SMED30035238

Overview
NameSMED30035238
Smed IDSMED30035238
Length (bp)741
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 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30035238 (SMED30035238) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035238 (SMED30035238) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30035238 (SMED30035238) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035238 (SMED30035238) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30035238

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
neoblastSMED30035238SMESG000057219.1 dd_Smed_v4_15701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30035238SMESG000057219.1 dd_Smed_v4_15701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035238SMESG000030578.1 SMESG000020466.1 Contig32548newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035238SMESG000030578.1 SMESG000020466.1 Contig32548uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035238 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003164:69800..70536 -3613
v31.022315:4345..5085 -3579
v31.000610:77488..78228 -3552
v31.019719:400..1140 +3543
v31.007384:6567..7307 -3543
v31.000318:106535..107275 +3543
v31.006261:14196..14936 -3516
v31.005415:15396..16136 +3516
v31.011833:3270..4010 -3498
v31.022671:7255..8043 +3460
v31.000051:94884..95617 -3453
v31.000550:100846..101633 +3446
v31.000749:60115..60854 -3430
v31.000967:100953..101692 -3400
v31.006131:28027..28806 -3389
v31.001745:8773..9552 +3389
v31.006812:5142..5918 +3281
v31.020318:8239..9044 +3267
v31.002280:26866..27672 +3266
v31.000096:53658..54409 -3264
v31.018025:1559..2365 -3257
v31.000264:36471..37277 -3257
v31.002044:19775..20572 -3229
v31.004936:10215..11018 +3222
v31.000410:82341..83157 -3219
v31.021844:6052..6858 -3212
v31.000058:200260..201063 +3203
v31.000824:49592..50395 +3183
v31.002682:15102..15912 -3167
v31.001636:70686..71466 +3164
v31.005054:19174..19977 -3149
v31.003123:22641..23413 +3129
v31.015035:1727..2527 +3078
v31.000403:91120..91923 +3041
v31.017671:2985..3752 -3036
v31.009312:8473..9627 -3036
v31.006137:3027..3830 -3032
v31.002648:22460..23263 +3023
v31.000327:80356..81159 -3005
v31.000752:52702..53508 -3003
v31.003573:27257..28050 -2932
v31.014147:8670..9406 -2907
v31.000671:84791..85584 +2901
v31.000485:54965..55761 +2901
v31.003764:57334..58119 -2897
v31.000018:49368..50161 -2883
v31.024612:3109..3912 +2853
v31.002596:60177..60980 +2849
v31.002704:28025..28826 -2828
v31.001936:60922..61724 -2821
v31.002290:27998..28745 +2641
v31.008052:6815..7495 +2577
v31.013739:13803..14433 +2526
v31.000147:8804..9442 +2501
v31.001088:24713..25538 +1483
Homology
[Close]
BLAST of SMED30035238 vs. Planmine SMEST
Match: SMESG000027090.1 (SMESG000027090.1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.025e-10
Identity = 72/173 (41.62%), Postives = 89/173 (51.45%), Query Frame = 2 
Query:   44 VLTKTPTKLQSPKKHFDNIINSTINHNTCSTPKNDLNKKSCYHQKNYLFNLSSNSSEX-XXXXXXXXXXXXXXXXKSLYSNNTFNLNTLPDYSNRNKNSINTYTN---YSSFKKSLPSLNYKFALTHYKIYNNT------TLNYPKYLTTNNKNIEAYKNSAYNFICTHYKLE 532
            +L+KTPTKLQS         N   N +TCSTPKND NK  C H  + LFN SS SSEI       + TT T+  + SLYSN     +  P     NK +  TY +    S+ +  L +L  +   THYKI  N       T  YP   TT N  I+A K+ A+ FICTHYK E
Sbjct:  128 ILSKTPTKLQS---------NYIKNLSTCSTPKNDCNKNPCNHFDD-LFNSSSKSSEIDLTNISDNTTTTTNYSNISLYSNENLTDHIDP----CNKLTSFTYDDNKPNSTLQSILTTLLKELIPTHYKIEKNINSLPINTTKYPPATTTKNL-IQASKSFAHYFICTHYKPE 285
[Close]
BLAST of SMED30035238 vs. Planmine SMEST
Match: SMESG000012636.1 (SMESG000012636.1)

