SMED30004839

Overview
NameSMED30004839
Smed IDSMED30004839
Length (bp)603
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30004839 (SMED30004839) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004839 (SMED30004839) 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




SMED30004839

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
eyeSMED30004839h1SMcG0002349 Contig28920uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30004839h1SMcG0002349 Contig28920newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004839 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016466:3121..3722 +2881
v31.004326:60738..61350 +2574
v31.028990:2295..2901 -2525
Homology
BLAST of SMED30004839 vs. Ensembl Celegans
Match: C32D5.11 (pep chromosome:WBcel235:II:6352542:6355911:-1 gene:WBGene00016318.1 transcript:C32D5.11.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:C32D5.11)

HSP 1 Score: 46.9802 bits (110), Expect = 3.900e-6
Identity = 18/53 (33.96%), Postives = 29/53 (54.72%), Query Frame = 1
Query:  112 DNMECCICLSNNCSQTAKAVGCEHQFCEDCIWKWIL--ITNKCPSCGSRIEEM 264
            + ++C ICLS   SQ  +  GC H FC  CI +W+   +   CP C   ++++
Sbjct:   64 EELQCTICLSTRFSQECRIEGCNHSFCFSCISEWVCQSLRPSCPMCRKDVDKV 116          
BLAST of SMED30004839 vs. UniProt/SwissProt
Match: sp|P29129|ICP0_SUHVF (E3 ubiquitin-protein ligase ICP0 OS=Suid herpesvirus 1 (strain Indiana-Funkhauser / Becker) OX=31523 GN=EP0 PE=2 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.055e-7
Identity = 24/61 (39.34%), Postives = 36/61 (59.02%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAE 300
            M+C ICL    ++ A+ + C H+FC DCI +W L +  CP C +R+  +  H  SD +F E
Sbjct:   44 MDCPICLDVAATE-AQTLPCMHKFCLDCIQRWTLTSTACPLCNARVTSILHHVDSDASFVE 103          
BLAST of SMED30004839 vs. Ensembl Medaka
Match: phrf1 (PHD and ring finger domains 1 [Source:NCBI gene;Acc:101165783])

HSP 1 Score: 47.3654 bits (111), Expect = 4.247e-6
Identity = 29/93 (31.18%), Postives = 42/93 (45.16%), Query Frame = 1
Query:  112 DNMECCICLSNNCSQ-TAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDS 387
            D+ +C ICL+    Q  A    CEH FC DCI +W    N CP   +    +YI         +++T+     KS E+      A+D D E +
Sbjct:  100 DSEKCPICLNTFSEQPVATPENCEHYFCFDCILEWTKNANSCPVDRTTFNSIYIRKCYGGKVKKMVTVQKPAQKSQED------AVDLDLEQT 186          
BLAST of SMED30004839 vs. Ensembl Medaka
Match: phrf1 (PHD and ring finger domains 1 [Source:NCBI gene;Acc:101165783])

HSP 1 Score: 46.9802 bits (110), Expect = 5.599e-6
Identity = 29/93 (31.18%), Postives = 42/93 (45.16%), Query Frame = 1
Query:  112 DNMECCICLSNNCSQ-TAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDS 387
            D+ +C ICL+    Q  A    CEH FC DCI +W    N CP   +    +YI         +++T+     KS E+      A+D D E +
Sbjct:  100 DSEKCPICLNTFSEQPVATPENCEHYFCFDCILEWTKNANSCPVDRTTFNSIYIRKCYGGKVKKMVTVQKPAQKSQED------AVDLDLEQT 186          
BLAST of SMED30004839 vs. Planmine SMEST
Match: SMESG000054764.1 (SMESG000054764.1)

HSP 1 Score: 275.789 bits (704), Expect = 4.366e-96
Identity = 135/139 (97.12%), Postives = 137/139 (98.56%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEKGIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF 534
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNF EILT PPL+NKSLEENWNLIRAIDSDEEDSEKGIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNF+RNIEARNNNEF
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTNPPLMNKSLEENWNLIRAIDSDEEDSEKGIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFMRNIEARNNNEF 139          
BLAST of SMED30004839 vs. Planmine SMEST
Match: SMESG000037691.1 (SMESG000037691.1)

HSP 1 Score: 237.269 bits (604), Expect = 1.018e-80
Identity = 120/142 (84.51%), Postives = 125/142 (88.03%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF 534
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNF EILTIPPLINKSLEENWNL+RAIDSDE DSE+    + C+EDLF +H LSDS  YVITNYIDES  LSN IRNIE  NNNE 
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGYLSNIIRNIEVNNNNEL 142          
BLAST of SMED30004839 vs. Planmine SMEST
Match: SMESG000054762.1 (SMESG000054762.1)

