SMED30002422

Overview
NameSMED30002422
Smed IDSMED30002422
Length (bp)2507
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.
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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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Alignments
SMED30002422 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009823:11467..16258 +12371
Homology
BLAST of SMED30002422 vs. TrEMBL
Match: A0A1S3JJT4 (microtubule-associated protein futsch OS=Lingula unguis OX=7574 GN=LOC106173549 PE=4 SV=1)

HSP 1 Score: 86.6557 bits (213), Expect = 2.192e-13
Identity = 48/161 (29.81%), Postives = 89/161 (55.28%), Query Frame = 3
Query: 1833 MLPSTDCLKQTFHVDHEDEELLQTPIIYD-ANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKL-QNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEE 2309
            ++P    ++Q+ HVD E+EE+    I+ + A+G   +  S T NF +V E V L I +  A + ++++ E    +NP++D WK+  V +TR+IE DL    ++R++ + I+   + +K ++++ D  G    +   +  L  KET  VF  L++   E+ E
Sbjct: 1927 LVPIPRNVRQSIHVDREEEEIQGGGILLNHADGSGYKTDSSTVNFDTVNECVDLGIENGVARVAVKVTCERIVPVNPVQDVWKKNAVIVTRLIEFDLEANPETRRMYERIINSRKTNKREVAYIDSRGREHIETQADRTLNAKETMKVFSTLMNAAGEKNE 2087          
BLAST of SMED30002422 vs. Planmine SMEST
Match: SMESG000074454.1 (SMESG000074454.1)

HSP 1 Score: 977.622 bits (2526), Expect = 0.000e+0
Identity = 476/477 (99.79%), Postives = 476/477 (99.79%), Query Frame = 3
Query: 1017 MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPIGSTRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY 2447
            MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPI STRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY
Sbjct:    1 MHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVKPKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKKEWVEYKQLPVETNHRSEIKRDYNSEILYPIDSTRSKNSNAVYFNNKLSDYKIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEEWTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTEKLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQPSKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY 477          
BLAST of SMED30002422 vs. Planmine SMEST
Match: SMESG000077614.1 (SMESG000077614.1)

