HTH_Tnp_Tc3_2 domain-containing protein

Overview
NameHTH_Tnp_Tc3_2 domain-containing protein
Smed IDSMED30031868
Length (bp)1067
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 HTH_Tnp_Tc3_2 domain-containing protein (SMED30031868) t-SNE clustered cells

Violin plots show distribution of expression levels for HTH_Tnp_Tc3_2 domain-containing protein (SMED30031868) 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 HTH_Tnp_Tc3_2 domain-containing protein (SMED30031868) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for HTH_Tnp_Tc3_2 domain-containing protein (SMED30031868) 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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Homology
BLAST of HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Match: A0A4Q9LLI7 (Uncharacterized protein (Fragment) OS=Hamiltosporidium tvaerminnensis OX=1176355 GN=CWI38_2203p0010 PE=4 SV=1)

HSP 1 Score: 195.667 bits (496), Expect = 1.918e-55
Identity = 89/177 (50.28%), Postives = 127/177 (71.75%), Query Frame = 2
Query:  164 ARPR*D*SKNEYFDGKFGIWSFIFKENAKRNSKNRLKGTSVTKVMEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDSALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYI--LQALQHQMVTKNIDYLISAVETAFQQLDRDTLDSVFLTLQTCLENLMI 688
            ARPR D  +  YFDGK GIW F+++E A+RNSKNR KGT +TK +E +     +NM+I NV+PAI+ KFP + K +T+Y+QQDNAKPH ++ND+ +      + W+++ K+QP NSP LN LDLG+   +Q+LQH+     ID LI+ V+ AF QL+ +TLD+VF TLQ C+E++M+
Sbjct:  208 ARPRYDAHRKNYFDGKIGIWPFVYQEPAQRNSKNRAKGTMITKNVESVTAVHCKNMIIDNVIPAIKSKFPPAYKKKTIYVQQDNAKPHFSDNDADIVALGSADDWNIKFKAQPANSPDLNVLDLGFFNSIQSLQHEASPHTIDELINCVQDAFHQLEANTLDNVFTTLQACMESIML 384          
BLAST of HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Match: A0A081AT54 (HTH_Tnp_Tc3_2 domain-containing protein OS=Phytophthora parasitica P1976 OX=1317066 GN=F444_03700 PE=4 SV=1)

HSP 1 Score: 179.104 bits (453), Expect = 1.730e-48
Identity = 81/176 (46.02%), Postives = 121/176 (68.75%), Query Frame = 2
Query:  164 ARPR*D*SKNEYFDGKFGIWSFIFKENAKRNSKNRLKGTSVTKVMEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDSALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYI--LQALQHQMVTKNIDYLISAVETAFQQLDRDTLDSVFLTLQTCLENLM 685
            ARPR D  + + FDGK GIW+F  +  AKR SKNR KGT V + +E + +E  +  +I +++PAI+ K+P+S K RT+YIQQDNAKPH++ +D  +       GW ++++ QPPNSP LN LDLGY   +Q+LQ+Q   + ++ L+ AV +AF  +  DTL+ +F+TLQTC+E ++
Sbjct:  211 ARPRYDAHRKQAFDGKIGIWAFAEEYEAKRTSKNRPKGTIVLRNVESVDREAYKATLIGDIIPAIKAKWPRSGKKRTIYIQQDNAKPHVSVDDPDIMAAGRSGGWDIRMRCQPPNSPDLNVLDLGYFRSIQSLQYQTECRGVEALLDAVNSAFSAMKADTLNKIFMTLQTCMECII 386          
BLAST of HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Match: W2ZV45 (HTH_Tnp_Tc3_2 domain-containing protein OS=Phytophthora parasitica P10297 OX=1317064 GN=F442_03611 PE=4 SV=1)

