SMED30031250

Overview
NameSMED30031250
Smed IDSMED30031250
Length (bp)310
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
Alignments
SMED30031250 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.024200:10082..10390 -1527
v31.003742:40149..40456 -1333
v31.005414:30268..30575 -1198
v31.006217:28799..29100 +1046
v31.000316:189486..189769 -1020
Homology
BLAST of SMED30031250 vs. TrEMBL
Match: A0A0N5BH91 (Paired domain-containing protein OS=Strongyloides papillosus OX=174720 PE=4 SV=1)

HSP 1 Score: 130.183 bits (326), Expect = 3.152e-34
Identity = 58/100 (58.00%), Postives = 82/100 (82.00%), Query Frame = -3
Query:    3 THAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 302
            T +   VPTIRGRS++LIA ++I+ M + K I+NSTV A+IF +Y++ELC ++R+++ ++ ACLILDN R+HKR++IERITS  N++FKFLS YSYMLNP
Sbjct:  200 TRSNVKVPTIRGRSVTLIASISISQMCHCKVISNSTVDADIFSEYLEELCMYIRDEMKLQAACLILDNARIHKRNEIERITSMFNFDFKFLSPYSYMLNP 299          
BLAST of SMED30031250 vs. TrEMBL
Match: A0A0N5BG34 (Paired domain-containing protein OS=Strongyloides papillosus OX=174720 PE=4 SV=1)

HSP 1 Score: 130.183 bits (326), Expect = 3.505e-34
Identity = 58/100 (58.00%), Postives = 82/100 (82.00%), Query Frame = -3
Query:    3 THAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 302
            T +   VPTIRGRS++LIA ++I+ M + K I+NSTV A+IF +Y++ELC ++R+++ ++ ACLILDN R+HKR++IERITS  N++FKFLS YSYMLNP
Sbjct:  200 TRSNVKVPTIRGRSVTLIASISISQMCHCKVISNSTVDADIFSEYLEELCMYIRDEMKLQAACLILDNARIHKRNEIERITSMFNFDFKFLSPYSYMLNP 299          
BLAST of SMED30031250 vs. TrEMBL
Match: A0A0N5CAE4 (DDE_3 domain-containing protein OS=Strongyloides papillosus OX=174720 PE=4 SV=1)

HSP 1 Score: 103.99 bits (258), Expect = 8.299e-27
Identity = 45/75 (60.00%), Postives = 62/75 (82.67%), Query Frame = -3
Query:    3 MGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 227
            M   K I+NSTV A+IF +Y++ELC ++R+++ ++ ACLILDN R+HKR++IERITS  N++FKFLS YSYMLNP
Sbjct:    1 MCCCKVISNSTVDADIFSEYLEELCMYIRDEMKLQAACLILDNARIHKRNEIERITSMFNFDFKFLSPYSYMLNP 75          
BLAST of SMED30031250 vs. TrEMBL
Match: A0A0A9XRL8 (Insertion element IS630 uncharacterized 39 kDa protein OS=Lygus hesperus OX=30085 GN=YIS5_1 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 2.194e-13
Identity = 35/100 (35.00%), Postives = 62/100 (62.00%), Query Frame = -3
Query:    3 THAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 302
            T AV +VPT+ GR++SLI  +   G+ +SK I   T +A +FV+++ EL + + +  N+    +I+DN R+HK + ++R   ++ ++  +L  YS M NP
Sbjct:   24 TRAVVTVPTVGGRNVSLILALNNRGVVHSKVIAQGTTNAELFVEFLAELRQKVPDPDNL----IIMDNARIHKAAAVKRFIEEVRFQVHYLPPYSPMFNP 119          
BLAST of SMED30031250 vs. TrEMBL
Match: A0A183GHU5 (DDE_3 domain-containing protein OS=Heligmosomoides polygyrus OX=6339 GN=HPBE_LOCUS22159 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.909e-12
Identity = 40/103 (38.83%), Postives = 60/103 (58.25%), Query Frame = -3
Query:    3 THAVPSVPTIRGR--SISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLN-MEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 302
            T A   +PT+RGR  + +LI  M   G+ ++  I + T     F  +V +L   +R  ++ M+ A LI+ N R+ K S++ RI  + +YE KFLS YSYMLNP
Sbjct:   88 TRANDVLPTVRGRWWTRTLILAMNTQGVIHTGIIDDRTCTGPKFCAFVDQLVSKMRGVMDGMDGAWLIMSNARIRKISELRRILEETSYELKFLSPYSYMLNP 190          
BLAST of SMED30031250 vs. Planmine SMEST
Match: SMESG000043845.1 (SMESG000043845.1)

HSP 1 Score: 176.407 bits (446), Expect = 5.426e-57
Identity = 85/101 (84.16%), Postives = 91/101 (90.10%), Query Frame = -3
Query:    6 QRTHAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLN 308
            Q T AV SVPTI GRSISLIA +TINGMGYSKTITNSTV+ANIF DY+QELC+FLRNDLN +KACLILDN R+HKRSDIERITSQ NYEFKFLS YSYMLN
Sbjct:   85 QGTRAVVSVPTISGRSISLIASITINGMGYSKTITNSTVNANIFADYLQELCQFLRNDLNKKKACLILDNARIHKRSDIERITSQFNYEFKFLSPYSYMLN 185          
BLAST of SMED30031250 vs. Planmine SMEST
Match: SMESG000044452.1 (SMESG000044452.1)

