SMED30021239

Overview
NameSMED30021239
Smed IDSMED30021239
Length (bp)3780
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 SMED30021239 (SMED30021239) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021239 (SMED30021239) 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 SMED30021239 (SMED30021239) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021239 (SMED30021239) 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




SMED30021239

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermal cellSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal region of the epidermisSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
head marginSMED30021239SMESG000010487.1 dd_Smed_v4_9329_1_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021239 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001739:32739..42380 +16725
Homology
BLAST of SMED30021239 vs. Planmine SMEST
Match: SMESG000010487.1 (SMESG000010487.1)

HSP 1 Score: 1235.71 bits (3196), Expect = 0.000e+0
Identity = 619/628 (98.57%), Postives = 625/628 (99.52%), Query Frame = 2
Query:  887 MDVSGQGNLATVNKPKRPSDGNGQPLSTPSVNVIDFLPVIKWKFKIIPTKVPDSGSNGGVISLNDDVKNTNNANSGGSTDKNPNHKXXXXXXXXXXXXXXPQTSGPVLLGSLSFSPNSDLSLWIIVGILLLTMAVVWAVTHFICYVSKQGKTRRNVCGWRKKFSKDDNHSWLGAYHVVNKSKSSTIDQLSLIKMKTEIQNSQTVKSTFGSTNQTKQLFSSGLINKDYTQSLRVSIPGSVRPNGLRSQSSTSLWSYQTTIADGTALISGSFTGPTMNNHIIENGNTGLIFTISELKCPNAWISKDSENVSHFENSQFEECLEVHFLLRESLLVGKMKNVRHRRNIGDFVIQIWNAFEGTLLKSVPDDLTEHSIACDAICTLRDEFLILIRQGEILVWNVKANAIMQAMKLPNIQTWKGKHAIQATQNMQDIIIMIFLPFSGVTHLYTYNFDDIVRGGCSCSFQYRSFPSQKTFYSLISNNSILIAGSTCVDIVLWNFSNNSESILSRNEEEQIQRILNSPSGELILIQTNNGISIWQTQFWLKISEIYISSTKICSMVFSKMIGSTCLLAAALEDGSICIYNAGDGKLVKIFQISIPIVYMRFNSLNNSSLIALADRASHYRLFILDIQ 2770
            MDVSGQGNLAT+NKPKRPSDGNGQPLSTPSVNVIDFLPVIKWKFKI+PTKVPDSGS GG ISLNDDVKNTNNANSGGSTDKNPNHKIFVQGVGYGVGIIIPQTSGPVLLGSLSFSPNSDLSLWIIVGILLLTMAVVWAVTHFICYVSKQGKTRRNVCGWRKKFSKDDN SWLGAYHVVNKSKSSTIDQLSLIKMKTEIQNSQTVKSTFGSTNQTKQLFSSGLINKDYTQSLRVSIPGSVRPNGLRSQSSTSLWSYQTTIADGTALISGSFTGPTMNNHIIENGNTGLIFTISELKCPN+WISKDSENVSHFENSQFEECLEVHFLLRESLLVGKMKNVRHRRNIGDFVIQIWNAFEGTLLKSVPDDLTEHSIACDAICTLRDEFLILIRQGEILVWNVKANAIMQAMKLPNIQTWKGKHAIQATQNMQDIIIMIFLPFSGVTHLYTYNFD+IVRGGCSCSFQYRSFPSQKTFYSLISNNSILIAGSTCVDIVLWNFS+NSESILSRNEEEQIQRILNSPSGELILIQTNNGISIWQTQFWLKISEIYISSTKICSMVFSKMIGSTCLLAAALEDGSICIYNAGDGKLVKIFQISIPIVYMRFNSL+NSSLIALADRASHYRLFILDIQ