HSP 1 Score: 178.333 bits (451), Expect = 1.802e-48
Identity = 81/176 (46.02%), Postives = 120/176 (68.18%), Query Frame = 2
Query:  164 ARPR*D*SKNEYFDGKFGIWSFIFKENAKRNSKNRLKGTSVTKVMEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDSALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYI--LQALQHQMVTKNIDYLISAVETAFQQLDRDTLDSVFLTLQTCLENLM 685
            ARPR D  + + FDGK GIW+F  +  AKR SKNR KGT V + +E + +E  +  +I +++PAI+ K+P+S K RT+YIQQDNAKPH++ +D  +       GW ++++ QPPNSP LN LDLGY   +Q+LQ+Q   + ++ L+ AV  AF  +  DTL+ +F+TLQTC+E ++
Sbjct:  185 ARPRYDAHRKQAFDGKIGIWAFAEEYEAKRTSKNRPKGTIVLRNVESVDREAYKATLIGDIIPAIKAKWPRSGKKRTIYIQQDNAKPHVSVDDPDIMAAGRSGGWDIRMRCQPPNSPDLNVLDLGYFRSIQSLQYQTECRGVEALLDAVNGAFSAMKADTLNKIFMTLQTCMECII 360          
BLAST of HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Match: W2QAD0 (Uncharacterized protein OS=Phytophthora parasitica (strain INRA-310) OX=761204 GN=PPTG_10854 PE=4 SV=1)

HSP 1 Score: 176.407 bits (446), Expect = 2.213e-48
Identity = 80/175 (45.71%), Postives = 118/175 (67.43%), Query Frame = 2
Query:  164 ARPR*D*SKNEYFDGKFGIWSFIFKENAKRNSKNRLKGTSVTKVMEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDSALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYI--LQALQHQMVTKNIDYLISAVETAFQQLDRDTLDSVFLTLQTCLENL 682
            ARPR D  + + FDGK GIW+F  +  AKR SKNR KGT V + +E + +E  +  +I +++PAI+ K+P+S K RT+YIQQDNAKPH++ +D  +       GW ++++ QPPNSP LN LDLGY   +Q+LQ+Q   + ++ L+  V +AF  +  DTL  +F+TLQTC+E +
Sbjct:  115 ARPRYDAHRKQAFDGKIGIWAFAEEYEAKRTSKNRPKGTIVLRNVESVDREAYKATLIGDIIPAIKAKWPRSGKKRTIYIQQDNAKPHVSVDDPDIMAAGRSGGWDIRMRCQPPNSPDLNVLDLGYFRSIQSLQYQTECRGVEALLDTVNSAFSAMKADTLSKIFMTLQTCMECI 289          
BLAST of HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Match: W2NW41 (HTH_Tnp_Tc3_2 domain-containing protein OS=Phytophthora parasitica OX=4792 GN=L914_03500 PE=4 SV=1)