HSP 1 Score: 52.373 bits (124), Expect = 1.029e-7
Identity = 90/255 (35.29%), Postives = 116/255 (45.49%), Query Frame = 2 
Query:  128 CSTPKNDLNKKSCYHQKNYLFNLSSNSSEXXXXXXXXXXXXXX-XXXKSLYSNNTFNLNTLPDYSNRNKNSINTYTNYSSFKKSLPSLNYKFALTHYKIYNNT------------TLNYPKYLTT--NNKNIEAYKNSAYNFICTHYKLE---------------------------XXXXXXXPXXXXXXXXXXXXXXQPPDKQTYNI-----------NSSYQDNQPDYHGDPDYADYLKSLQYEEEYSDGDY 733
            CSTPK DLNK+S Y+  + LFN S NSS+ID+TNL+ NTTD S + + SLY  +  NLN                TNY+ +       +  F  THYKI +N             T N PK+ +T  NN  I+ YK+ A  FICTHYKLE                            N +   P  N + T DN T +QP  KQ+ +I           +  Y     +Y+   DY  Y+K    EEEYSD DY
Sbjct:  169 CSTPKTDLNKQS-YNCFDDLFNSSCNSSQIDLTNLTANTTDKSNSSTNSLYKTDITNLNI-------------DSTNYTPYP-----FDNNFVPTHYKIESNLNNHINIDSISIDTQNNPKHSSTYTNNILIQVYKSLANIFICTHYKLENNIINHDNDDSITTTNCYNQDYSIESSKNDLATNPFLNTNNTIDNTTIEQPSTKQSCHITDVSSYDCSYDSDEYYGGGDEYYEGADYLAYIKGQYEEEEYSDDDY 404
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BLAST of SMED30035238 vs. Planmine SMEST
Match: SMESG000009401.1 (SMESG000009401.1)

HSP 1 Score: 51.2174 bits (121), Expect = 2.336e-7
Identity = 77/179 (43.02%), Postives = 94/179 (52.51%), Query Frame = 2 
Query:   44 VLTKTPTKLQSPKKHFDNIINSTINHNTCSTPKNDLNKKSCYHQKNYLFNLSSNSSEXXXXXXXXXXXXXXXXXKSLYSNNTFNLNT-LPDYSNRNKNSINTYTNY-----SSFKKSLPSLNYKFALTHYKIYNN----------TTLNYPKYLTTNNKNIEAYKNSAYNFICTHYKLE 532
            +L KTPTK QS         N   N   CSTPKND NKK C H  + LFN SS SSEID TN+SDN T T+N     YSN T + N  L D+ +   N I ++T+      S+ +  L +L      THYK   N           TLN PKY  +N K  +A K+ A+ FICTHYK E
Sbjct:  226 ILYKTPTKFQS---------NYIKNLTICSTPKNDCNKKPCNHFDD-LFNSSSKSSEIDRTNISDNITTTTN-----YSNITLHSNENLTDHIDL-CNKITSFTSEDDKPNSTLQPILTTLLKDLIPTHYKTEKNNHVNNNSLPINTLNNPKY--SNKK--KASKSFAHYFICTHYKPE 384
[Close]
BLAST of SMED30035238 vs. Planmine SMEST
Match: SMESG000017552.1 (SMESG000017552.1)

HSP 1 Score: 48.9062 bits (115), Expect = 1.329e-6
Identity = 63/162 (38.89%), Postives = 81/162 (50.00%), Query Frame = 2 
Query:   56 TPTKLQSPKKHFDNIINSTINHNTCSTPKNDLNKKS--CYHQKNYLFNLSSNSSEXX-XXXXXXXXXXXXXXXKSLYSNNTFNLNTLPDYSNRNKNSINTYTNYSSFKKSLPSLNYKFALTHYKIYNN--TTLNYPKYLTT-NNKNIEAYKNSAYNFICTHY 523
            TPTK++S K               CSTPK D NK+S  C+     LFN S NSS+ID     ++ T  +++   SLY  +T NLN          +  NTYTNY+ +       +  F  THYKI NN  +T N PK+    +N  I AYK SAY FI  HY
Sbjct:  223 TPTKIRSNKNPI------------CSTPKTDFNKQSYNCFDN---LFNSSCNSSQIDPTYLTNNTTDKSNSSINSLYETDTTNLNI---------DLTNTYTNYTPY-----PFDNNFVSTHYKIENNHVSTHNNPKHTNFYHNHLIRAYKKSAYKFIYKHY 355
[Close]
BLAST of SMED30035238 vs. Planmine SMEST
Match: SMESG000017552.1 (SMESG000017552.1)