Sbjct:    1 MDVSGQGNLATINKPKRPSDGNGQPLSTPSVNVIDFLPVIKWKFKIMPTKVPDSGSIGGAISLNDDVKNTNNANSGGSTDKNPNHKIFVQGVGYGVGIIIPQTSGPVLLGSLSFSPNSDLSLWIIVGILLLTMAVVWAVTHFICYVSKQGKTRRNVCGWRKKFSKDDNDSWLGAYHVVNKSKSSTIDQLSLIKMKTEIQNSQTVKSTFGSTNQTKQLFSSGLINKDYTQSLRVSIPGSVRPNGLRSQSSTSLWSYQTTIADGTALISGSFTGPTMNNHIIENGNTGLIFTISELKCPNSWISKDSENVSHFENSQFEECLEVHFLLRESLLVGKMKNVRHRRNIGDFVIQIWNAFEGTLLKSVPDDLTEHSIACDAICTLRDEFLILIRQGEILVWNVKANAIMQAMKLPNIQTWKGKHAIQATQNMQDIIIMIFLPFSGVTHLYTYNFDEIVRGGCSCSFQYRSFPSQKTFYSLISNNSILIAGSTCVDIVLWNFSSNSESILSRNEEEQIQRILNSPSGELILIQTNNGISIWQTQFWLKISEIYISSTKICSMVFSKMIGSTCLLAAALEDGSICIYNAGDGKLVKIFQISIPIVYMRFNSLDNSSLIALADRASHYRLFILDIQ 628          
The following BLAST results are available for this feature:
BLAST of SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 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 SMED30021239 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000010487.10.000e+098.57SMESG000010487.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021239 ID=SMED30021239|Name=SMED30021239|organism=Schmidtea mediterranea sexual|type=transcript|length=3780bp
TTTAAAGATTTTCTTTGTATTTATTTCGACATTTCTTGACTAATAGTGTT
TTTGATCAAACTCAAAATATTTATGACAGCCACTATTATTGTTCCTTGAC
TTGAGGATTTTGCTTCCGAAAATTCAATGATTTAATTTTTGCATGGTTTC
CGGTATTAGATTTTTTTTCGCCAATTGTTCCTGAAATCTTTCCGTGCCCC
CCGTTTCTCTTTTATGTTTGATTTGTTTTAATTTTTATTATTCTAGAGAT
TCGTCAACAAATAATAAAGTAAAACGTTTCTCTAAATATAAAATTGATGC
ACAAGTAAGGATTTCACTATATATTTATCACTGTACCACAAATAGATCCA
ATTTGGGCCCTGAAAGTCACGTCTCGTTTCAAATCGTCCTGTTAAGTCCC
CCAATTCTCATGATCTGATCAGAATTATAATTTAAACAATATTAAGAAAC
TGACGTAAGGCATCTGAAAGTAAAAATTATGAATAATAATTGATGTGACT
CATTGAGAAGGTGGACATTTGATCTGAATCAAAAGGGTGATGGTGTGCTT
GATCAGCCTAATAATCCGACTTATTGAAACAAATTCATTGAGTAGTCGCT
ATCTTCAAGGTCTACTGGTCAACACAAACCGTCAGCAACAAATTATAATA
AAAAATTTCAATAGTAATCCTGACACTTGCAGCAATGGACTATGCAAATG
TTCTGCTTGGTCCGATGCTGCCAATCGTCACGGCCGAGTGAAACGCTTAT
TGGCCATTGAAAACTCACCATTTTGTTGGCGATCTATTCAATTGTTCAGT
TGGTCATCATATGGACATCATTTAGGTCGCTGAGAATTGTAAAACATTTC
AGAATTTCTAGAATCTCACTCTCTTGTCAATCTCGAATGGATGTGTCGGG
ACAGGGAAATCTAGCCACCGTTAATAAACCCAAACGTCCTAGTGATGGGA
