SMED30006228

Overview
NameSMED30006228
Smed IDSMED30006228
Length (bp)940
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




SMED30006228

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30006228SMESG000004998.1 SmedASXL_001150SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006228 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000357:54095..60048 -4536
Homology
BLAST of SMED30006228 vs. Planmine SMEST
Match: SMESG000004999.1 (SMESG000004999.1)

HSP 1 Score: 437.958 bits (1125), Expect = 8.751e-157
Identity = 212/241 (87.97%), Postives = 223/241 (92.53%), Query Frame = 2
Query:  179 LDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFALNSIKQ 901
            +++ +KCNIE+FDLIGFKGSE IS+ +I IQR SL N   S  + PKISHVGLAVHGKDMKPFM DVLSEFHGKI+EQEIYVFESTKSGT FDQG+DVF+TF FGVQLRSL MVIENYPGKIYWSPKRFETN  HHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFALNSIKQ
Sbjct:    1 METNEKCNIETFDLIGFKGSELISDFVISIQRISLKNGNISPIHTPKISHVGLAVHGKDMKPFMADVLSEFHGKISEQEIYVFESTKSGTPFDQGKDVFNTFSFGVQLRSLNMVIENYPGKIYWSPKRFETNETHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFALNSIKQ 241          
BLAST of SMED30006228 vs. Planmine SMEST
Match: SMESG000004998.1 (SMESG000004998.1)

HSP 1 Score: 435.261 bits (1118), Expect = 9.760e-156
Identity = 206/237 (86.92%), Postives = 220/237 (92.83%), Query Frame = 2
Query:  170 MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQF 880
            MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKE+ YKPYE+S KTLFAS+ K   A ETK S FCSELVARCLQ+S++L  T+NPE+VVPLDFY+DPN P  TLD+  EIP+LYENP++I+ 
Sbjct:    1 MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEYYYKPYEKSFKTLFASVSKRFKAKETKGSLFCSELVARCLQKSNLLLDTVNPEKVVPLDFYKDPNQPNRTLDIHHEIPILYENPIQIKL 237          
BLAST of SMED30006228 vs. Planmine SMEST
Match: SMESG000005002.1 (SMESG000005002.1)

HSP 1 Score: 327.02 bits (837), Expect = 5.591e-113
Identity = 156/235 (66.38%), Postives = 188/235 (80.00%), Query Frame = 2
Query:  179 LDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFA 883
            LDS  + NIE+FDLIGFKGSEFIS  II IQR +LH+  FS  N P+ISHVGLA+HGKDMKPFM +VLSEF GKINE EIYVFEST SGT FD+ +DVF  F FGVQLRSL ++I+ YPGKIYWS K F+TN DH+LKLA CIK+ N+KP+E+S+K L ++  ++    +TK+SFFCSELVAR LQRS+IL   INPE+VVP DFY DP NPE TLD+D E+P+LY+NPV I+F 
Sbjct:    2 LDSADEFNIETFDLIGFKGSEFISKLIIHIQRNALHDRHFSIDNFPEISHVGLAIHGKDMKPFMGNVLSEFCGKINESEIYVFESTASGTPFDRAKDVFKQFHFGVQLRSLNILIDKYPGKIYWSSKLFKTNEDHYLKLANCIKDLNHKPFEKSLKVLLSNFCEFSKVKQTKNSFFCSELVARILQRSNILPRKINPEKVVPFDFYIDPRNPEKTLDVDGEVPILYKNPVRIKFV 236          
BLAST of SMED30006228 vs. Planmine SMEST
Match: SMESG000005001.1 (SMESG000005001.1)

HSP 1 Score: 288.5 bits (737), Expect = 3.213e-98
Identity = 143/243 (58.85%), Postives = 177/243 (72.84%), Query Frame = 2
Query:  167 IMIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFALNSI 895
            +M+ LDS+ + NIE+FDLIGFKGSE IS+ +I IQR SL+N+  S +NLP+ISH+GLAVHGKDMKPFM+++L EF GKINE+EIYV EST+SGT FD+GRDVF   FFGVQLRS+ ++I+NYPG                              +   +K L       +N  ET+DSFFCSELVARCLQ+SDILSST+NPERVVPLDFYQDPNNPE TLD+D EIP+LYENP +I+  +NS+
Sbjct:    1 MMVLLDSEDEVNIETFDLIGFKGSELISSLVIFIQRNSLNNKHISKENLPEISHIGLAVHGKDMKPFMKNILKEFRGKINEREIYVLESTQSGTLFDRGRDVFKRSFFGVQLRSMKIIIKNYPGN-----------------------------WRSVLKNLI------INPKETEDSFFCSELVARCLQKSDILSSTVNPERVVPLDFYQDPNNPEITLDVDGEIPVLYENPNQIKLTVNSL 208          
BLAST of SMED30006228 vs. Planmine SMEST
Match: SMESG000004927.1 (SMESG000004927.1)

