SMED30001937

Overview
NameSMED30001937
Smed IDSMED30001937
Length (bp)1499
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



SMED30001937

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30001937SMESG000070717.1 Contig27094newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30001937SMESG000070717.1 Contig27094uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
testisSMED30001937SMESG000070717.1 PL06016B1C09ncbi_smed_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30001937SMESG000070717.1 Contig5486GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001937 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018670:3535..5033 -7423
Homology
[Close]
BLAST of SMED30001937 vs. TrEMBL
Match: A0A504YUN8 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_04125 PE=4 SV=1)

HSP 1 Score: 103.99 bits (258), Expect = 3.888e-20
Identity = 45/85 (52.94%), Postives = 59/85 (69.41%), Query Frame = -3 
Query:  274 IQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAF 528
            I+YTFY++D D   +PFYDRR+ AIA+  +C I  H K    +KP+YYKG  V PVTI++  M  LKRC+  +D Q+PYFN KAF
Sbjct:  371 IEYTFYINDTDAYQRPFYDRRVEAIARASQCNICLH-KPPPGQKPIYYKGNRVLPVTISARTMVTLKRCMARLDMQYPYFNVKAF 454
[Close]
BLAST of SMED30001937 vs. TrEMBL
Match: A0A4E0RXM1 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_006260 PE=4 SV=1)

HSP 1 Score: 103.605 bits (257), Expect = 5.690e-20
Identity = 45/85 (52.94%), Postives = 59/85 (69.41%), Query Frame = -3 
Query:  274 IQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAF 528
            I+YTFY++D D   +PFYDRR+ AIA+  +C I  H K    +KP+YYKG  V PVTI++  M  LKRC+  +D Q+PYFN KAF
Sbjct:  371 IEYTFYINDTDAYQRPFYDRRVEAIARASQCNICLH-KPPPGQKPIYYKGNRVLPVTISARTMVTLKRCMARLDMQYPYFNVKAF 454
[Close]
BLAST of SMED30001937 vs. TrEMBL
Match: A0A419PHI1 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CSKR_1389s PE=4 SV=1)

HSP 1 Score: 102.449 bits (254), Expect = 1.449e-19
Identity = 46/91 (50.55%), Postives = 61/91 (67.03%), Query Frame = -3 
Query:  274 EQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAF 546
            +Q+   I+YTFY++D +   +PFYDRR+ AIA+  +C I  H K     KP+YYKG  V PVTI+S  M  LKRC+  +D Q+PYFN KAF
Sbjct:  366 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLH-KPPPGHKPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 455
[Close]
BLAST of SMED30001937 vs. TrEMBL
Match: A0A4V6RGN9 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_010519 PE=4 SV=1)

HSP 1 Score: 102.064 bits (253), Expect = 1.884e-19
Identity = 46/91 (50.55%), Postives = 61/91 (67.03%), Query Frame = -3 
Query:  274 EQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAF 546
            +Q+   I+YTFY++D +   +PFYDRR+ AIA+  +C I  H K     KP+YYKG  V PVTI+S  M  LKRC+  +D Q+PYFN KAF
Sbjct:  369 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLH-KPPPGHKPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 458
[Close]
BLAST of SMED30001937 vs. TrEMBL
Match: A0A074ZW82 (Uncharacterized protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=T265_12942 PE=4 SV=1)

HSP 1 Score: 102.064 bits (253), Expect = 2.067e-19
Identity = 46/91 (50.55%), Postives = 61/91 (67.03%), Query Frame = -3 
Query:  274 EQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAF 546
            +Q+   I+YTFY++D +   +PFYDRR+ AIA+  +C I  H K     KP+YYKG  V PVTI+S  M  LKRC+  +D Q+PYFN KAF
Sbjct:  369 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLH-KPPPGHKPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 458
[Close]
BLAST of SMED30001937 vs. Planmine SMEST
Match: SMESG000070717.1 (SMESG000070717.1)

