SMED30028280

Overview
NameSMED30028280
Smed IDSMED30028280
Length (bp)1117
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 SMED30028280 (SMED30028280) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028280 (SMED30028280) 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 SMED30028280 (SMED30028280) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028280 (SMED30028280) 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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Alignments
SMED30028280 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002808:28144..30441 +5482
Homology
BLAST of SMED30028280 vs. TrEMBL
Match: R7TBF7 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_218860 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.839e-7
Identity = 42/181 (23.20%), Postives = 84/181 (46.41%), Query Frame = 2
Query:   47 NILNYLVILCSLDMAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCK---CNEEHKDGLEVGVVVLSRI---------NREQSNCKLMENYFE---CFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYF---GSNADKSMSSFCISRI 535
             +L + ++  +   A     +  + + NP  ++  C  G+  R YICDP   L  +   +++ LL  I++ + C C    CN  H  G ++G+ ++ +I           E+    +++   E    F+  +LK W+M +CG D++I+    D     N+++   G  A+K +++  I  I
Sbjct:   15 QLLVFAIVCWASAFAQDGDIYAADEYPNPFFDTQACGRGT-QRSYICDPSFILKAEEAQQLEALLGIIRNETACPCADHYCNAAHP-GYKIGIALVKKIAPSNPMKTGEDEKDPSFVIQQNLEKSSLFAYTLLKRWQMGACGEDVIILYSVVD-----NVFYTITGEVAEKKLTASMIGDI 188          
BLAST of SMED30028280 vs. TrEMBL
Match: A0A3M6TW21 (Uncharacterized protein OS=Pocillopora damicornis OX=46731 GN=pdam_00013131 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.739e-6
Identity = 46/161 (28.57%), Postives = 79/161 (49.07%), Query Frame = 2
Query:   59 YLVIL---CSLDMAHSFRYWTHNNFVNPLINSNFC-KLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGND---MLIVIEKNDGLLKSNIYF--GSNADKSMS 514
            +LVI    C L    + R W   +F NP  +   C + G  +  +ICDPE  L YK   +I+ L++++  N+   C  +E  K G ++GV VL+R+       + +E   + F++++  +W +   G D   ML++      +L   +Y   G  A KS+S
Sbjct:    8 FLVIFAAFCFLQEGRTTREWYKEDFPNPTRDVKGCGRRGEVS--WICDPENILSYKAANKIEELIYSVVKNTYSGCSNDE--KPGFQIGVAVLNRMRGIPG--EPVEETAKTFAKHLHDSWGVGHAGCDDGAMLLI-----SILDRQLYVSTGKRAMKSLS 157          
BLAST of SMED30028280 vs. TrEMBL
Match: A0A1E1WXB3 (Putative conserved secreted protein (Fragment) OS=Amblyomma aureolatum OX=187763 PE=2 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.790e-6
Identity = 26/120 (21.67%), Postives = 59/120 (49.17%), Query Frame = 2
Query:  104 YWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCK-CNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKND 460
            YW  + + +P+    +C    +   ++CDP++ +  K    +D ++  I++ + C C  C++    G+ +GV ++  I+R  +    M      F+  + + W +  C +D+L++I   D
Sbjct:   43 YWRVDEYPHPITQPRYCN--RYRASFVCDPDRVINKKQADSLDRIIERIRNETLCICPTCDKSQASGITLGVAIMEHIHRPHN--LPMSEAVRLFAERLRRQWGLGHCDDDILLLISAKD 158          
BLAST of SMED30028280 vs. Ensembl Nematostella
Match: EDO30764 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SZU4])

HSP 1 Score: 45.8246 bits (107), Expect = 4.099e-6
Identity = 26/122 (21.31%), Postives = 55/122 (45.08%), Query Frame = 2
Query:  101 RYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMS--SCGNDMLIVIEKND 460
            + W+  NF NP+ ++  C     +  +ICDP++ L Y     ++ +L NI+  +  +  C    K G ++ V ++ +I          E     F+ ++  +W +    CG+  + ++   D
Sbjct:    3 KEWSKENFPNPIKDTEMCGRRGVS-SWICDPDEVLSYADANTLEEMLRNIEQKT--TSGCEHSRKPGYQIAVALMKKIKHHYGISG--EELARDFAVHLHDSWGVGHRGCGDGAVFLLSVTD 119          
BLAST of SMED30028280 vs. Planmine SMEST
Match: SMESG000016792.1 (SMESG000016792.1)

