SMED30026906

Overview
NameSMED30026906
Smed IDSMED30026906
Length (bp)679
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 SMED30026906 (SMED30026906) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026906 (SMED30026906) 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 SMED30026906 (SMED30026906) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026906 (SMED30026906) 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



SMED30026906

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
gutSMED30026906h1SMcG0015285 dd_Smed_v4_5549_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30026906h1SMcG0015285 dd_Smed_v4_14418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30026906h1SMcG0015285 dd_Smed_v6_5549_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026906 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000524:101211..102100 +3269
Homology
[Close]
BLAST of SMED30026906 vs. Planmine SMEST
Match: SMESG000021439.1 (SMESG000021439.1)

HSP 1 Score: 441.039 bits (1133), Expect = 2.125e-152
Identity = 226/226 (100.00%), Postives = 226/226 (100.00%), Query Frame = 2 
Query:    2 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTXXXXXXXXXXXXLPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 679
            FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTIRIHHHPSRIHILPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI
Sbjct:  127 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTIRIHHHPSRIHILPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 352

HSP 2 Score: 110.153 bits (274), Expect = 1.659e-27
Identity = 47/94 (50.00%), Postives = 68/94 (72.34%), Query Frame = 2 
Query:  392 PNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSI 673
            P I +  + N+T++CY++DG+P+P + +QLIEGP NA Q+Y    NG QIYI+SN+PTGS W FKC+MKSI+ N  K+  + ++F IA +P  I
Sbjct:  452 PIIKKRFRSNSTIKCYIKDGFPYPKINWQLIEGPKNADQFYVITGNGDQIYINSNSPTGSKWKFKCTMKSILVNSNKMLYETISFAIAKNPMEI 545

HSP 3 Score: 77.0258 bits (188), Expect = 4.320e-16
Identity = 34/96 (35.42%), Postives = 59/96 (61.46%), Query Frame = 2 
Query:  392 PNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 679
            P  + +++ N+T+ C   DGYP    ++++  GP N+S YY    NG+QI++  N PT S W  +C++K+ + NV     + + F+IA+HP+S+ I
Sbjct:  354 PMPDGIVEPNSTINCSPADGYPVAKAKWKVFAGPENSSLYYNIIGNGTQIHLKKNCPTKSEWKIECTVKNCLENVCVTLNQTILFKIANHPSSLYI 449
[Close]
BLAST of SMED30026906 vs. Planmine SMEST
Match: SMESG000021439.1 (SMESG000021439.1)

HSP 1 Score: 441.039 bits (1133), Expect = 2.308e-152
Identity = 226/226 (100.00%), Postives = 226/226 (100.00%), Query Frame = 2 
Query:    2 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTXXXXXXXXXXXXLPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 679
            FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTIRIHHHPSRIHILPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI
Sbjct:  131 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTIRIHHHPSRIHILPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 356

HSP 2 Score: 110.153 bits (274), Expect = 1.778e-27
Identity = 47/94 (50.00%), Postives = 68/94 (72.34%), Query Frame = 2 
Query:  392 PNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSI 673
            P I +  + N+T++CY++DG+P+P + +QLIEGP NA Q+Y    NG QIYI+SN+PTGS W FKC+MKSI+ N  K+  + ++F IA +P  I
Sbjct:  456 PIIKKRFRSNSTIKCYIKDGFPYPKINWQLIEGPKNADQFYVITGNGDQIYINSNSPTGSKWKFKCTMKSILVNSNKMLYETISFAIAKNPMEI 549

HSP 3 Score: 77.0258 bits (188), Expect = 4.536e-16
Identity = 34/96 (35.42%), Postives = 59/96 (61.46%), Query Frame = 2 
Query:  392 PNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 679
            P  + +++ N+T+ C   DGYP    ++++  GP N+S YY    NG+QI++  N PT S W  +C++K+ + NV     + + F+IA+HP+S+ I
Sbjct:  358 PMPDGIVEPNSTINCSPADGYPVAKAKWKVFAGPENSSLYYNIIGNGTQIHLKKNCPTKSEWKIECTVKNCLENVCVTLNQTILFKIANHPSSLYI 453
[Close]
BLAST of SMED30026906 vs. Planmine SMEST
Match: SMESG000014539.1 (SMESG000014539.1)

HSP 1 Score: 324.709 bits (831), Expect = 2.970e-111
Identity = 172/229 (75.11%), Postives = 189/229 (82.53%), Query Frame = 2 
Query:    2 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDH--LNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTXXXXXXXXXXXXLPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHP-TSILI 679
            FSAPN F R+KY+K LSLAKRLFHE+IDL IPSTL LSV P+ V R EIIIND +MASCRAF GIPQ KPRFEDH  LNVTEIIYNKTANEIRMNLRA L DHLTNFSC AGNVTE F IRIHHHPS+IHI P+I ++LQ N  +QCY QDGYP P L FQLI+GPSNAS YYE R+NGS+IYI S+APTGS W+FKC MKS IA VA  KEKN+ F+IAS P TSILI
Sbjct:  128 FSAPNKFVRKKYLKNLSLAKRLFHELIDLFIPSTLALSVFPIKVDRKEIIINDIVMASCRAFSGIPQEKPRFEDHAHLNVTEIIYNKTANEIRMNLRASLDDHLTNFSCSAGNVTETFVIRIHHHPSKIHIKPDIKDILQANRAIQCYAQDGYPQPSLHFQLIKGPSNASHYYETRKNGSKIYIRSSAPTGSAWMFKCLMKSTIAGVAMTKEKNINFRIASKPYTSILI 356
[Close]
BLAST of SMED30026906 vs. Planmine SMEST
Match: SMESG000014539.1 (SMESG000014539.1)