HSP 1 Score: 73.9442 bits (180), Expect = 2.020e-13
Identity = 49/155 (31.61%), Postives = 78/155 (50.32%), Query Frame = 3
Query: 1833 MLPSTDCLKQTFHVDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKAL-IKIEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCRMDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSIT 2294
            MLP     KQ FHV  ++EELL  P+IYD NG +I NL  TN F  V+E V++ IS L  + + + I V  + +   I+  W +KT+ + R I +++       K++ ++     +K +    D   S+     ++  LTG     VF  L+ I 
Sbjct:  281 MLPVGTFAKQKFHVVQDEEELLGRPVIYDLNGLQIPNLEITNEFDCVSESVSINISKLTNVEVVVTILVSKYISKKQIDKPWTKKTIEIIRTISINVEASGKKEKVEKLINDLMKNKSE--KFDIKASIYRLKGEKIQLTGYSALKVFKILMKIA 433          
The following BLAST results are available for this feature:
BLAST of SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1S3JJT42.192e-1329.81microtubule-associated protein futsch OS=Lingula u... [more]
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BLAST of SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 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 SMED30002422 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000074454.10.000e+099.79SMESG000074454.1[more]
SMESG000077614.12.020e-1331.61SMESG000077614.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002422 ID=SMED30002422|Name=SMED30002422|organism=Schmidtea mediterranea sexual|type=transcript|length=2507bp
TTAATATCAGATTTTGTTAACCATAAAAATCAGTTCAAGTTTTCATTTTT
GATATAGTTTGAATTTTTTAAATGACTGAAGTAATAGAACAGAGAAGAGT
TGAAAAAGTTATAAAAACACATCATAAGATTCAGGAAGATGAGCCAATGA
TTCACAAGAAAATTATAGATATAACCATACATCCAGTTGATGACGCTGAG
AGCTTTGTCATTAATAAATCATCAAAAGAATTAAATGAGTCCATTGGAAA
TGGAGGGATTAAAGAATCCATGATCACCAAAAAAGTTCATTCAATAAAAG
ATCAAACTGAGTTTTATGATAACGGTACATTGACTGAAAATCACCATGAA
ATGCATAATGGCCACGGGATAAATAATACCAAAATACACGCATCAAACGG
AGAGCATTTAGTAAAATTAGATAACACTGCTATTCAAAAGCAAATTGTGA
ATGTAGCTATAACTCCTGTCGAGGAAGAAAATTATGAAGAAGAGCTTAAA
AAATCGGAAACCATAAATAAGACTCGGACTATAATTACAAGCGAGAGAAA
TGTGAATGAAAATGTAAATAACTCAAATCATCTAAAAGTGGTGAAAAGAA
ATGAATTTGATACTCGTTCTGTTGAATTGAACCAAAAACCTCCAAAAGAT
AATGACCGAGATTCTCGTTCAGTTTGCTCGGTTGGCGACGGGAAACATTG
GGAGATAAAGTCTATCAAGTCAATTGAGGATGAATTTAGATTAGTACCAA
AACTAAACCCTGAACAAGAATCACTGGAGAAAGTAGAAAATTACTTAAAA
TCTCAAGACTCGAATTTTATTTTAGTAAACGATAGTAAAATTGAAAATAT
ACAACATCCTCCTGGCACCGTAGACAATTTTATTATCGAAAATCGTATGG
GGAAAAATATGAATTTGAATATAAATTATATCAAATCTGTCGATGGGGAT
AACAAATCAGCTCGGTCAAACTCAGTTATAATAAATGAAAAGTGGACCGA
ATATCATCCACAAAAAATGCATTCTTCAACATCTGAAATTGAAATTAAAG
AACCGGAAAAAAATTTAAGTTTCACAATTGATAAAGTTCAAGAATACAAC
TACACCAACAACACAGTCAAACCGAAGGAAAGAGAACGGCCTCGCGTTAA
AGAATCATCGACAGTTGAAATGAAGATCCACTCACCCAAACCGGAAATAG
ATTTTGTCAACATAGAGATTTATAATGGCAATGAACCTCCAGTCAGATCC
GATTCAGTGAAAATGAAAAAAGAATGGGTTGAATATAAACAACTACCGGT
TGAGACAAATCATCGCAGCGAAATAAAAAGAGATTATAACTCCGAAATTT
TGTATCCCATTGGTAGTACAAGATCAAAGAATTCTAATGCTGTATATTTC
AATAACAAATTAAGTGACTATAAAATAAAACCAACGGAGACTTCAAGTTT
TGAACAAATATCTAAAGGCTACTCATCTAAAGACCTATGTGACACTCACA
ACAGTTATGTTCCTAGCATGTATAATACTGGTCAAACTGGGAAATCTGAT
TCAGTAACAATGAAAGAAGAATGGACGGAATTCCTTACAGTTCCCATTTT
TTCCACTTCAGCCAATTCAATAACACAAAAAGAAAATCCCAAAAGTAACG
CAACTTATCCATATGCTTCCAAAATATACGATCATTACAGCTATCGATAT
GAAGATCCTATAAAGACGGAAAAGTTACAAAACTTAGCTAGCACAACCTT
GGAAAACGCACCAAGAACATATCATTCATCCGAGAGAGTTGTCCAAGCAC
TTTATGATTCATTAAGCAAAAAACATAAACCAATGTTGCCATCAACAGAT
TGCTTGAAACAGACTTTTCACGTTGATCACGAAGACGAGGAGTTACTGCA
GACTCCTATCATTTATGACGCCAATGGGGAACGGATTGAAAACTTGTCTG
AAACCAACAATTTCAAATCTGTAACAGAATACGTGACATTGCGAATTTCT
GATTTGAAGGCGTTAATAAAAATTGAAATCTCTGTCGAAATGTTCCATAA
TATAAATCCAATCGAAGACAATTGGAAAAGAAAAACCGTCAGATTAACAC
GAATGATTGAGCTTGATTTGTCAAAAATAAAAGATAGCAGAAAACTTCAA
AATATTATGAAGAGATGCCGTATGGACAAGCCGCAAATATCTTGGACCGA
TGAAAATGGCAGTGTTGTCAATCAGTACAATCAAGAAAATGTTTTAACTG
GAAAAGAAACATTCGATGTGTTTTTTAACTTGTTGTCTATAACTCACGAA
GAAGAAGAACAGTGCCAACCTTCAAAAGTCAACAAGGATGAATTCTATTT
AACTCGGAGTCCAAGTGGGCAAATAACTAACGTACCTTGTGAACCACAAT
ATTTGATTAATGGATATTCGAATGTTGAAAGATCTTATCTATACTATTGA
GATTTTATTATTATGACTTTTATTAAAAACGATTTATTCTGATTATTTGT
GTTATGA
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protein sequence of SMED30002422-orf-1

>SMED30002422-orf-1 ID=SMED30002422-orf-1|Name=SMED30002422-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=793bp
MTEVIEQRRVEKVIKTHHKIQEDEPMIHKKIIDITIHPVDDAESFVINKS
SKELNESIGNGGIKESMITKKVHSIKDQTEFYDNGTLTENHHEMHNGHGI
NNTKIHASNGEHLVKLDNTAIQKQIVNVAITPVEEENYEEELKKSETINK
TRTIITSERNVNENVNNSNHLKVVKRNEFDTRSVELNQKPPKDNDRDSRS
VCSVGDGKHWEIKSIKSIEDEFRLVPKLNPEQESLEKVENYLKSQDSNFI
LVNDSKIENIQHPPGTVDNFIIENRMGKNMNLNINYIKSVDGDNKSARSN
SVIINEKWTEYHPQKMHSSTSEIEIKEPEKNLSFTIDKVQEYNYTNNTVK
PKERERPRVKESSTVEMKIHSPKPEIDFVNIEIYNGNEPPVRSDSVKMKK
EWVEYKQLPVETNHRSEIKRDYNSEILYPIGSTRSKNSNAVYFNNKLSDY
KIKPTETSSFEQISKGYSSKDLCDTHNSYVPSMYNTGQTGKSDSVTMKEE
WTEFLTVPIFSTSANSITQKENPKSNATYPYASKIYDHYSYRYEDPIKTE
KLQNLASTTLENAPRTYHSSERVVQALYDSLSKKHKPMLPSTDCLKQTFH
VDHEDEELLQTPIIYDANGERIENLSETNNFKSVTEYVTLRISDLKALIK
IEISVEMFHNINPIEDNWKRKTVRLTRMIELDLSKIKDSRKLQNIMKRCR
MDKPQISWTDENGSVVNQYNQENVLTGKETFDVFFNLLSITHEEEEQCQP
SKVNKDEFYLTRSPSGQITNVPCEPQYLINGYSNVERSYLYY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0000421tail
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 30..51
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 33..51