HSP 1 Score: 641.343 bits (1653), Expect = 0.000e+0
Identity = 315/315 (100.00%), Postives = 315/315 (100.00%), Query Frame = 2
Query:   44 MNILNYLVILCSLDMAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQSELPPNYLDITKIDKESIEDSKPEILLVDTIVIGQDPPSYSDVLRFSKLKY 988
            MNILNYLVILCSLDMAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQSELPPNYLDITKIDKESIEDSKPEILLVDTIVIGQDPPSYSDVLRFSKLKY
Sbjct:    1 MNILNYLVILCSLDMAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQSELPPNYLDITKIDKESIEDSKPEILLVDTIVIGQDPPSYSDVLRFSKLKY 315          
BLAST of SMED30028280 vs. Planmine SMEST
Match: SMESG000016792.1 (SMESG000016792.1)

HSP 1 Score: 516.153 bits (1328), Expect = 0.000e+0
Identity = 252/256 (98.44%), Postives = 253/256 (98.83%), Query Frame = 2
Query:   86 MAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQSELPPN 853
            MAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQS   P+
Sbjct:    1 MAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSNIVRPFRQTAATVNQSGESPD 256          
BLAST of SMED30028280 vs. Planmine SMEST
Match: SMESG000073734.1 (SMESG000073734.1)