HSP 1 Score: 237.269 bits (604), Expect = 1.030e-80
Identity = 121/142 (85.21%), Postives = 125/142 (88.03%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF 534
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNF EILTIPPLINKSLEENWNLIRAIDSDE DSE+    + C+EDLF +H LSDS  YVITNYIDES  LSN IRNIE  NNNE 
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLSNIIRNIEVNNNNEL 142          
BLAST of SMED30004839 vs. Planmine SMEST
Match: SMESG000037688.1 (SMESG000037688.1)

HSP 1 Score: 235.728 bits (600), Expect = 3.045e-80
Identity = 119/142 (83.80%), Postives = 125/142 (88.03%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF 534
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNF EILTIPPLINKSLEENWNL+RAIDSDE DSE+    + C++DLF +H LSDS  YVITNYIDES  LSN IRNIE  NNNE 
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVDDLFCNHSLSDSNNYVITNYIDESGYLSNIIRNIEVNNNNEL 142          
BLAST of SMED30004839 vs. Planmine SMEST
Match: SMESG000054763.1 (SMESG000054763.1)

HSP 1 Score: 235.728 bits (600), Expect = 4.138e-80
Identity = 120/142 (84.51%), Postives = 125/142 (88.03%), Query Frame = 1
Query:  118 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF 534
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNF EILTIPPLINKSLEENWNLI+AIDSDE DSE+    + C+EDLF +H LSDS  YVITNYIDES  LSN IRNIE  NNNE 
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIQAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLSNIIRNIEVNNNNEL 142          
The following BLAST results are available for this feature:
BLAST of SMED30004839 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 SMED30004839 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
C32D5.113.900e-633.96pep chromosome:WBcel235:II:6352542:6355911:-1 gene... [more]
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BLAST of SMED30004839 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 SMED30004839 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 SMED30004839 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 SMED30004839 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 SMED30004839 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P29129|ICP0_SUHVF2.055e-739.34E3 ubiquitin-protein ligase ICP0 OS=Suid herpesvir... [more]
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BLAST of SMED30004839 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 SMED30004839 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 SMED30004839 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 SMED30004839 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 SMED30004839 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 SMED30004839 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 2
Match NameE-valueIdentityDescription
phrf14.247e-631.18PHD and ring finger domains 1 [Source:NCBI gene;Ac... [more]
phrf15.599e-631.18PHD and ring finger domains 1 [Source:NCBI gene;Ac... [more]
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BLAST of SMED30004839 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054764.14.366e-9697.12SMESG000054764.1[more]
SMESG000037691.11.018e-8084.51SMESG000037691.1[more]
SMESG000054762.11.030e-8085.21SMESG000054762.1[more]
SMESG000037688.13.045e-8083.80SMESG000037688.1[more]
SMESG000054763.14.138e-8084.51SMESG000054763.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004839 ID=SMED30004839|Name=SMED30004839|organism=Schmidtea mediterranea sexual|type=transcript|length=603bp
GTCAACTTTTTTCAATTAAAACTTTATCAAACTTTATAAATTTTTACGGA
AATGATTATGACGTCATTGCATTAATTTTGTTTTAATTAAAAATATGTTC
TGATATTTTCTGATAATATGGAGTGCTGTATTTGCTTATCAAATAATTGT
TCCCAAACCGCGAAGGCAGTTGGATGTGAACATCAATTCTGTGAAGATTG
CATATGGAAATGGATCCTAATTACGAACAAGTGCCCATCGTGTGGATCAA
GAATTGAAGAAATGTATATTCACAATAAAAGTGATGATAACTTTGCGGAA
ATTTTAACGATTCCTCCACTGATAAACAAATCTCTCGAGGAAAATTGGAA
CTTGATTCGAGCCATAGATTCAGATGAAGAAGACAGTGAAAAGGGCATTG
GCTGTATTGAGGATCTATTTCGCGATCATTTTTTGTCTGATAGTAAAAAA
TATGTCATAACAAATTACATAGATGAATCTGAATGCCTTTCCAATTTTAT
AAGGAATATCGAAGCTAGAAATAACAATGAATTTTAAATGAATTGGGATT
GCAAAATTGTTTGTGATTTATTCCCGTCCCTGTTTATAACGCTGTGTTGA
TTA
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protein sequence of SMED30004839-orf-1

>SMED30004839-orf-1 ID=SMED30004839-orf-1|Name=SMED30004839-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMY
IHNKSDDNFAEILTIPPLINKSLEENWNLIRAIDSDEEDSEKGIGCIEDL
FRDHFLSDSKKYVITNYIDESECLSNFIRNIEARNNNEF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000036eye
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
GO:0016874ligase activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001841Zinc finger, RING-typeSMARTSM00184ring_2coord: 3..42
e-value: 6.6E-4
score: 29.0
IPR001841Zinc finger, RING-typePFAMPF13639zf-RING_2coord: 2..42
e-value: 6.5E-7
score: 29.6
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 3..42
score: 10.837
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 1..63
e-value: 4.6E-10
score: 40.6
IPR017907Zinc finger, RING-type, conserved sitePROSITEPS00518ZF_RING_1coord: 20..29
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 2..49