SMED30029693

Overview
NameSMED30029693
Smed IDSMED30029693
Length (bp)321
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



SMED30029693

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
parenchymaSMED30029693 dd_Smed_v4_38734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30029693 dd_Smed_v6_38734_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
SMED30029693 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000392:55368..55686 +1310
v31.012198:4072..4386 -1280
v31.009094:12097..12411 +1265
v31.000516:117818..118137 -1120
v31.010018:12826..13129 +1095
v31.000166:188948..189261 -1060
v31.001117:12102..12399 -1025
v31.006766:2747..3010 -969
Homology
[Close]
BLAST of SMED30029693 vs. TrEMBL
Match: A0A2B4T023 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene666 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 6.212e-13
Identity = 39/94 (41.49%), Postives = 54/94 (57.45%), Query Frame = 2 
Query:   38 KLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            +L ++ I  F G  + Y+ W+  F A VD A      KL+ LRQYL G+ L+++E LGY A  Y TA ERLE  +GG  R+    L E++ F P
Sbjct:  181 QLKRVSIPVFNGDER-YEGWKMAFMAFVDKAPATPEYKLLQLRQYLSGEALKVVEPLGYSATAYETATERLERKFGGKRRQVALHLEELENFKP 273
[Close]
BLAST of SMED30029693 vs. TrEMBL
Match: A0A2B4RC04 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene20623 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 9.207e-13
Identity = 38/94 (40.43%), Postives = 53/94 (56.38%), Query Frame = 2 
Query:   38 KLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            +L  + I  F G   +Y+ W+  F+AC+D A      KL+ LRQYL G+ L+ IE+LG+ A+ Y  A  RLE  YGG  R+    L E+  F P
Sbjct:  287 QLKGVSIPLFNGDKTNYESWKAAFEACIDKAEY----KLLQLRQYLSGEALKAIENLGHSASAYEAAKSRLEGKYGGRRRQIALHLEELDNFKP 376
[Close]
BLAST of SMED30029693 vs. TrEMBL
Match: A0A2B4R783 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene23326 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.000e-9
Identity = 32/91 (35.16%), Postives = 47/91 (51.65%), Query Frame = 2 
Query:   41 LNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEF 313
            L ++ I  + G  K    W+  F +CVD        KL+ LR+ L G+ L++IE+LG+    Y  A  RLE  YGG+ R     L E++ F
Sbjct:   91 LKRVSIPRYAGYKKHCASWKAAFCSCVDQVKAAPQYKLLRLRECLQGEALRVIENLGHSTTAYEAARSRLERKYGGEGRALTLRLEELEAF 181
[Close]
BLAST of SMED30029693 vs. TrEMBL
Match: A0A2B4R8Z1 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene21000 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.759e-8
Identity = 31/93 (33.33%), Postives = 48/93 (51.61%), Query Frame = 2 
Query:   41 LNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            + K  +  F G    Y  W+ +F+  VD        K+M L+  L G PL+++E LGY +  Y TAL++L+   GG++R  +R L  I    P
Sbjct:  372 IKKPALTVFSGDKNLYHDWKAQFEIFVDRMKAPAKTKMMMLKNSLTGKPLRVVERLGYTSKHYQTALQKLDQKNGGEERLLQRYLEAILHASP 464
[Close]
BLAST of SMED30029693 vs. TrEMBL
Match: A7SRU1 (Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g216455 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.040e-7
Identity = 31/77 (40.26%), Postives = 43/77 (55.84%), Query Frame = 2 
Query:   41 LNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGD 271
            L K  +  F G    Y   R +FD  V    V +  K+M L+  ++G PL++IE LGY  A Y TALE+L+  YGG+
Sbjct:  238 LKKPQLAIFSGDKDLYHDLRAQFDVFVHQTKVPEKVKMMMLKSAVLGKPLKVIERLGYSPAQYKTALEKLDQKYGGE 314
[Close]
BLAST of SMED30029693 vs. Ensembl Nematostella
Match: EDO33575 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SRU1])

HSP 1 Score: 58.5362 bits (140), Expect = 1.438e-11
Identity = 31/77 (40.26%), Postives = 43/77 (55.84%), Query Frame = 2 
Query:   41 LNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGD 271
            L K  +  F G    Y   R +FD  V    V +  K+M L+  ++G PL++IE LGY  A Y TALE+L+  YGG+
Sbjct:  238 LKKPQLAIFSGDKDLYHDLRAQFDVFVHQTKVPEKVKMMMLKSAVLGKPLKVIERLGYSPAQYKTALEKLDQKYGGE 314
[Close]
BLAST of SMED30029693 vs. Planmine SMEST
Match: SMESG000042730.1 (SMESG000042730.1)

HSP 1 Score: 213.386 bits (542), Expect = 5.287e-73
Identity = 102/102 (100.00%), Postives = 102/102 (100.00%), Query Frame = 2 
Query:   14 MESFKFLGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            MESFKFLGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP
Sbjct:    1 MESFKFLGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 102
[Close]
BLAST of SMED30029693 vs. Planmine SMEST
Match: SMESG000046963.1 (SMESG000046963.1)