ACGGCCAACCACTGAGCACTCCATCGGTGAATGTTATAGATTTTCTACCG
GTCATTAAATGGAAATTCAAAATCATACCTACCAAGGTTCCAGATTCCGG
TTCCAATGGTGGAGTGATATCACTGAATGATGACGTCAAAAACACCAACA
ATGCCAACTCAGGTGGATCAACGGACAAAAATCCAAATCACAAAATCTTT
GTCCAAGGGGTCGGATATGGCGTTGGAATTATAATTCCTCAAACTTCAGG
CCCAGTTTTATTGGGGAGCCTTTCATTTAGTCCCAACTCCGATTTATCGT
TATGGATAATTGTTGGAATATTGCTATTAACTATGGCCGTTGTCTGGGCT
GTCACGCATTTCATTTGTTACGTAAGCAAGCAGGGAAAGACACGGAGGAA
TGTTTGTGGGTGGAGAAAAAAGTTCTCAAAAGACGACAATCACAGCTGGC
TGGGAGCTTACCATGTAGTGAATAAGTCCAAAAGCAGTACAATTGACCAG
TTATCGCTAATAAAAATGAAAACTGAAATTCAGAACAGTCAAACTGTAAA
GTCTACTTTTGGAAGTACCAACCAAACGAAGCAATTATTTTCTTCGGGTC
TAATTAATAAAGACTATACTCAATCTCTGCGAGTCAGCATTCCGGGTTCC
GTCAGGCCCAATGGACTGAGATCGCAATCTTCGACATCTTTATGGAGCTA
CCAGACGACAATCGCTGATGGGACGGCATTAATCAGCGGGTCCTTCACGG
GCCCCACCATGAACAATCATATCATTGAGAATGGAAACACAGGGTTGATA
TTTACCATATCTGAGCTCAAATGCCCAAACGCGTGGATTAGTAAGGATTC
CGAAAACGTCTCGCATTTTGAGAATTCACAATTCGAAGAATGTTTGGAAG
TCCATTTTCTCTTGAGAGAATCATTGCTAGTTGGAAAGATGAAAAACGTG
CGACATAGAAGGAATATTGGGGACTTTGTTATTCAGATCTGGAACGCTTT
TGAAGGAACTTTACTAAAAAGCGTGCCAGATGATTTGACAGAGCATAGCA
TTGCCTGTGATGCAATATGTACTCTCCGTGATGAGTTCCTTATATTGATA
CGACAAGGGGAAATTCTCGTATGGAACGTAAAGGCCAACGCAATCATGCA
GGCAATGAAATTGCCAAATATCCAAACTTGGAAAGGAAAACATGCAATCC
AAGCAACTCAGAATATGCAAGACATCATCATTATGATCTTCCTTCCTTTC
AGTGGAGTCACTCATTTATACACCTACAATTTCGATGACATTGTTCGTGG
CGGCTGCTCATGCTCTTTTCAATACAGAAGTTTTCCTTCTCAAAAAACCT
TTTATTCATTGATCTCAAACAACTCGATTTTGATTGCAGGCTCCACGTGC
GTTGACATCGTACTTTGGAATTTTTCAAACAATTCCGAATCTATTCTTTC
CAGAAATGAAGAGGAGCAAATTCAGAGAATTTTGAACTCACCGAGTGGAG
AGTTGATTCTCATTCAAACGAATAACGGGATTTCAATTTGGCAGACCCAG
TTCTGGTTGAAAATATCAGAAATATATATCTCTTCGACAAAGATATGTTC
AATGGTATTTTCAAAAATGATCGGATCAACATGTTTGTTAGCAGCTGCGT
TAGAGGACGGCTCGATCTGCATTTACAATGCCGGTGATGGGAAACTTGTA
AAGATATTTCAAATCAGCATTCCAATAGTCTATATGCGGTTCAATAGTCT
TAACAATTCTAGCCTCATTGCCTTGGCAGACCGTGCCAGTCATTACCGAT
TGTTCATCCTGGACATTCAGTAAACTAATCACCCCGTCACCAAGCCTCCT
AACAACAAGGACGTGGTGAAAGTTTCAGACATTAAGAAATTATAAGTTTT
TCGACCTAATTTCAATGTAGGAAAATCTTTTGATTGTTTTGTCGTGACCA
CTCGGCAAACGTTTTTGTTTCCTTTGTGTAAATATGAATTTTATTTCTTT
TCAATGTTTTACATCTAGTAAATGTTCCGCTGTCATGCTTACTTTCATGG
AGCTTGTAAACTTTTTATTTATTTTATCCAAATTTGTTTCGTTTTGCCAT
TCAATGATTTGTAACAATACTTCTTTTATTGAATTTTACACACCTTAATG
AGTTTGAATTTTTGTTTTATATTATCGGTTTTATTTGTCGGTTACAATTG
