 
Query:  287 TKCDKCENEVIPKLKYKIGSFTWCMCVVXXXXXXXXXXXXXX--SNNYKDIYHKCPVCDHTLYVTRR 481
            T C KCE +V   + YK G++ W MC++F     IL         N++KD+YH CP C   L++ ++
Sbjct:   84 TNCPKCERQVETVVDYKAGTYAWLMCLLFICCGLILLCCLIPFFMNSFKDVYHSCPNCHKILHIEKK 150
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BLAST of LITAF domain-containing protein vs. Planmine SMEST
Match: SMESG000020869.1 (SMESG000020869.1)

HSP 1 Score: 184.111 bits (466), Expect = 6.755e-60
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 2 
Query:   74 MDNKDTSNXXXXXXXGFATNQHFIXXXXXXXXXXXXXXXXXXXXXXLILGRNQMIVTNQGVVANIGLVYLKTKCDKCENEVIPKLKYKIGSFTWCMCVVXXXXXXXXXXXXXXSNNYKDIYHKCPVCDHTLYVTRRC 484
            MDNKDTSNPPPPPP GFATNQHFISEQSQYQSHSVQVVYPHVHQQQLILGRNQMIVTNQGVVANIGLVYLKTKCDKCENEVIPKLKYKIGSFTWCMCVVFFLIFPILFFLPFISNNYKDIYHKCPVCDHTLYVTRRC
Sbjct:    1 MDNKDTSNPPPPPPLGFATNQHFISEQSQYQSHSVQVVYPHVHQQQLILGRNQMIVTNQGVVANIGLVYLKTKCDKCENEVIPKLKYKIGSFTWCMCVVFFLIFPILFFLPFISNNYKDIYHKCPVCDHTLYVTRRC 137
[Close]
BLAST of LITAF domain-containing protein vs. Planmine SMEST
Match: SMESG000020865.1 (SMESG000020865.1)

HSP 1 Score: 67.3958 bits (163), Expect = 2.558e-14
Identity = 37/77 (48.05%), Postives = 45/77 (58.44%), Query Frame = 2 
Query:  257 VANIGLVYLKTKCDKCENEVIPKLKYKIGSFTWCMC-VVXXXXXXXXXXXXXXSNNYKDIYHKCPVCDHTLYVTRRC 484
            V  I     K +CDKCENEV P + YK G FTW MC ++F         +PF  N +KD  +KCP+CDH LY  RRC
Sbjct:   63 VTKINYGSSKVRCDKCENEVFPAISYKSGGFTWLMCFIIFLFAPIGCCLIPFCINGFKDEKYKCPICDHKLYELRRC 139
The following BLAST results are available for this feature:
BLAST of LITAF 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 LITAF 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 LITAF 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 LITAF 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 LITAF 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 LITAF 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 LITAF 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 LITAF domain-containing protein 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 LITAF 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 LITAF 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 LITAF 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 LITAF 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 LITAF domain-containing protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 2
Match NameE-valueIdentityDescription
si:ch211-157c3.45.258e-635.82lipopolysaccharide-induced tumor necrosis factor-a... [more]
si:ch211-157c3.47.069e-635.82lipopolysaccharide-induced tumor necrosis factor-a... [more]
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BLAST of LITAF domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000020869.16.755e-6099.27SMESG000020869.1[more]
SMESG000020865.12.558e-1448.05SMESG000020865.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028698 ID=SMED30028698|Name=LITAF domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=596bp
ACTACTTATTCCGAAACCTATTCACTCAAACAATCAAAACTTTTTTCACT
AATTAACAATTAAATAAACTAAAATGGATAACAAAGATACTAGTAATCCG
CCACCCCCTCCTCCACCAGGATTTGCAACCAACCAGCATTTTATTTCTGA
ACAGAGTCAGTACCAGTCGCATTCAGTACAGGTAGTCTATCCACATGTTC
ATCAACAGCAGTTAATACTTGGGAGAAATCAAATGATTGTTACAAATCAA
GGCGTCGTTGCTAATATTGGGCTCGTATATCTAAAGACGAAATGTGATAA
ATGCGAAAACGAAGTAATTCCTAAACTAAAATATAAAATTGGAAGTTTTA
CATGGTGTATGTGTGTGGTTTTTTTTTTAATATTTCCTATACTATTTTTC
CTACCTTTCATTTCGAATAATTACAAGGATATTTATCACAAATGTCCAGT
TTGCGATCACACCTTATATGTAACTCGACGTTGCTGACGAGTTTTCAAGT
GAAAGAAAATTTATATCAAATCTCTAATTACATTTTGTGAAAAATTAAAT
TTATTTACATTTTTTTACATATTTTGTCTTAAAACTATATTGGTAC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR037519LITAF_fam
IPR006629LITAF
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006629LPS-induced tumour necrosis factor alpha factorSMARTSM00714litafcoord: 69..136
e-value: 2.3E-8
score: 43.8
IPR006629LPS-induced tumour necrosis factor alpha factorPFAMPF10601zf-LITAF-likecoord: 72..133
e-value: 2.6E-15
score: 56.4
IPR006629LPS-induced tumour necrosis factor alpha factorPROSITEPS51837LITAFcoord: 51..136
score: 12.782
IPR037519LITAF domain containing proteinPANTHERPTHR23292LIPOPOLYSACCHARIDE-INDUCED TRANSCRIPTION FACTOR REGULATING TUMOR NECROSIS FACTOR ALPHAcoord: 9..136
NoneNo IPR availableTMHMMTMhelixcoord: 91..113