SMED30009080
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Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast Population▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Overview
Single cell RNA-seq of pluripotent neoblasts and its early progeniesWe 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
Neoblast Population
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30009080 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30009080 aligns in the following genomic locations: Homology
BLAST of SMED30009080 vs. Planmine SMEST
Match: SMESG000011199.1 (SMESG000011199.1) HSP 1 Score: 266.159 bits (679), Expect = 6.986e-87 Identity = 151/171 (88.30%), Postives = 157/171 (91.81%), Query Frame = 1
Query: 1 AIDDRIKAIDTFKNALSHYKIESSQLLNDFETFKKDVAKNIQTSNLKDIKYNNKAFVYYAIEEQSSTISFKIKTNPTTLFGDKDHTFNLFRNHDDFFVMFVYNGQNIEINKIRIMGSKGTFIRAIIGNKRKTLHLRNNSFSVSEPLSKXXXXXXXXXXXXXXXXXHREFEK 513
AIDDR+K IDT KN +SHYKIESSQLLNDFETFKKDVAK IQTSNLKDIKYNNKAF YYAIEE SS ISF IK NPTT FGDKDHTFNLFR+HDDFFVMFVYNGQNIEI KIRIMGSKGTFIRAIIGNKRKTL L NNSFSVSEP+SKLTIGG+GIILDLLIN G+REFEK
Sbjct: 109 AIDDRMKIIDTLKNEISHYKIESSQLLNDFETFKKDVAKYIQTSNLKDIKYNNKAFDYYAIEEPSSMISFIIKNNPTTFFGDKDHTFNLFRHHDDFFVMFVYNGQNIEIKKIRIMGSKGTFIRAIIGNKRKTLQLSNNSFSVSEPMSKLTIGGSGIILDLLINHGYREFEK 279
BLAST of SMED30009080 vs. Planmine SMEST
Match: SMESG000073213.1 (SMESG000073213.1) HSP 1 Score: 210.305 bits (534), Expect = 1.004e-65 Identity = 103/119 (86.55%), Postives = 109/119 (91.60%), Query Frame = 1
Query: 28 DTFKNALSHYKIESSQLLNDFETFKKDVAKNIQTSNLKDIKYNNKAFVYYAIEEQSSTISFKIKTNPTTLFGDKDHTFNLFRNHDDFFVMFVYNGQNIEINKIRIMGSKGTFIRAIIGN 384
+T KN +SHYKIESSQLLNDFETFKKDVA+NIQTSNLK++KYNNKAF YYAIEEQSS I F IK NPTTLFGDKDHTFNLFR+HDDFFVMFVYNG NIEINKIRIMGSK TFIRAI GN
Sbjct: 127 NTLKNEISHYKIESSQLLNDFETFKKDVAENIQTSNLKELKYNNKAFDYYAIEEQSSMIYFIIKNNPTTLFGDKDHTFNLFRHHDDFFVMFVYNGHNIEINKIRIMGSKKTFIRAITGN 245
BLAST of SMED30009080 vs. Planmine SMEST
Match: SMESG000026577.1 (SMESG000026577.1) HSP 1 Score: 199.519 bits (506), Expect = 1.013e-58 Identity = 126/146 (86.30%), Postives = 131/146 (89.73%), Query Frame = 2
Query: 671 MEREINEEIIYPTFQERKIYPFLNEQNVFNYIENLPTEKIKAAMNKNSMNNPLINQINEFLLEKKTLDERLIHYKKIKSRRTKADTGIKIACXXXXXXXXXXXXXXXXXXXXXVAPFVSIIMSSIFGGSNVLLLFLGEGISIVLTC 1108
MEREINEEIIYPTFQER+IYP LNEQNVFNYIENLP EKIKA MNK+ NNP IN+INEFLLEKK LDER+IHYKKIKSR TKADTGIKIACLSITGILTISTSIFSG+SLIGVA FVSIIMS IF GSN LLLFL EGISI LT
Sbjct: 1 MEREINEEIIYPTFQERRIYPSLNEQNVFNYIENLPIEKIKAPMNKDCTNNPSINKINEFLLEKKKLDERVIHYKKIKSRWTKADTGIKIACLSITGILTISTSIFSGISLIGVAHFVSIIMSLIFRGSNALLLFLWEGISIGLTS 146
BLAST of SMED30009080 vs. Planmine SMEST
Match: SMESG000025592.1 (SMESG000025592.1) HSP 1 Score: 124.79 bits (312), Expect = 2.798e-45 Identity = 87/103 (84.47%), Postives = 90/103 (87.38%), Query Frame = 2
Query: 800 MNKNSMNNPLINQINEFLLEKKTLDERLIHYKKIKSRRTKADTGIKIACXXXXXXXXXXXXXXXXXXXXXVAPFVSIIMSSIFGGSNVLLLFLGEGISIVLTC 1108
MNK S NNP IN+INEFLLEKK LDERLIHYKK KSR T+ADTGIKI CLSITGILTIS SIFSG+SLIGVAPFVSIIMSSIFGGSN LLLFL E ISI LT
Sbjct: 1 MNKGSTNNPSINKINEFLLEKKKLDERLIHYKKRKSRWTEADTGIKIVCLSITGILTISNSIFSGISLIGVAPFVSIIMSSIFGGSNALLLFLSERISIGLTS 103 HSP 2 Score: 77.0258 bits (188), Expect = 2.798e-45 Identity = 37/44 (84.09%), Postives = 41/44 (93.18%), Query Frame = 3
Query: 1110 IYREVCEELNHGINKLYLYQVKALEDGIL*PTEIEESNKIIDEI 1241
IYREV ++LNHGINKLYLYQVKAL+DGIL PTEIE SNKIIDE+
Sbjct: 108 IYREVYKKLNHGINKLYLYQVKALKDGILSPTEIESSNKIIDEM 151
BLAST of SMED30009080 vs. Planmine SMEST
Match: SMESG000076736.1 (SMESG000076736.1) HSP 1 Score: 141.354 bits (355), Expect = 6.619e-41 Identity = 75/96 (78.12%), Postives = 79/96 (82.29%), Query Frame = 2
Query: 674 EREINEEIIYPTFQERKIYPFLNEQNVFNYIENLPTEKIKAAM-----NKNSMNNPLINQINEFLLEKKTLDERLIHYKKIKSRRTKADTGIKIAC 946
+ EINEEIIY TFQERKIY LNEQNVFNYIENLP EKIKA M NK+ MNNP IN+INEFLLEKK LDERLIHYKKIKSR TKADTGIK+
Sbjct: 10 QSEINEEIIYSTFQERKIYSSLNEQNVFNYIENLPIEKIKAPMNITFKNKDYMNNPSINKINEFLLEKKKLDERLIHYKKIKSRWTKADTGIKLLV 105 The following BLAST results are available for this feature:
BLAST of SMED30009080 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30009080 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30009080 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30009080 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30009080 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30009080 ID=SMED30009080|Name=SMED30009080|organism=Schmidtea mediterranea sexual|type=transcript|length=1241bpback to top protein sequence of SMED30009080-orf-1 >SMED30009080-orf-1 ID=SMED30009080-orf-1|Name=SMED30009080-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=177bp AIDDRIKAIDTFKNALSHYKIESSQLLNDFETFKKDVAKNIQTSNLKDIKback to top protein sequence of SMED30009080-orf-2 >SMED30009080-orf-2 ID=SMED30009080-orf-2|Name=SMED30009080-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp MEREINEEIIYPTFQERKIYPFLNEQNVFNYIENLPTEKIKAAMNKNSMNback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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