SMED30022994

Overview
NameSMED30022994
Smed IDSMED30022994
Length (bp)2110
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 SMED30022994 (SMED30022994) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022994 (SMED30022994) 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 SMED30022994 (SMED30022994) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022994 (SMED30022994) 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.
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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30022994

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
X1 cellSMED30022994SMESG000030881.1 SmedASXL_017371SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30022994SMESG000030881.1 SmedASXL_017368SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022994 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005788:36142..38564 +10414
v31.009278:10636..13067 +9987
Homology
[Close]
BLAST of SMED30022994 vs. Planmine SMEST
Match: SMESG000030881.1 (SMESG000030881.1)

HSP 1 Score: 719.539 bits (1856), Expect = 0.000e+0
Identity = 438/514 (85.21%), Postives = 448/514 (87.16%), Query Frame = -2 
Query:    1 KKKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNTDDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEFKSKISENEMNNYHLKRFGSKNINSKVSWKCSTCSSENSNDSLECKNCENISNRNVVLISENAIPTSFDXXXXXXXXXXXXXXSAEITLSNESTNIVSTAGFDFTQTPASLTNIDLKLSNFNTSPAIMNNDQKVKNXXXXXXXXXXXXXXXSAATFGQLPVTTSKTESITLSISNTISFGHSEISKTFSTVSNTTMSTPVVFSTGTTSNVTISSAPVSTSSKMFAFNQXXXXXXXXXXXXXXXXXXXXSLVSTSNSFAFGQKSSTGNLPFGSLLNAGTVSTSFETSKPS-------------------SFGNITT------------------TEIFSPSTTFETS------------KPFSLNQRP--NAETPKPFAFGQVPTTSVETPKPFAF 1389
            +KKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNTDDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEFKSKISENEMNNYH K FGSKNINSKVSWKCSTCSSENS DSLECKNCENISNRNVVLISENAIPTSFDKSNLL+TLLENETTSAEITLSNES NIVSTAGFD TQTPASLTN DLKLSNFN SP IMNNDQKVKNSSGISSFGFSSTVSPSAATFGQLPVTTSKTESITLSISNTISFGHSEISKTFSTVSNTTMSTPVVFSTGTTSNVTISSAPVSTSSKMFAFNQTSTASISILGSISSSEGNSTSLVSTSNSFAFGQKSSTGNLPFGSLLNAGTVSTSFETSKPS                   SFGN+++                  + I + ST+FETS            KPF+  Q P  + ETPKPFAFGQVPTTSVETPKPFAF
Sbjct:   91 RKKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNTDDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEFKSKISENEMNNYHQKLFGSKNINSKVSWKCSTCSSENSYDSLECKNCENISNRNVVLISENAIPTSFDKSNLLRTLLENETTSAEITLSNESRNIVSTAGFDLTQTPASLTNTDLKLSNFNISPTIMNNDQKVKNSSGISSFGFSSTVSPSAATFGQLPVTTSKTESITLSISNTISFGHSEISKTFSTVSNTTMSTPVVFSTGTTSNVTISSAPVSTSSKMFAFNQTSTASISILGSISSSEGNSTSLVSTSNSFAFGQKSSTGNLPFGSLLNAGTVSTSFETSKPSFGNLSSIGTVSTSFDTSKPSFGNLSSIGNVSTSFDTSKPSFGNLSSIGTVSTSFETSKPSSFGNITTTPKPFAFGQVPTTSVETPKPFAFGQVPTTSVETPKPFAF 604

HSP 2 Score: 193.356 bits (490), Expect = 0.000e+0
Identity = 92/93 (98.92%), Postives = 93/93 (100.00%), Query Frame = -1 
Query: 1382 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGKKK 1660
            MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIG+KK
Sbjct:    1 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKK 93
[Close]
BLAST of SMED30022994 vs. Planmine SMEST
Match: SMESG000003624.1 (SMESG000003624.1)

HSP 1 Score: 244.588 bits (623), Expect = 3.700e-79
Identity = 154/254 (60.63%), Postives = 169/254 (66.54%), Query Frame = -2 
Query:  634 KKKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNT-DDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEFKSKISENEMNNYHLKRFGSKNINSKVSWKCSTCSSENSNDSLECKNCENISNRNVVLISENAIPTSFDXXXXXXXXXXXXXXSAEITLSNESTNIVSTAGFDFTQTPASLTNIDLKLSNFNT-SPAIMNNDQK 1389
            +KKPIPIKAVTVSATSKDLCQSNCG IR KKRIG SDDVDLDSESI G+YKYPVLNDSAKI+FSNIPM+KKSVSTNT  DTYLVN D+ELSDL+F  RPPQTI D+DYLHNLQ                         G  N N+                              VVLIS+NAIPT F KSNLL+T LENETT AEITLSNES NI  TAGF   QTPA+L + D+KL N++T   AIMNND K
Sbjct:   53 RKKPIPIKAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESIFGNYKYPVLNDSAKITFSNIPMVKKSVSTNTAGDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQ-------------------------GEVNSNA------------------------------VVLISDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDHK 251