ATCCGTTTCCGTATTGCTCTTTAATATCAAAATCAGAATTAATCCGGCAA
GAACTTTATTTAAACCAGTTTTTCCCAAACCGGAGTAAGCGTACCCTTGG
CGGTACGCAGGTCTTTTCAATCTTCTATTATCTAAATATTAAAAGATAAA
TAAAAAAAATTTAATTAGATTAAAATGTCTTATTAAAGTTTTATTACTGC
AGAAAAATATAAATATAATCTTGTTTTTTATTTATTGTTCATATTTTTGA
ATCAATAACATATTTTTAGAAATAAAAATTTCTTTAAATTTTTTTTAATT
TTTAAATTTCAAGGAGAAATTTATCTTAGCATAAGCAATTTCATCCTTCT
CATTAATTACAAAAAAAATTAATTATAGTATTTTTTATTTTACATTAATT
TAAAGGCCAAATATAATTTTAAAGCAAAGGGGTACATTATATGGTGAAAA
TGATCAAGGGGTACGCAGTACCAAATGTTTGGCAAACACTGATCTAGAGC
TGATAGCCAACCAGTTTCATCGCTGTTATTCTCAGATTATCGATACGTCA
AAGTATGTTGATTTGTCGTTACTTCGGGGAAGACATTCAGCTGTAGTTCG
GTGTAAAATAAATGAAACAAATATAAATTG
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protein sequence of SMED30021239-orf-1

>SMED30021239-orf-1 ID=SMED30021239-orf-1|Name=SMED30021239-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=629bp
MDVSGQGNLATVNKPKRPSDGNGQPLSTPSVNVIDFLPVIKWKFKIIPTK
VPDSGSNGGVISLNDDVKNTNNANSGGSTDKNPNHKIFVQGVGYGVGIII
PQTSGPVLLGSLSFSPNSDLSLWIIVGILLLTMAVVWAVTHFICYVSKQG
KTRRNVCGWRKKFSKDDNHSWLGAYHVVNKSKSSTIDQLSLIKMKTEIQN
SQTVKSTFGSTNQTKQLFSSGLINKDYTQSLRVSIPGSVRPNGLRSQSST
SLWSYQTTIADGTALISGSFTGPTMNNHIIENGNTGLIFTISELKCPNAW
ISKDSENVSHFENSQFEECLEVHFLLRESLLVGKMKNVRHRRNIGDFVIQ
IWNAFEGTLLKSVPDDLTEHSIACDAICTLRDEFLILIRQGEILVWNVKA
NAIMQAMKLPNIQTWKGKHAIQATQNMQDIIIMIFLPFSGVTHLYTYNFD
DIVRGGCSCSFQYRSFPSQKTFYSLISNNSILIAGSTCVDIVLWNFSNNS
ESILSRNEEEQIQRILNSPSGELILIQTNNGISIWQTQFWLKISEIYISS
TKICSMVFSKMIGSTCLLAAALEDGSICIYNAGDGKLVKIFQISIPIVYM
RFNSLNNSSLIALADRASHYRLFILDIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000096ventral epidermis
PLANA:0002032epidermal cell
PLANA:0007561head margin
Vocabulary: INTERPRO
TermDefinition
IPR036322WD40_repeat_dom_sf
IPR015943WD40/YVTN_repeat-like_dom_sf
IPR017986WD40_repeat_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR015943WD40/YVTN repeat-like-containing domain superfamilyGENE3DG3DSA:2.130.10.10coord: 442..626
e-value: 1.4E-8
score: 36.3
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..27
NoneNo IPR availableTMHMMTMhelixcoord: 87..109
NoneNo IPR availableTMHMMTMhelixcoord: 430..447
NoneNo IPR availableTMHMMTMhelixcoord: 124..146
IPR036322WD40-repeat-containing domain superfamilySUPERFAMILYSSF50978WD40 repeat-likecoord: 346..623