HSP 1 Score: 720.309 bits (1858), Expect = 0.000e+0
Identity = 350/367 (95.37%), Postives = 353/367 (96.19%), Query Frame = -3 
Query:  259 MGICHGRIPRTETRSAQTELNPFFEYSSRELINARYPNYRPTSVHSRNNVSKQRGENIQLKNSIISDWKHPNRFDYNFTKTDNPLIDNSGQIFPEMPRQKLEINKNNGDSTPTPSGVWPINGSGDCNFINLQKKKNIISQSRGQLNRDLEKSSVNINGNYSDEEDIETQKNTLFNEIDNNGFDINSKFPSQLPISTSSEFKTAKKSNCRKLSSQRNSRQKEYTRMKSSRKLSNQKIQLGNNNSNNYHTLVDDKALNNAVGISQKFHSSSLLEQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAFLSLSS 1359
            MGICHGRIPRTETRSAQTELNPFFEYSSRELINARYPNYRPTSVHSRNNVSKQRGENIQLKNSIISDWKHPNRFDYNFTKTDNPL+DNSGQIFPEMPRQKLEINKNNGDSTPTPSGVWPINGSGDCNFINLQKKKNIISQSRGQLNRDLEKSSVNINGNYSDEEDIETQKNTLFNE+DNNGFDIN             +FKTAKKSNCRKLSSQRNSRQKE TRMKSSRKLSNQKIQLGNNNSNNYHTLVDDKALNNAVGISQKFHSSSLLEQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAFLSLSS
Sbjct:    1 MGICHGRIPRTETRSAQTELNPFFEYSSRELINARYPNYRPTSVHSRNNVSKQRGENIQLKNSIISDWKHPNRFDYNFTKTDNPLMDNSGQIFPEMPRQKLEINKNNGDSTPTPSGVWPINGSGDCNFINLQKKKNIISQSRGQLNRDLEKSSVNINGNYSDEEDIETQKNTLFNEVDNNGFDIN-------------KFKTAKKSNCRKLSSQRNSRQKECTRMKSSRKLSNQKIQLGNNNSNNYHTLVDDKALNNAVGISQKFHSSSLLEQDCYPIQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAFLSLSS 354
[Close]
BLAST of SMED30001937 vs. Planmine SMEST
Match: SMESG000045132.1 (SMESG000045132.1)