HSP 1 Score: 143.28 bits (360), Expect = 2.394e-43
Identity = 68/82 (82.93%), Postives = 74/82 (90.24%), Query Frame = 2 
Query:   71 GQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFY 316
            GQLK+Y+ WRNEFDA VDSAS NDGEKLMHLRQYLVG+PL+IIE+LGY+AAVY TALERLEM YGGDDRR   MLAEIKEFY
Sbjct:  171 GQLKNYERWRNEFDAYVDSASANDGEKLMHLRQYLVGEPLRIIENLGYEAAVYKTALERLEMRYGGDDRRCHGMLAEIKEFY 252
[Close]
BLAST of SMED30029693 vs. Planmine SMEST
Match: SMESG000071974.1 (SMESG000071974.1)

HSP 1 Score: 98.9821 bits (245), Expect = 3.238e-28
Identity = 48/81 (59.26%), Postives = 59/81 (72.84%), Query Frame = 2 
Query:   77 LKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            +KD + W+N F+  VDS S N GEKLMHLRQY+VG+ L+IIE+LG    V+N A E LE  Y GDD RY  +LA+IKEFYP
Sbjct:    1 MKDNEQWKNGFNLFVDSTSANGGEKLMHLRQYMVGESLRIIEYLGNHTPVHNMAQETLETRYRGDDMRYCGILAKIKEFYP 81
[Close]
BLAST of SMED30029693 vs. Planmine SMEST
Match: SMESG000010152.1 (SMESG000010152.1)

HSP 1 Score: 106.301 bits (264), Expect = 3.464e-28
Identity = 52/68 (76.47%), Postives = 56/68 (82.35%), Query Frame = 2 
Query:    5 NYSMESFKFLGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHL 208
            N SMESFK LGKL KIVIK F GQ+KDY+  RNEFDA VDS S NDGE LM LRQYLVG+PL+IIEHL
Sbjct:  424 NKSMESFKCLGKLKKIVIKQFAGQMKDYERRRNEFDAYVDSGSANDGENLMRLRQYLVGEPLRIIEHL 491
[Close]
BLAST of SMED30029693 vs. Planmine SMEST
Match: SMESG000057422.1 (SMESG000057422.1)

HSP 1 Score: 99.3673 bits (246), Expect = 1.848e-25
Identity = 45/96 (46.88%), Postives = 66/96 (68.75%), Query Frame = 2 
Query:   32 LGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHLRQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEFYP 319
            L KL ++ I  F GQ++++  W+  F+  V+ A  +  EKL HLR+YLVG+PL++I+ LGY A  Y+ ALERLE  YGG++R YR +L E++ F P
Sbjct:  513 LDKLKRLTIPVFNGQIREFPAWKAAFEVRVNKALGSKEEKLQHLRKYLVGEPLKLIDTLGYSAGAYDAALERLESNYGGEERLYRNLLQELERFRP 608
The following BLAST results are available for this feature:
BLAST of SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2B4T0236.212e-1341.49Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4RC049.207e-1340.43Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4R7831.000e-935.16Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4R8Z11.759e-833.33Uncharacterized protein OS=Stylophora pistillata O... [more]
A7SRU11.040e-740.26Predicted protein OS=Nematostella vectensis OX=453... [more]
back to top
BLAST of SMED30029693 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 SMED30029693 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 SMED30029693 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 SMED30029693 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO335751.438e-1140.26Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
back to top
BLAST of SMED30029693 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 SMED30029693 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042730.15.287e-73100.00SMESG000042730.1[more]
SMESG000046963.12.394e-4382.93SMESG000046963.1[more]
SMESG000071974.13.238e-2859.26SMESG000071974.1[more]
SMESG000010152.13.464e-2876.47SMESG000010152.1[more]
SMESG000057422.11.848e-2546.88SMESG000057422.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029693 ID=SMED30029693|Name=SMED30029693|organism=Schmidtea mediterranea sexual|type=transcript|length=321bp
GTAAAATTATAGCATGGAATCCTTTAAATTTCTGGGCAAACTAAATAAAA
TTGTAATAAAGTCATTCGAGGGTCAATTGAAGGATTATAAACTGTGGAGA
AATGAATTTGACGCCTGTGTTGACTCAGCAAGCGTCAATGATGGAGAAAA
GTTGATGCATTTAAGACAATACCTGGTAGGAGACCCTCTGCAAATAATTG
AGCATTTAGGATATGATGCTGCAGTTTATAACACGGCTCTGGAAAGACTA
GAGATGATGTACGGAGGAGATGATAGAAGATACCGTAGAATGCTAGCAGA
AATAAAGGAGTTCTATCCAGT
back to top

protein sequence of SMED30029693-orf-1

>SMED30029693-orf-1 ID=SMED30029693-orf-1|Name=SMED30029693-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MESFKFLGKLNKIVIKSFEGQLKDYKLWRNEFDACVDSASVNDGEKLMHL
RQYLVGDPLQIIEHLGYDAAVYNTALERLEMMYGGDDRRYRRMLAEIKEF
YP
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR005312DUF1759