HSP 1 Score: 49.2914 bits (116), Expect = 1.348e-6
Identity = 63/162 (38.89%), Postives = 82/162 (50.62%), Query Frame = 2 
Query:   56 TPTKLQSPKKHFDNIINSTINHNTCSTPKNDLNKKS--CYHQKNYLFNLSSNSSEXX-XXXXXXXXXXXXXXXKSLYSNNTFNLNTLPDYSNRNKNSINTYTNYSSFKKSLPSLNYKFALTHYKIYNN--TTLNYPKYLTT-NNKNIEAYKNSAYNFICTHY 523
            TPTK++S K            +  CSTPK D NK+S  C+     LFN S NSS+ID     ++ T  +++   SLY  +T NLN          +  NTYTNY+ +       +  F  THYKI NN  +T N PK+    +N  I AYK SAY FI  HY
Sbjct:  263 TPTKIRSNK------------NPICSTPKTDFNKQSYNCFDN---LFNSSCNSSQIDPTYLTNNTTDKSNSSINSLYETDTTNLNI---------DLTNTYTNYTPY-----PFDNNFVSTHYKIENNHVSTHNNPKHTNFYHNHLIRAYKKSAYKFIYKHY 395
The following BLAST results are available for this feature:
BLAST of SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 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 SMED30035238 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000027090.12.025e-1041.62SMESG000027090.1[more]
SMESG000012636.11.029e-735.29SMESG000012636.1[more]
SMESG000009401.12.336e-743.02SMESG000009401.1[more]
SMESG000017552.11.329e-638.89SMESG000017552.1[more]
SMESG000017552.11.348e-638.89SMESG000017552.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035238 ID=SMED30035238|Name=SMED30035238|organism=Schmidtea mediterranea sexual|type=transcript|length=741bp
TTCAACTCCTACTAACACCTATGATTCAATTTCTGATGTCTCTGTTCTTA
CTAAAACACCAACAAAACTTCAATCACCTAAAAAACACTTTGACAACATC
ATAAATAGCACTATTAATCATAACACATGTTCAACTCCTAAAAATGATCT
CAATAAAAAATCATGTTATCACCAAAAAAATTATCTCTTCAACCTATCAT
CCAACTCGTCTGAAATTGATATTACAAACTTGTCTGATAATACTACTGAC
ACATCAAATATCTCCAAATCACTATATAGTAATAACACTTTTAATTTAAA
TACCTTACCTGACTACTCAAATCGCAATAAAAATTCAATTAATACCTACA
CAAACTACTCTTCTTTCAAAAAATCACTACCATCTCTCAATTATAAATTT
GCTCTAACACATTACAAAATTTACAATAATACTACACTAAACTACCCAAA
ATACTTGACTACCAATAATAAAAATATTGAAGCATACAAAAATTCAGCTT
ACAACTTTATTTGCACACACTACAAACTTGAAAACAACATTATCATCAAC
ATCCCTCTTACTAATAATTCAACTACCTCTGACAATCTAACTTCAGATCA
ACCTCCAGATAAGCAAACTTACAACATTAATAGTTCTTATCAAGACAACC
AACCTGATTATCATGGTGATCCTGATTACGCTGATTACCTGAAAAGCTTA
CAGTATGAAGAAGAATATTCTGATGGTGACTACTGATGTCG
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protein sequence of SMED30035238-orf-1

>SMED30035238-orf-1 ID=SMED30035238-orf-1|Name=SMED30035238-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=245bp
STPTNTYDSISDVSVLTKTPTKLQSPKKHFDNIINSTINHNTCSTPKNDL
NKKSCYHQKNYLFNLSSNSSEIDITNLSDNTTDTSNISKSLYSNNTFNLN
TLPDYSNRNKNSINTYTNYSSFKKSLPSLNYKFALTHYKIYNNTTLNYPK
YLTTNNKNIEAYKNSAYNFICTHYKLENNIIINIPLTNNSTTSDNLTSDQ
PPDKQTYNINSSYQDNQPDYHGDPDYADYLKSLQYEEEYSDGDY*
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 14..37
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 14..29