HSP 1 Score: 97.4413 bits (241), Expect = 3.294e-22
Identity = 42/92 (45.65%), Postives = 60/92 (65.22%), Query Frame = -3 
Query:  271 IQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAK------ADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAFL 528
            I+YTFYV D +IC +P  D+R+ +I   C C +  H +      A++  + ++YKG PV PVTI S  M+ L++C+G +D QFPYFN KAFL
Sbjct:  216 IEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAFL 307
The following BLAST results are available for this feature:
BLAST of SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A504YUN83.888e-2052.94Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A4E0RXM15.690e-2052.94Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A419PHI11.449e-1950.55Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A4V6RGN91.884e-1950.55Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A074ZW822.067e-1950.55Uncharacterized protein (Fragment) OS=Opisthorchis... [more]
back to top
BLAST of SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 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 SMED30001937 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000070717.10.000e+095.37SMESG000070717.1[more]
SMESG000045132.13.294e-2245.65SMESG000045132.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001937 ID=SMED30001937|Name=SMED30001937|organism=Schmidtea mediterranea sexual|type=transcript|length=1499bp
CGCAGTCTGAATCAATTGGATTACTATAATTCATTGTAATTCCAACCAAC
TTTTCATTAGTTGCATCATAAATCATAGTTATGTTACTCTTGAACGACTA
GTTAAATAGTGTAGTAACGAGTTAATTTGACTGAAATAATTTCATATTAC
ACATTTAGAAAAACAATGTGTCAGTGGTATGGAAAAATGAAATAAAGTCT
GATTATTTATTTATTATGGTGCGAATTTATCAATTCTCCTATTTACGTAA
TAATATTAGCTGCTTAAACTTAAAAAAGCTTTACAATTAAAGTAAGGAAA
CTGCGAGTCTATAGATCCTAAACATCGTTTAAGACATGCCATATCAGGAG
ATGTAATAGTGACTGGTCTGACTGGTTTCCCTTTATAATATAAAGGTTTT
TCTGCTTCGTCGGCTTTTGCGTGAAAATATATTCGACATCGACAGGTTTT
TGCAATAGCAACCATTCGTCTATCATAAAATGGTTTTGTGCAGATGTCGT
TGTCGTCGACGTAAAATGTATACTGTATAGGATAACAATCCTGTTCCAAT
AAGCTGGACGAATGGAACTTTTGTGAAATACCAACTGCATTGTTCAAAGC
TTTATCATCTACAAGAGTATGATAGTTATTAGAATTGTTATTGCCCAATT
GAATTTTCTGATTTGAAAGCTTTCTTGAAGATTTCATTCGAGTGTATTCT
TTTTGCCTAGAATTTCTTTGGGAACTCAATTTGCGACAGTTAGATTTCTT
TGCTGTCTTAAATTCTGAACTTGTTGAAATAGGAAGTTGAGAAGGAAACT
TACTATTAATATCAAATCCATTATTGTCTATTTCATTGAACAGTGTATTC
TTTTGCGTTTCTATGTCTTCTTCGTCACTGTAATTTCCATTGATATTCAC
GCTTGATTTTTCTAAGTCTCGGTTGAGTTGCCCACGTGATTGGGAAATTA
TATTTTTCTTTTTCTGTAAATTTATGAAATTACAATCTCCACTTCCGTTT
ATTGGCCAAACTCCGCTAGGAGTCGGCGTAGAATCGCCGTTGTTTTTATT
AATTTCCAATTTCTGTCTTGGCATTTCTGGAAAGATTTGACCGGAATTGT
CAATTAGTGGATTATCTGTTTTTGTGAAATTATAATCAAAACGATTTGGG
TGCTTCCAGTCGCTTATTATTGAGTTTTTCAGCTGGATATTCTCTCCGCG
CTGCTTGGAAACGTTGTTCCTTGAATGGACCGACGTCGGTCTGTAATTTG
GATAGCGAGCATTTATCAATTCACGGCTTGAATACTCAAAAAATGGATTG
AGTTCGGTTTGAGCGGATCTCGTTTCCGTTCGGGGTATTCGTCCATGACA
AATGCCCATGGGAATTTTTTTAACTTTATTTTTTCTATGGTTTGTTATCG
TTTTTGGATTAAATACCACATGCTGTTTAATATTCTTTGCAATAGGACAT
AATATATAAAACTTTAAATAATTTTTTATCAATAACTATTGAACATTTT
back to top

protein sequence of SMED30001937-orf-1

>SMED30001937-orf-1 ID=SMED30001937-orf-1|Name=SMED30001937-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=368bp
MGICHGRIPRTETRSAQTELNPFFEYSSRELINARYPNYRPTSVHSRNNV
SKQRGENIQLKNSIISDWKHPNRFDYNFTKTDNPLIDNSGQIFPEMPRQK
LEINKNNGDSTPTPSGVWPINGSGDCNFINLQKKKNIISQSRGQLNRDLE
KSSVNINGNYSDEEDIETQKNTLFNEIDNNGFDINSKFPSQLPISTSSEF
KTAKKSNCRKLSSQRNSRQKEYTRMKSSRKLSNQKIQLGNNNSNNYHTLV
DDKALNNAVGISQKFHSSSLLEQDCYPIQYTFYVDDNDICTKPFYDRRMV
AIAKTCRCRIYFHAKADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSI
DSQFPYFNCKAFLSLSS*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0002089reproductive organ