HSP 1 Score: 108.612 bits (270), Expect = 2.416e-32
Identity = 56/77 (72.73%), Postives = 62/77 (80.52%), Query Frame = -3
Query:   81 RTHAVPSVPTIRG--RSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKR 305
            + H   SV  + G  R ISLIA +TINGM YS TITNSTV+ANI+ DYVQELC+FLRNDLNMEKACLILDN RVHKR
Sbjct:    6 KEHVHLSVFQLSGEDRYISLIASITINGMEYSITITNSTVNANIYTDYVQELCQFLRNDLNMEKACLILDNARVHKR 82          
BLAST of SMED30031250 vs. Planmine SMEST
Match: SMESG000059107.1 (SMESG000059107.1)

HSP 1 Score: 58.5362 bits (140), Expect = 2.889e-11
Identity = 35/100 (35.00%), Postives = 53/100 (53.00%), Query Frame = -3
Query:    3 THAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 302
            T A  +VPTIR R+IS+   M  NG+ + K+  N  ++   F++Y+ EL   L  D  + +   I+DN + HK  ++    +  N   KFL  YS  LNP
Sbjct: 1412 TPATLNVPTIRSRNISIACAMNKNGLLFYKSF-NRALNKEKFIEYITELKEVLI-DKEIHRCVFIMDNAKFHKSPEVLSAINNENTTVKFLPPYSPFLNP 1509          
BLAST of SMED30031250 vs. Planmine SMEST
Match: SMESG000076350.1 (SMESG000076350.1)

HSP 1 Score: 50.0618 bits (118), Expect = 3.363e-8
Identity = 33/103 (32.04%), Postives = 53/103 (51.46%), Query Frame = -3
Query:    3 QRTHAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDL-NMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 308
            + + A   V   RGR+ISL+  +T  G+  S  I   + + +IF++Y++   R L+    N     L++DN   H R D+  + S LN    +L  YS +LNP
Sbjct:  713 KNSKAFCRVQANRGRNISLMVAITKRGV-LSYDIQEGSYNGDIFIEYIK---RGLKTHFENNPNDILVMDNCAFHHRRDVTELFSNLNINVNYLPQYSPLLNP 811          
BLAST of SMED30031250 vs. Planmine SMEST
Match: SMESG000076350.1 (SMESG000076350.1)

HSP 1 Score: 49.6766 bits (117), Expect = 3.438e-8
Identity = 33/103 (32.04%), Postives = 53/103 (51.46%), Query Frame = -3
Query:    3 QRTHAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQELCRFLRNDL-NMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYMLNP 308
            + + A   V   RGR+ISL+  +T  G+  S  I   + + +IF++Y++   R L+    N     L++DN   H R D+  + S LN    +L  YS +LNP
Sbjct:  712 KNSKAFCRVQANRGRNISLMVAITKRGV-LSYDIQEGSYNGDIFIEYIK---RGLKTHFENNPNDILVMDNCAFHHRRDVTELFSNLNINVNYLPQYSPLLNP 810          
The following BLAST results are available for this feature:
BLAST of SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0N5BH913.152e-3458.00Paired domain-containing protein OS=Strongyloides ... [more]
A0A0N5BG343.505e-3458.00Paired domain-containing protein OS=Strongyloides ... [more]
A0A0N5CAE48.299e-2760.00DDE_3 domain-containing protein OS=Strongyloides p... [more]
A0A0A9XRL82.194e-1335.00Insertion element IS630 uncharacterized 39 kDa pro... [more]
A0A183GHU51.909e-1238.83DDE_3 domain-containing protein OS=Heligmosomoides... [more]
back to top
BLAST of SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 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 SMED30031250 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043845.15.426e-5784.16SMESG000043845.1[more]
SMESG000044452.12.416e-3272.73SMESG000044452.1[more]
SMESG000059107.12.889e-1135.00SMESG000059107.1[more]
SMESG000076350.13.363e-832.04SMESG000076350.1[more]
SMESG000076350.13.438e-832.04SMESG000076350.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031250 ID=SMED30031250|Name=SMED30031250|organism=Schmidtea mediterranea sexual|type=transcript|length=310bp
ATGGGATTAAGCATGTATGAATAAAGGGACAAAAATTTAAATTCGTAGTT
TAATTGTGAAGTAATTCTTTCAATATCACTTCTTTTATGAACCCTAACAT
TATCTAATATCAGGCAAGCCTTTTCCATATTAAGATCATTTCTGAGAAAT
CGACACAATTCTTGAACATAATCGACAAAAATATTGGCATGGACTGTTGA
ATTTGTAATTGTTTTAGAATATCCCATGCCATTAATAGTCATTATAGCAA
TTAATGAAATAGATCTTCCCCTGATAGTTGGAACACTGGGAACTGCATGT
GTTCGTTGCA
back to top

protein sequence of SMED30031250-orf-1

>SMED30031250-orf-1 ID=SMED30031250-orf-1|Name=SMED30031250-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
QRTHAVPSVPTIRGRSISLIAIMTINGMGYSKTITNSTVHANIFVDYVQE
LCRFLRNDLNMEKACLILDNVRVHKRSDIERITSQLNYEFKFLSLYSYML
NP
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland