SMED30022734

Overview
NameSMED30022734
Smed IDSMED30022734
Length (bp)407
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 SMED30022734 (SMED30022734) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022734 (SMED30022734) 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



SMED30022734

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
head regionSMED30022734 SmedASXL_001801SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30022734 SmedASXL_001801SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022734 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.022376:810..1541 +1835
Homology
[Close]
BLAST of SMED30022734 vs. Planmine SMEST
Match: SMESG000043411.1 (SMESG000043411.1)

HSP 1 Score: 159.073 bits (401), Expect = 1.477e-51
Identity = 94/95 (98.95%), Postives = 94/95 (98.95%), Query Frame = -1 
Query:  105 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFXXXXXXXXXXXXXXKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSCS 389
            MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFSEMEVNEDKEENESKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTS CKPRRFSCS
Sbjct:    1 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFSEMEVNEDKEENESKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSTCKPRRFSCS 95
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BLAST of SMED30022734 vs. Planmine SMEST
Match: SMESG000040596.1 (SMESG000040596.1)

HSP 1 Score: 93.2041 bits (230), Expect = 1.217e-25
Identity = 53/97 (54.64%), Postives = 73/97 (75.26%), Query Frame = -1 
Query:  108 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFXXXXX---XXXXXXXXXKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSC 389
            MKLIILL T+FFVGSI+C+E+ ++   N++  +VK   E E+   N+ +EEN++KLFK+ ++CG+R C  FFGRR F CT+RFYR   +CKPRRFSC
Sbjct:    1 MKLIILLLTIFFVGSIYCAEEENEALTNDESFDVKSLKEEELEEGNDKEEENDTKLFKRRRYCGLRTCRFFFGRRWFTCTVRFYRSRRLCKPRRFSC 97
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BLAST of SMED30022734 vs. Planmine SMEST
Match: SMESG000043393.1 (SMESG000043393.1)

HSP 1 Score: 90.8929 bits (224), Expect = 9.526e-25
Identity = 51/97 (52.58%), Postives = 72/97 (74.23%), Query Frame = -1 
Query:  108 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFXXXXXXX---XXXXXXXKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSC 389
            MKLIILL T+FFVGSI+C+E+ ++   N++  +VK   E E+ E    +EEN++KLF K ++CG+R C ++FGRR F CT+RFYR   +CKPRRF+C
Sbjct:    1 MKLIILLLTIFFVGSIYCAEEENEALTNDESFDVKSLKEEEIEEGNDKEEENDTKLFIKHRYCGLRTCRLYFGRRWFTCTVRFYRIGRLCKPRRFAC 97
[Close]
BLAST of SMED30022734 vs. Planmine SMEST
Match: SMESG000043388.1 (SMESG000043388.1)

HSP 1 Score: 85.5001 bits (210), Expect = 1.499e-22
Identity = 49/97 (50.52%), Postives = 69/97 (71.13%), Query Frame = -1 
Query:  108 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFXXXXXXX---XXXXXXXKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSC 389
            MKLIILL T+FFVGSI+C+E+ ++   N++  +VK   E E+ E    +EEN++KL  K ++CG+R C + FGRR F CT+RFYR   +CKP RF+C
Sbjct:    1 MKLIILLLTIFFVGSIYCAEEENEALTNDESFDVKSLKEEEIEEGNDKEEENDTKLLIKHRYCGLRTCRLHFGRRWFTCTVRFYRIGRLCKPSRFNC 97
[Close]
BLAST of SMED30022734 vs. Planmine SMEST
Match: SMESG000043391.1 (SMESG000043391.1)

HSP 1 Score: 73.9442 bits (180), Expect = 4.159e-18
Identity = 50/97 (51.55%), Postives = 74/97 (76.29%), Query Frame = -1 
Query:  108 MKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFXXXXX---XXXXXXXXXKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSC 389
            MKLIILL T+FFVGSI+C+E+ ++   N++  +VK   E E+   ++ +EEN++KLF K ++CG+R C ++FGRR F CT+RFYR+  +CKPRRF+C
Sbjct:    1 MKLIILLLTIFFVGSIYCAEEENEALTNDESFDVKSLKEEELEEGSDKEEENDTKLFIKHRYCGLRTCRLYFGRRWFTCTVRFYRRRRLCKPRRFAC 97
The following BLAST results are available for this feature:
BLAST of SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 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 SMED30022734 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043411.11.477e-5198.95SMESG000043411.1[more]
SMESG000040596.11.217e-2554.64SMESG000040596.1[more]
SMESG000043393.19.526e-2552.58SMESG000043393.1[more]
SMESG000043388.11.499e-2250.52SMESG000043388.1[more]
SMESG000043391.14.159e-1851.55SMESG000043391.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022734 ID=SMED30022734|Name=SMED30022734|organism=Schmidtea mediterranea sexual|type=transcript|length=407bp
TCGTTCTTCTAAATTTTATTTTAATGAAACTAAATGTTAACACAAAAGAT
CATAACTACGAGTTTATTTTGTTAGAATTGAAGTTAAAATTAGAAGTTCA
TTTAAGAACATGAAAACCTTCGAGGTTTGCAGATTGAAGTTTGACGGTAG
AATCTAATAGTGCAATTGAACTTTCGTCTTCCGAAGAACACTATGCATCT
TCTAACTCCACAAAATTTAGGTTTCTTGAATAACTTAGACTCATTCTCTT
CTTTGTCTTCATTAACTTCCATTTCACTGAAATCTTTAACTTCCAAATCA
TCTTCATTAGCAGCTACGTCATGATGATCTTCAGAACAGAAAATCGATCC
AACAAAGAATAAAGTGAAAAGTAAAATGATCAACTTCATGATTCCCCATG
TACTCTG
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protein sequence of SMED30022734-orf-1

>SMED30022734-orf-1 ID=SMED30022734-orf-1|Name=SMED30022734-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
QSTWGIMKLIILLFTLFFVGSIFCSEDHHDVAANEDDLEVKDFSEMEVNE
DKEENESKLFKKPKFCGVRRCIVFFGRRKFNCTIRFYRQTSICKPRRFSC
S*
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.865