HSP 1 Score: 200.29 bits (508), Expect = 3.166e-63
Identity = 96/225 (42.67%), Postives = 147/225 (65.33%), Query Frame = 2
Query:  203 IESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPKISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRDVFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFNYKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINPERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQ 877
            +++FDLIGF+G EF+S  I+ ++++++ N+       PKISHVG+ V GKD++ + +      H  I+  +IY+FEST +G   D+ +DV+  +FFG QLR L  VI +Y G ++ S K F    +      E ++E+N++PYE+S ++LF +I + +   E  DS FCSELV+  L  S +L++T+NPE VVPLDFY DP N   TLD+D EIPL+Y +PV ++
Sbjct:   14 VKTFDLIGFRGREFVSKLIVHMEKKAIKNKDIHID--PKISHVGIVVEGKDLQEYHD---CSLHSAIDVNKIYIFESTATGRIIDKVKDVYGKYFFGAQLRDLKKVISSYKGCVFHSSKLFPVTREQVKLFVEFVQEYNHRPYEKSCRSLFGNICRCIEIRENTDSVFCSELVSLALINSGVLANTVNPELVVPLDFYPDPINIGRTLDVDGEIPLIYSDPVAMK 233          
The following BLAST results are available for this feature:
BLAST of SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 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 SMED30006228 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004999.18.751e-15787.97SMESG000004999.1[more]
SMESG000004998.19.760e-15686.92SMESG000004998.1[more]
SMESG000005002.15.591e-11366.38SMESG000005002.1[more]
SMESG000005001.13.213e-9858.85SMESG000005001.1[more]
SMESG000004927.13.166e-6342.67SMESG000004927.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006228 ID=SMED30006228|Name=SMED30006228|organism=Schmidtea mediterranea sexual|type=transcript|length=940bp
CTTAAATAGACCATGACTGCTTGGTAAAGGTTTTATGACTGATGTGAGTG
TTCAACCGGATTGATCGGTTCAATGATCATTTAGTTGTTCAACATTTTCT
ACAACAGTTCTTGACAATGCACAAGTAAATCTAACAAACTAAACAACATT
TCAGAACATAAATTCAATCATGATTTGGCTTGACTCAAAGAAGAAATGCA
ACATTGAAAGTTTTGATTTAATTGGATTCAAGGGATCTGAGTTTATATCA
AATTCAATTATTTGTATTCAAAGAAGAAGTCTACACAATGAAAGATTTTC
AACAAAAAACTTACCAAAAATTTCACACGTCGGACTAGCTGTCCATGGGA
AAGATATGAAGCCGTTTATGGAGGATGTTTTAAGCGAATTTCATGGGAAA
ATAAATGAACAAGAAATTTATGTATTTGAATCGACGAAATCTGGAACGTC
TTTTGATCAAGGTAGAGATGTTTTCAGCACTTTCTTTTTCGGTGTCCAAC
TGAGATCCTTAACTATGGTAATTGAGAATTATCCTGGAAAAATTTATTGG
TCCCCAAAGCGTTTTGAGACAAATGGAGATCATCATTTGAAATTGGCGGA
GTGTATAAAAGAATTTAATTATAAACCATATGAAAGGTCTATTAAAACTT
TATTTGCTAGTATTTTTAAATGGTTAAATGCTGATGAAACAAAAGATTCG
TTTTTTTGCTCAGAATTAGTAGCAAGGTGTCTGCAAAGATCTGATATATT
ATCAAGCACAATAAATCCGGAAAGAGTTGTCCCTCTGGACTTTTATCAGG
ACCCTAACAATCCTGAAACAACTCTTGATTTAGACGCTGAAATTCCACTT
TTATACGAAAACCCAGTAGAAATACAATTTGCTCTAAATTCCATTAAACA
GTAACAATTACATTTATTCTTTATTTTATTATTTGTTTAT
back to top

protein sequence of SMED30006228-orf-1

>SMED30006228-orf-1 ID=SMED30006228-orf-1|Name=SMED30006228-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=245bp
MIWLDSKKKCNIESFDLIGFKGSEFISNSIICIQRRSLHNERFSTKNLPK
ISHVGLAVHGKDMKPFMEDVLSEFHGKINEQEIYVFESTKSGTSFDQGRD
VFSTFFFGVQLRSLTMVIENYPGKIYWSPKRFETNGDHHLKLAECIKEFN
YKPYERSIKTLFASIFKWLNADETKDSFFCSELVARCLQRSDILSSTINP
ERVVPLDFYQDPNNPETTLDLDAEIPLLYENPVEIQFALNSIKQ*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head