HSP 1 Score: 80.8777 bits (198), Expect = 9.002e-17
Identity = 81/320 (25.31%), Postives = 130/320 (40.62%), Query Frame = 2
Query:  101 RYWTHNNFVNPLINSNFCKLGSFNRQYICDPEQYLPYKIKYEIDTLLFNIKSNSRCSCKCNE-----EHKDGLEVGVVVLSRINREQSNCKLMENYFECFSRNILKNWEMSSC-GNDMLIVIEKNDGLLKSNIYFGSNADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFDIGENTWEFKAEMLLGLII------GFSVITIVLIFVVPCCKRRNS-SVDDSRPRNSNIVRPFRQTAA-------TVNQSELPPNYLDITKIDKESIEDSKPEILLVDTI-----------VIGQDPPSYSDVL 967
            + W  +   NPLIN  FC++       ICDPE  L   +K  +   L +    S   C CNE     ++K  L  G+V++S IN    N     + +E FS  IL NW +S C GN++LI++ K     ++ IYFG+   K + + C+ R++  +   +     L  I   I  ++     C+ +       W       +G+I+      G S   +V  F      R N  S   +RPR      P R            ++ +  PP+Y  +    K    +  P+I +  T             I + PP+Y+ V 
Sbjct:   19 KVWNADEIKNPLINPEFCQVNFNEPSLICDPENELAITLKKTLSKYLLHGFPVST-PCFCNEGCDAFDYKRRLMAGIVIVSSINETSVNYSGDLDIYESFSERILSNWNISQCLGNNVLILVTKK----QTQIYFGTAVRKRIPNSCLKRLKSLIRQYIPLPYNLRTIFKNIIEYIRKPCMCNDSCTYRHLKWLTNVVFFMGVIVLVTCIGGMSRRALVAKFHDRPFPRSNLISNAFTRPR-----LPARSNVTNNGNDILQMSGNHNPPDYSTLGPFTKPPPYNPSPDISVPKTQEYSSTNQTTRDQIQESPPAYTLVF 328          
The following BLAST results are available for this feature:
BLAST of SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
R7TBF71.839e-723.20Uncharacterized protein OS=Capitella teleta OX=283... [more]
A0A3M6TW211.739e-628.57Uncharacterized protein OS=Pocillopora damicornis ... [more]
A0A1E1WXB31.790e-621.67Putative conserved secreted protein (Fragment) OS=... [more]
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BLAST of SMED30028280 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 SMED30028280 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 SMED30028280 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 SMED30028280 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO307644.099e-621.31Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30028280 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 SMED30028280 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016792.10.000e+0100.00SMESG000016792.1[more]
SMESG000016792.10.000e+098.44SMESG000016792.1[more]
SMESG000073734.19.002e-1725.31SMESG000073734.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028280 ID=SMED30028280|Name=SMED30028280|organism=Schmidtea mediterranea sexual|type=transcript|length=1117bp
TACAATTTTTATAAAATACGAAACCAATTAAAATTAAAATTTCATGAATA
TCTTGAATTACTTAGTAATTCTTTGTTCGCTTGATATGGCTCACAGTTTC
AGATATTGGACTCATAATAATTTTGTAAATCCATTAATAAATTCAAATTT
TTGCAAATTAGGCTCATTTAACAGACAATATATTTGTGATCCTGAACAGT
ATCTGCCATACAAAATCAAATATGAAATTGACACTCTTTTATTTAATATT
AAATCAAATTCTCGATGTTCCTGTAAATGCAATGAAGAACATAAAGATGG
CTTGGAAGTTGGAGTTGTTGTTTTATCAAGAATCAATCGAGAGCAATCTA
ATTGTAAGTTGATGGAAAACTATTTCGAATGTTTTTCTCGGAATATTTTG
AAAAATTGGGAAATGTCATCTTGCGGTAATGATATGCTAATTGTCATAGA
AAAAAATGATGGATTATTAAAGTCAAATATATATTTCGGATCTAATGCAG
ATAAATCTATGTCGTCATTTTGTATTAGTCGCATCAGAAAAGATGTTGAA
GTATCTCTCACATCAGTCAATAAATTGCTTGCAATTCTCAATCGAATCAA
CCTATTTGTCACTGACAACCGATATTGCAGCAGAGCATTTGATATCGGTG
AAAATACATGGGAATTTAAAGCTGAAATGCTACTAGGATTAATCATTGGA
TTCTCAGTCATAACAATTGTTTTGATATTTGTTGTGCCTTGCTGTAAACG
GCGTAATTCCAGTGTTGATGACTCCAGGCCAAGAAACAGCAATATTGTCC
GTCCATTTCGTCAGACAGCAGCAACTGTCAACCAATCAGAACTCCCACCG
AATTATTTGGACATTACCAAGATAGACAAAGAAAGCATCGAAGATAGTAA
ACCAGAAATTCTTCTCGTTGACACTATCGTTATTGGACAAGATCCTCCAT
CGTATTCAGATGTTTTGCGCTTTTCTAAATTGAAATATTGATTTGAAATA
ATTATTTTTACCGTTGCATTTACATTAAAATTTCTTTAATTTGATTAATT
CTTACTTTTGTAATAAGCTCAAAGAATTTTTTTAATATTTTGTATTGAAA
ATAAATTTCAAATGGCG
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protein sequence of SMED30028280-orf-1

>SMED30028280-orf-1 ID=SMED30028280-orf-1|Name=SMED30028280-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=316bp
MNILNYLVILCSLDMAHSFRYWTHNNFVNPLINSNFCKLGSFNRQYICDP
EQYLPYKIKYEIDTLLFNIKSNSRCSCKCNEEHKDGLEVGVVVLSRINRE
QSNCKLMENYFECFSRNILKNWEMSSCGNDMLIVIEKNDGLLKSNIYFGS
NADKSMSSFCISRIRKDVEVSLTSVNKLLAILNRINLFVTDNRYCSRAFD
IGENTWEFKAEMLLGLIIGFSVITIVLIFVVPCCKRRNSSVDDSRPRNSN
IVRPFRQTAATVNQSELPPNYLDITKIDKESIEDSKPEILLVDTIVIGQD
PPSYSDVLRFSKLKY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0000418head
PLANA:0002089reproductive organ
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR033438MOLO1
Vocabulary: cellular component
TermDefinition
GO:0005892acetylcholine-gated channel complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR033438Modulator of levamisole receptor-1PFAMPF17175MOLO1coord: 22..139
e-value: 1.5E-18
score: 67.1
NoneNo IPR availablePANTHERPTHR33748:SF5coord: 6..254
NoneNo IPR availablePANTHERPTHR33748FAMILY NOT NAMEDcoord: 6..254
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.554
NoneNo IPR availableTMHMMTMhelixcoord: 212..234