SMED30014115

Overview
NameSMED30014115
Smed IDSMED30014115
Length (bp)375
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30014115

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30014115 dd_Smed_v4_101649_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014115 dd_Smed_v4_101649_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30014115 dd_Smed_v4_101649_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014115 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000853:12014..12442 -1852
Homology
[Close]
BLAST of SMED30014115 vs. Planmine SMEST
Match: SMESG000058758.1 (SMESG000058758.1)

HSP 1 Score: 72.0182 bits (175), Expect = 1.246e-15
Identity = 41/105 (39.05%), Postives = 58/105 (55.24%), Query Frame = 1 
Query:   28 QDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKF-LIKTEGIFNDDSKFECFDYVKVDNIYDCITKSLDKSYYKSGFFDSDRQECILSKYVSSLLPHSMKKS 339
            +DCV I N KL++  C    N+ C+  S  EI +R      T  IFN+D +  C+D V   ++ +C   SL K YY+S +FD  + +C+L KYV S LP S   S
Sbjct:  787 EDCVVI-NTKLYDTSCKGNFNYFCIANSYDEIHARNLKRNSTRPIFNNDVEVGCYDIVSARSVLECGAISLTKPYYRSFYFDKIQSDCVLVKYVDSTLPLSFNTS 890
[Close]
BLAST of SMED30014115 vs. Planmine SMEST
Match: SMESG000058775.1 (SMESG000058775.1)

HSP 1 Score: 70.0922 bits (170), Expect = 1.702e-15
Identity = 42/120 (35.00%), Postives = 64/120 (53.33%), Query Frame = 1 
Query:    4 QPDVNNNYQDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKFLIKTEGI---FNDDSKFECFDYVKVDNIYDCITKSLDKSYYKSGFFDSDRQECILSKYVSSLLPHSMKKSSENNI 354
            +P+   + +DCV I N K ++  C    N+ C+  S  EI +R   +K+  I   FN+D +  C+D V   ++ +C   SL K YY+S +FD  + +C+L KYV S LP S   S    I
Sbjct:  107 EPNSMPSGEDCVVI-NTKFYDTSCKGNFNYFCIANSYDEIHAR--FLKSNSIRPIFNNDVEVGCYDIVSARSVLECGAISLTKPYYRSFYFDKIQSDCVLVKYVDSTLPLSFNTSDRQWI 223
[Close]
BLAST of SMED30014115 vs. Planmine SMEST
Match: SMESG000058770.1 (SMESG000058770.1)

HSP 1 Score: 62.3882 bits (150), Expect = 1.257e-12
Identity = 45/135 (33.33%), Postives = 67/135 (49.63%), Query Frame = 1 
Query:    4 QPDVNNNYQDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKFLIK---TEGIFNDDSKFECFDYVKVDNI------YDC---------ITKSLDKSYYKSGFFDSDRQECILSKYVSSLLPHSMKKSSENNI 354
            +P+   + +DCV I   KL++  C    N+ C+  S  EI +R  ++K   T  IFN+D +  C+D V   ++      YDC           +SL K YY+S +FD  + +C+L KYV S LP S   S    I
Sbjct:  107 EPNSLYSGEDCVVIKT-KLYDTSCKGNFNYFCIANSYDEIHTR--ILKSNSTRPIFNNDVEVGCYDIVSAKSVLECGARYDCCIGIFLCFVTCRSLTKPYYRSFYFDKIQSDCVLVKYVDSTLPLSFNTSDRQWI 238
[Close]
BLAST of SMED30014115 vs. Planmine SMEST
Match: SMESG000058753.1 (SMESG000058753.1)

HSP 1 Score: 54.299 bits (129), Expect = 9.928e-10
Identity = 36/124 (29.03%), Postives = 62/124 (50.00%), Query Frame = 1 
Query:    1 TQPDVNNNYQDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKFLI-KTEGIFNDDSKFECFDYVKVDN------IYDCIT-----------KSLDKSYYKSGFFDSDRQECILSKYVSSLL 318
            +QP+     +DCV I N  + + +C     ++CV     + + R F+   +  I+N+D +  C+D  K +       +Y+ +T           +SL  S YKS +FDS+ ++C+ SKYV S L
Sbjct:   74 SQPNSLRAGEDCVVIQNNAIFDIECEETYKYVCVKSEEFKFRFRNFVSNASRPIYNNDIQSGCYDAYKAETTLQCAMLYELVTYYIFFIAILFHRSLSHSNYKSFYFDSESKDCVWSKYVDSTL 197
[Close]
BLAST of SMED30014115 vs. Planmine SMEST
Match: SMESG000024541.1 (SMESG000024541.1)

HSP 1 Score: 53.1434 bits (126), Expect = 2.629e-9
Identity = 29/106 (27.36%), Postives = 56/106 (52.83%), Query Frame = 1 
Query:    4 QPDVNNNYQDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKFLIKTEGIFNDDSKFECFDYVKVDNIYDCITKSLDKSYYKSGFFDSDRQECILSKYVSSLLP 321
            +P+     +DCV ++N  +++ KCT     ICV++      SR F + +  IFN D++  C++ +   + ++C  K ++    KS F++ +   C+ + Y  S LP
Sbjct:  111 EPNGGYISEDCVGMNNAGMYDIKCTEYLGTICVLDDGFRPSSRVFQLDSSIIFNGDAEKGCYESIGPLSRFNCAMKCVNTKKCKSFFYEDNEGFCVHADYADSTLP 216
The following BLAST results are available for this feature:
BLAST of SMED30014115 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30014115 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058758.11.246e-1539.05SMESG000058758.1[more]
SMESG000058775.11.702e-1535.00SMESG000058775.1[more]
SMESG000058770.11.257e-1233.33SMESG000058770.1[more]
SMESG000058753.19.928e-1029.03SMESG000058753.1[more]
SMESG000024541.12.629e-927.36SMESG000024541.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014115 ID=SMED30014115|Name=SMED30014115|organism=Schmidtea mediterranea sexual|type=transcript|length=375bp
ACGCAACCCGATGTCAACAATAATTATCAAGATTGCGTGACTATATCGAA
TGGAAAACTTCATAATTGTAAATGTACATTGGAAAATAACTTTATCTGCG
TAATGGAATCAGTAAAAGAAATCAAATCCAGGAAATTCTTAATTAAAACG
GAAGGCATATTCAACGATGATTCCAAGTTTGAATGCTTTGACTATGTAAA
AGTGGATAACATATACGATTGCATAACAAAAAGTTTGGACAAGTCATATT
ATAAATCTGGTTTCTTCGATAGCGATAGGCAAGAGTGCATCTTGAGCAAG
TACGTCAGTAGCCTTTTACCGCACTCGATGAAGAAATCAAGTGAAAATAA
TATTTTTCAATTTTATTAACTTGGG
back to top

protein sequence of SMED30014115-orf-1

>SMED30014115-orf-1 ID=SMED30014115-orf-1|Name=SMED30014115-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
TQPDVNNNYQDCVTISNGKLHNCKCTLENNFICVMESVKEIKSRKFLIKT
EGIFNDDSKFECFDYVKVDNIYDCITKSLDKSYYKSGFFDSDRQECILSK
YVSSLLPHSMKKSSENNIFQFY*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR016186C-type_lectin-like/link_sf
IPR016187CTDL_fold
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR016187C-type lectin foldSUPERFAMILYSSF56436C-type lectin-likecoord: 2..36