HSP 2 Score: 71.2478 bits (173), Expect = 3.700e-79
Identity = 38/68 (55.88%), Postives = 44/68 (64.71%), Query Frame = -1 
Query: 1382 MAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGKKK 1585
            M IR++K  +SSP K ILEKLDK TT ITEADKLA+  +              SNPYSRP PPIG+KK
Sbjct:    1 MPIRYTKVVVSSPGKNILEKLDKFTTAITEADKLAASFL-------------TSNPYSRPPPPIGRKK 55
[Close]
BLAST of SMED30022994 vs. Planmine SMEST
Match: SMESG000002138.1 (SMESG000002138.1)

HSP 1 Score: 157.532 bits (397), Expect = 3.035e-44
Identity = 114/213 (53.52%), Postives = 129/213 (60.56%), Query Frame = -2 
Query:  628 ESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNT-DDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEFKSKISENEMNNYHLKRFGSKNINSKVSWKCSTCSSENSNDSLECKNCENISNRNVVLISENAIPTSFDXXXXXXXXXXXXXXSAEITLSNESTNIVSTAGFDFTQTPASLTNIDLKLSNFNT-SPAIMNNDQKVK 1260
            ESICGDYKYPVLNDSAKI+FSNIPM+KKSVSTN  DDTYLVN D+ELSDL+F  RPPQTI D                     E+ ++N      G  N N+                              VVL S+NAIPT F KSNLL+T LENETT AEITLSNES NI  TAGF   QTPA+L + D+KL N++T   AIMNNDQKVK
Sbjct:   15 ESICGDYKYPVLNDSAKINFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITD---------------------EDYLHNLQ----GEVNSNA------------------------------VVLKSDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDQKVK 172
[Close]
BLAST of SMED30022994 vs. Planmine SMEST
Match: SMESG000004159.1 (SMESG000004159.1)