HSP 1 Score: 177.563 bits (449), Expect = 5.788e-48
Identity = 81/176 (46.02%), Postives = 120/176 (68.18%), Query Frame = 2
Query:  164 ARPR*D*SKNEYFDGKFGIWSFIFKENAKRNSKNRLKGTSVTKVMEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDSALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYI--LQALQHQMVTKNIDYLISAVETAFQQLDRDTLDSVFLTLQTCLENLM 685
            ARPR D  + + FDGK GIW+F  +  AKR SKNR KGT V + +E + +E  +   I +++PAI+ K+P+S K RT+YIQQDNAKPH++ +D  +       GW ++++ QPPNSP LN LDLGY   +Q+LQ+Q   + ++ L+ AV +AF  +  DTL+ +F+TLQTC+E ++
Sbjct:  211 ARPRYDAHRKQAFDGKIGIWAFAEEYEAKRTSKNRPKGTIVLRNVESVDREAYKATHIGDIIPAIKAKWPRSGKKRTIYIQQDNAKPHVSVDDPDIMAAGRSGGWDIRMRCQPPNSPDLNVLDLGYFRSIQSLQYQTECRGVEALLDAVNSAFSAMKADTLNKIFMTLQTCMECII 386          
The following BLAST results are available for this feature:
BLAST of HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Q9LLI71.918e-5550.28Uncharacterized protein (Fragment) OS=Hamiltospori... [more]
A0A081AT541.730e-4846.02HTH_Tnp_Tc3_2 domain-containing protein OS=Phytoph... [more]
W2ZV451.802e-4846.02HTH_Tnp_Tc3_2 domain-containing protein OS=Phytoph... [more]
W2QAD02.213e-4845.71Uncharacterized protein OS=Phytophthora parasitica... [more]
W2NW415.788e-4846.02HTH_Tnp_Tc3_2 domain-containing protein OS=Phytoph... [more]
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BLAST of HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 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 HTH_Tnp_Tc3_2 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031868 ID=SMED30031868|Name=HTH_Tnp_Tc3_2 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1067bp
ATTTGACTAATTTTGTTAAAGATTTGCTAAATTTGTACTGTTTTAATTAT
TTTTCTAAAAGTGCAAATTTAAGAAAAAAAAATTAGTAGTATTTAGTTAA
AAAATTAAAGAAATAAAGTACTAGTACGAATGTGCCTTGTTTAAAATTTG
TACGCGCGGACACGCAAGACCAAGATGAGATTAATCTAAAAACGAATATT
TCGATGGAAAATTTGGAATCTGGTCATTCATTTTCAAAGAAAATGCCAAA
AGGAACTCTAAAAATCGTCTAAAGGGAACTTCGGTAACGAAAGTTATGGA
ACAGATCGGCAAAGAAGAAATTCAAAATATGATGATTAAAAATGTTTTGC
CAGCTATACGCGAAAAATTTCCAAAAAGTGAAAAATCACGTACTGTTTAC
ATACAGCAAGACAATGCCAAGCCTCATTTAACAAATAATGATTCTGCTTT
ACAAGAAGAACTTATAAAAGAAGGTTGGAGTCTGCAATTAAAATCTCAAC
CTCCGAATAGTCCAGTCTTAAATTTTTTGGATCTTGGGTATATACTACAA
GCATTGCAACATCAGATGGTCACTAAAAATATTGATTATTTAATTAGTGC
AGTAGAAACAGCTTTCCAACAATTGGATCGAGACACACTTGATAGTGTAT
TCTTAACACTACAAACATGTTTGGAAAATCTCATGATAAAAATCTCATAA
ATAAAGAAAAACTTCGAAGAGAAAGTCGTCGACTCCCAATACATTTAAAA
TGTAATGCCGAAGCCGTGGAGAATACAAAAGATTTTTTAAATATTGAATA
ACTGAAATAAATGTTACTACTATAGAATTAATAAAGAACTTATTTCCAAC
TTGTAATTTTTTTATTCACCTATTTTTAAATGCCCAAGCTTTTTAGAAAG
CCTTGAGTAACCCTTTTCAACAAGCTATTACTTTTGAAAATCGGTCTAAC
ACAAGCGAAGCAATAGCTATAAAAGTTTTATCAAATGGGACAAGTATTAT
GGAACAGAGGTAGTACTATTTAAGAGATTGAATAATGATCTCATAACTTT
GCTAGATCTCAATTCAA
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protein sequence of SMED30031868-orf-1

>SMED30031868-orf-1 ID=SMED30031868-orf-1|Name=SMED30031868-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MEQIGKEEIQNMMIKNVLPAIREKFPKSEKSRTVYIQQDNAKPHLTNNDS
ALQEELIKEGWSLQLKSQPPNSPVLNFLDLGYILQALQHQMVTKNIDYLI
SAVETAFQQLDRDTLDSVFLTLQTCLENLMIKIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
Vocabulary: biological process
TermDefinition
GO:0006313transposition, DNA-mediated
GO:0015074DNA integration
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0000419prepharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR014760Serum_albumin_N
Vocabulary: cellular component
TermDefinition
GO:0005615extracellular space