HSP 1 Score: 324.709 bits (831), Expect = 3.030e-111
Identity = 172/229 (75.11%), Postives = 189/229 (82.53%), Query Frame = 2 
Query:    2 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDH--LNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTXXXXXXXXXXXXLPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHP-TSILI 679
            FSAPN F R+KY+K LSLAKRLFHE+IDL IPSTL LSV P+ V R EIIIND +MASCRAF GIPQ KPRFEDH  LNVTEIIYNKTANEIRMNLRA L DHLTNFSC AGNVTE F IRIHHHPS+IHI P+I ++LQ N  +QCY QDGYP P L FQLI+GPSNAS YYE R+NGS+IYI S+APTGS W+FKC MKS IA VA  KEKN+ F+IAS P TSILI
Sbjct:  130 FSAPNKFVRKKYLKNLSLAKRLFHELIDLFIPSTLALSVFPIKVDRKEIIINDIVMASCRAFSGIPQEKPRFEDHAHLNVTEIIYNKTANEIRMNLRASLDDHLTNFSCSAGNVTETFVIRIHHHPSKIHIKPDIKDILQANRAIQCYAQDGYPQPSLHFQLIKGPSNASHYYETRKNGSKIYIRSSAPTGSAWMFKCLMKSTIAGVAMTKEKNINFRIASKPYTSILI 358
[Close]
BLAST of SMED30026906 vs. Planmine SMEST
Match: SMESG000014554.1 (SMESG000014554.1)

HSP 1 Score: 319.701 bits (818), Expect = 1.129e-109
Identity = 166/228 (72.81%), Postives = 185/228 (81.14%), Query Frame = 2 
Query:    2 FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEIIINDTLMASCRAFDGIPQYKPRFEDH--LNVTEIIYNKTANEIRMNLRAFLSDHLTNFSCRAGNVTEVFTXXXXXXXXXXXXLPNINEMLQGNTTVQCYVQDGYPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKSIIANVAKIKEKNVTFQIASHPTSILI 679
            FSAPN F RRKY+K LSLAKRLFHE+IDL IPSTL L++ P+ V R +IIIND +MASCRAF GIPQ KPRFEDH  LNVTEIIYN+TANEI MNLR  L DHLTNFSC AGNVTE F I IHHHPS+IHI P+I ++LQ N  +QCY QDGYP P L FQLI+GPSNAS YYE R+NGS+IYI SNAPT S W+FKC M S IA VA  KEKN+ F+IASHPTSILI
Sbjct:  127 FSAPNKFVRRKYLKNLSLAKRLFHELIDLFIPSTLALTLLPIKVDRKDIIINDMVMASCRAFGGIPQEKPRFEDHAQLNVTEIIYNETANEISMNLRTSLDDHLTNFSCSAGNVTETFIICIHHHPSKIHIKPDIKDILQANRAIQCYAQDGYPQPSLHFQLIKGPSNASHYYETRKNGSEIYIRSNAPTRSAWMFKCLMISTIAGVAMTKEKNINFRIASHPTSILI 354
The following BLAST results are available for this feature:
BLAST of SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 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 SMED30026906 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021439.12.125e-152100.00SMESG000021439.1[more]
SMESG000021439.12.308e-152100.00SMESG000021439.1[more]
SMESG000014539.12.970e-11175.11SMESG000014539.1[more]
SMESG000014539.13.030e-11175.11SMESG000014539.1[more]
SMESG000014554.11.129e-10972.81SMESG000014554.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026906 ID=SMED30026906|Name=SMED30026906|organism=Schmidtea mediterranea sexual|type=transcript|length=679bp
CTTTTCTGCGCCAAATATATTTCAACGTCGAAAATATATGAAGAAACTTT
CCCTTGCCAAGCGTTTATTTCATGAAGTTATTGATTTGCTTATCCCATCC
ACATTGGAACTCTCTGTGCGCCCACTCGATGTCAAAAGAAATGAAATAAT
AATAAATGATACGCTAATGGCGTCTTGCAGAGCTTTCGATGGTATACCGC
AATATAAACCGAGATTCGAGGATCACTTGAATGTGACGGAAATAATTTAT
AATAAAACGGCCAATGAAATCAGAATGAATTTACGCGCATTTCTCAGTGA
CCATCTCACTAATTTCAGCTGTAGAGCCGGAAATGTCACAGAAGTTTTCA
CCATTCGCATTCATCATCACCCATCCAGGATTCACATATTGCCAAATATT
AATGAGATGTTGCAAGGAAATACAACGGTCCAATGCTATGTCCAAGATGG
TTATCCTCACCCTTTATTACAGTTTCAACTCATTGAAGGTCCATCAAATG
CATCTCAGTATTATGAAAATAGAGAAAACGGATCTCAAATTTACATCCAT
TCAAATGCTCCAACCGGATCAATGTGGATATTCAAATGCTCAATGAAAAG
CATCATTGCAAATGTAGCAAAAATCAAGGAAAAGAATGTTACCTTTCAAA
TAGCAAGCCATCCGACATCAATCCTGATC
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protein sequence of SMED30026906-orf-1

>SMED30026906-orf-1 ID=SMED30026906-orf-1|Name=SMED30026906-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=226bp
FSAPNIFQRRKYMKKLSLAKRLFHEVIDLLIPSTLELSVRPLDVKRNEII
INDTLMASCRAFDGIPQYKPRFEDHLNVTEIIYNKTANEIRMNLRAFLSD
HLTNFSCRAGNVTEVFTIRIHHHPSRIHILPNINEMLQGNTTVQCYVQDG
YPHPLLQFQLIEGPSNASQYYENRENGSQIYIHSNAPTGSMWIFKCSMKS
IIANVAKIKEKNVTFQIASHPTSILI
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