HSP 1 Score: 89.3521 bits (220), Expect = 3.337e-21
Identity = 65/92 (70.65%), Postives = 73/92 (79.35%), Query Frame = -2 
Query:  625 NCENISNRN-VVLISENAIPTSFDXXXXXXXXXXXXXXSAEITLSNESTNIVSTAGFDFTQTPASLTNIDLKLSNFNT-SPAIMNNDQKVKN 894
            NCEN+SNRN VVLI +NAIPT   KSNLL+T LENETT AEI LSNES NI  TAGFD  QTPASLT+ D+KL N++T   AIMNNDQK +N
Sbjct:    3 NCENMSNRNAVVLIFDNAIPTGLGKSNLLRTPLENETTCAEIALSNESRNIAFTAGFDLAQTPASLTDSDIKLPNYSTIESAIMNNDQKGEN 94
The following BLAST results are available for this feature:
BLAST of SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 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 SMED30022994 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000030881.10.000e+085.21SMESG000030881.1[more]
SMESG000003624.13.700e-7960.63SMESG000003624.1[more]
SMESG000002138.13.035e-4453.52SMESG000002138.1[more]
SMESG000004159.13.337e-2170.65SMESG000004159.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022994 ID=SMED30022994|Name=SMED30022994|organism=Schmidtea mediterranea sexual|type=transcript|length=2110bp
AAATGCGAACGGTTTCGGTGTTTCAACTGATGTTGTAGGAACTTGTCCAA
ATGCGAACGGTTTTGGTGTTTCTGCATTTGGTCTTTGATTCAATGAGAAC
GGTTTTGAAGTTTCAAATGTTGTGCTAGGTGAAAATATTTCAGTTGTCGT
TATATTTCCAAATGATGAAGGTTTAGATGTTTCAAAACTCGTCGATACAG
TTCCAGCATTTAAAAGACTCCCAAAAGGCAAATTTCCGGTACTTGATTTT
TGGCCAAAAGCAAAGGAATTTGATGTTGATACTAAGGAAGTAGAATTACC
TTCAGAACTTGAGATTGATCCCAAAATTGAAATAGAAGCTGTAGATGTTT
GATTAAATGCGAACATTTTCGATGATGTCGACACAGGTGCGGAAGATATA
GTCACATTAGATGTCGTGCCTGTTGAAAACACAACTGGTGTTGACATGGT
TGTATTAGACACAGTTGAGAATGTTTTCGATATTTCTGAGTGACCAAATG
AAATTGTATTTGAAATGGATAATGTAATTGATTCGGTTTTCGAAGTGGTC
ACTGGTAATTGCCCAAATGTAGCAGCTGATGGTGACACAGTTGATGAGAA
TCCGAACGAAGAAATTCCCGATGAATTTTTCACCTTTTGATCATTATTCA
TAATAGCTGGTGAAGTGTTAAAATTCGATAATTTTAAATCGATATTTGTC
AAACTTGCCGGGGTTTGTGTGAAATCAAAACCAGCCGTAGAAACAATGTT
TGTTGACTCATTTGATAAAGTGATTTCTGCAGAAGTGGTTTCGTTTTCTA
AAAGTGTTTTCAGGAGATTTGATTTGTCAAAACTGGTAGGAATGGCATTT
TCGGATATGAGGACGACATTTCTATTTGAAATGTTTTCGCAATTTTTGCA
TTCGAGTGAATCATTAGAGTTTTCTGAGGAGCAAGTGCTACATTTCCATG
AGACTTTAGAATTAATATTTTTACTACCAAATCGTTTCAGGTGATAATTA
TTCATTTCATTTTCACTAATTTTCGATTTGAATTCATACGAATTGACTTC
TTTTTGTAAGTTGTGCAAATAGTCGTCATCATTAATTGTTTGTGGTGGCC
TAAAAGAAAATTCCAAATCGGACAATTCCTCGTCATTATTCACTAAATAT
GTATCATCTGTATTTGTCGACACAGACTTCTTTAACATTGGAATATTTGA
GAAACTTATTTTTGCAGAATCATTTAAAACAGGATATTTATAGTCACCAC
AAATGGATTCTGAATCTAAATCAACATCATCGGAAAACCCAATACGTTTT
TTCGAGCGAATAGGACCACAATTACTTTGACAAAGATCTTTAGATGTTGC
TGATACTGTCACAGCTTTAATCGGTATTGGTTTTTTTTTTACCGATAGGA
GGAGTTGGCCTACTATACGGATTAGAAGCCTTTAGCCTGTCGACATTATT
AATTGGTGCCTTTACCCTGACCAATAGACTTGCCAATTTATCCGCCTCCG
TTATTGGAGTAGTAAGTTTATCAAGCTTTTCTAAAATTTTTTTGGCTGGT
GAACTAATAAAATCTTTAGAATGTCTGATTGCCATGTGTGAAACTGAAGA
ATTTGGTTTTTGCGACACGTTTAAATTTCTTGGATATTTATAATTATTCT
GTATTTGCATATCTTCCACAAGTCCTAAATTAAACCTTTTTGATGAACGT
GGATGAAGCGATGATACACCACTCGTCGAGACGGAAACATTGCTTGTATC
ACTGAAATCTGAAGCAGTATCATTAAAATTATTATTGTACGCATTATATC
GATCTGGTAAGTGAGTAGTAATTGGTTTCACTATCCTTGATGTCGGTAAG
GATTTAAGGTCATAATGCAGTCTTGCTCTCTTTATTCTTAATTCATCATC
GTCTCTACCAAATGCTTCGGATGCTAGTCGTCGATTAGAACTTGTAATCG
GCGACAAATTTCTATCAAAAGAAACATTAGATATGTCTTCTCTAGTAGTT
GAATTAAAAGGAAATATGCTTGAGAAAGAGTCGCTCAGCTTTTGAAAAAA
TGATTTATTTTTAGACATTTTATTTAAATTTTTAGTAAATGTGTCGCGCG
ATTAAACATA
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protein sequence of SMED30022994-orf-1

>SMED30022994-orf-1 ID=SMED30022994-orf-1|Name=SMED30022994-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=234bp
MSKNKSFFQKLSDSFSSIFPFNSTTREDISNVSFDRNLSPITSSNRRLAS
EAFGRDDDELRIKRARLHYDLKSLPTSRIVKPITTHLPDRYNAYNNNFND
TASDFSDTSNVSVSTSGVSSLHPRSSKRFNLGLVEDMQIQNNYKYPRNLN
VSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLV
RVKAPINNVDRLKASNPYSRPTPPIGKKKTNTD*
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protein sequence of SMED30022994-orf-2

>SMED30022994-orf-2 ID=SMED30022994-orf-2|Name=SMED30022994-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=396bp
MLKKSVSTNTDDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNS
YEFKSKISENEMNNYHLKRFGSKNINSKVSWKCSTCSSENSNDSLECKNC
ENISNRNVVLISENAIPTSFDKSNLLKTLLENETTSAEITLSNESTNIVS
TAGFDFTQTPASLTNIDLKLSNFNTSPAIMNNDQKVKNSSGISSFGFSST
VSPSAATFGQLPVTTSKTESITLSISNTISFGHSEISKTFSTVSNTTMST
PVVFSTGTTSNVTISSAPVSTSSKMFAFNQTSTASISILGSISSSEGNST
SLVSTSNSFAFGQKSSTGNLPFGSLLNAGTVSTSFETSKPSSFGNITTTE
IFSPSTTFETSKPFSLNQRPNAETPKPFAFGQVPTTSVETPKPFAF
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR001876Znf_RanBP2
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding