SMED30000214

Overview
NameSMED30000214
Smed IDSMED30000214
Length (bp)1487
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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Anatomical Expression

PAGE et. al., 2020




SMED30000214

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30000214h1SMcG0005860 GDAG01079171.1SmedSxl_ww_GDAG01PMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
nervous systemSMED30000214h1SMcG0005860 dd_Smed_v4_75078_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000214h1SMcG0005860 dd_Smed_v4_75078_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30000214h1SMcG0005860 dd_Smed_v4_75078_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30000214h1SMcG0005860 dd_Smed_v6_101901_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
testisSMED30000214h1SMcG0005860 PL030011A20H07smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30000214h1SMcG0005860 Contig52213uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30000214h1SMcG0005860 Contig52213newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30000214h1SMcG0005860 Contig44827uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30000214h1SMcG0005860 Contig44827newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000214 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004960:30029..33691 +5937
Homology
BLAST of SMED30000214 vs. TrEMBL
Match: Q868D5 (Uncharacterized protein Dryg OS=Dugesia ryukyuensis OX=79738 GN=Dryg PE=2 SV=1)

HSP 1 Score: 140.584 bits (353), Expect = 6.117e-32
Identity = 119/450 (26.44%), Postives = 191/450 (42.44%), Query Frame = 1
Query:  175 LQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGK-----------DEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNK--DSVSIDFTCWSLLKCK---KRNNLMTPFNNKMTTETVQ----CTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIF-KTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMT 1461
            +Q  D    YY+ +C  N  T P K  FC Y K+    +   FPT  EC TC   ++ + WN+H+E A+ NL+ YT + +C  VK S K +C   +N  K  + +FL K+M    FC++ L C    D     +F ++  +  D Y   FFE+F+ + NY  +F  Y  FN     Q      Y + Q F +   P+  N +  +  ++YF++  N     +  +FF  +F ++             D  F   Y        +  +  C  CE I       W   + +           C +  N  E  +  EII +    I ++  + +S+   C+ + +C    +  N M  F       T Q    C VCK FS++ S   +   F +   D F  ++C  +F K +  C  FL  +  N+L  L   I + YLC   C  K++
Sbjct:   16 IQGHDYHN-YYEHYCDGNYYTSPTKFYFCHYLKTTTESETVPFPTISECKTCKELLKRITWNSHSEKAVENLLDYTTKHFCENVKRSTKVECQSKLNEYKPKMKEFLVKIMKNGKFCEVLLKCAEKKDVLFTTYFTEYTTDWTDFYSMPFFEYFFNRENYSEDFYPYHFFNYFYHYQDNEHPTY-YHQYFYET--PHTENHMFPHEYFQYFYK--NKTTNYFPHQFFHEYFFNNQYTSPTFNHNNFYDYFFTDEYHGFFERDQKPSEKFCNRCENIPESKFLKWAKSVDIKMLTDAGYKVMCSEL-NTTESERCREIISHIGTVILHELENVLSVKNVCYKIYRCPMNLETTNEMHSFYYDTFDFTRQTSKRCEVCKAFSDVFSSGIDRDLFEEMVVDQFEKVYCNKLFPKKEHMCKKFLKNELPNILNKLRVSIHRDYLCNSTCNGKLS 458          
BLAST of SMED30000214 vs. Planmine SMEST
Match: SMESG000000723.1 (SMESG000000723.1)

HSP 1 Score: 884.789 bits (2285), Expect = 0.000e+0
Identity = 446/447 (99.78%), Postives = 447/447 (100.00%), Query Frame = 1
Query:  127 MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI 1467
            MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQ+KSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGFNFYYFFNNYIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI
Sbjct:    1 MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQEKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISHGKDEGFNFYYFFNNYIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSI 447          
BLAST of SMED30000214 vs. Planmine SMEST
Match: SMESG000000719.1 (SMESG000000719.1)

HSP 1 Score: 155.992 bits (393), Expect = 6.771e-41
Identity = 125/487 (25.67%), Postives = 217/487 (44.56%), Query Frame = 1
Query:  142 CLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKSFQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLVKASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNHFYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIYEFFQGFIKNLKPNRNNSLISYWDYKYFF-------------------EESNNINEIYSWKFFEHFFIS-----HGKDEGXXXXXXXXXXIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQILINPKTCKDFSNIK--ECYKTIEIIINYWKGIRNK--DSVSIDFTCWSLLKCKKRNNLMTPFNNKMTTE-------------TVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIFCPSIF-KTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIAC---PNKMTSI 1467
            C L+ LS+I    ++D    +Y  +C  +  T P K  FC+Y K   + +   FPT  EC+ C  F++ + WN+H+E A+ NL+KYT   +C  VK +   +C   +N  +  I +FL KMM    FC++ L C+        ++F  +  +  D Y   FFE+F+   +Y  +F  Y  FN   + Q+     Y + + F +N  P  ++++  Y  ++YFF                   + S+  ++ Y + FF+ FF       + KD+             ++F    C+ CE I       W + + +   ++L +       SN+K  E  K  E+I++  + I +K    +S+   C  + +C        P N +M TE             T QC VC   + + S   ++  F K   + F++ +C  +F K + EC  FL  +  N+L  +   + + YLC + C   PN + S+
Sbjct:    6 CSLLLLSAIQIQGSYD----FYSHYCSGSYYTDPSKVYFCQYVKGPSDMEKVPFPTGGECTACKEFLKRITWNSHSEEAVDNLLKYTTNHFCEDVKRTTSSECKTKLNEYRPKIKEFLVKMMKDSSFCEVLLKCSEKKGVLFMSYFSQYKPDWMDFYSMPFFEYFFNLKSYSHDFYPYHFFNYFYNYQETGFPSYTYLEHFYEN--PKNDSTMHPYRFFEYFFSNDSSKSTFFPFKFFEYFFKNSHYESDFYPYTFFQEFFSDEYYNYYSKDQKPT----------DKF----CKRCENIPAERFLKWANSIDI---KMLTDAGYIAMCSNMKSTEKEKCREMILHVGRVILHKLESVLSVKSICHQIYRC--------PMNIEMKTEDFTFYEKPHPKKPTKQCEVCSLITNVYSNAMDKDIFEKYVVEIFQMKYCNKLFPKKENECKKFLKNELPNILNKIRVSLHKNYLCNLTCNANPNSLWSM 461          
The following BLAST results are available for this feature:
BLAST of SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
Q868D56.117e-3226.44Uncharacterized protein Dryg OS=Dugesia ryukyuensi... [more]
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BLAST of SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 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 SMED30000214 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000000723.10.000e+099.78SMESG000000723.1[more]
SMESG000000719.16.771e-4125.67SMESG000000719.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000214 ID=SMED30000214|Name=SMED30000214|organism=Schmidtea mediterranea sexual|type=transcript|length=1487bp
CTAAAAGTCTAGAAACAACTGATATCTTGCATAGCATAAACAACTCAAAG
CTTACGCGGTACTTTGAAGTATAGAAAAACAATTGCTATAAATATAAATC
GTAGAATATCTCCACAAAACTTCAAAATGTCGACAATTGGATGTTTGCTG
ATATTTCTAAGCTCAATTGTGGCTTTGCAAGCGTTTGATTTAGAAACGGT
TTATTACAAACAATTTTGCAGACAAAATCTGATTACAGGCCCATTGAAAA
CTGGATTTTGTGAATATTTCAAAAGTTTTCAAAATTTCAAAGCAAAATCC
TTTCCAACGTTTCAAGAATGCAGCACTTGCAATGCCTTCATAGAACTGTT
GATTTGGAACAATCACACGGAAACGGCTTTGTCAAATCTTATGAAATACA
CCCAGGAGACATATTGCAACTTAGTAAAAGCTTCGAAAAAGCAAAAATGT
ACAATTATGATCAATAGTAAAAAAAGTTATATTTTGAAGTTCCTTAGAAA
AATGATGACAAAGGAATTGTTTTGTAAAATCTTTCTGAACTGCACAAACC
CCTCTGATCAGACATTAAGGAATCATTTTTATGATTTTTTGTTGAACTCA
AAAGATGTCTATCCGACTGAATTCTTTGAATTTTTCTACCAAAAACATAA
TTATCCGTGGAATTTTTCTGAATATAGCATGTTTAATAGTCTGTCAAGTC
GACAGAAGAAATCTTCACATATTTATGAATTTTTTCAAGGTTTTATTAAA
AATCTTAAACCAAATCGAAACAATTCGCTGATCTCTTACTGGGATTACAA
ATATTTCTTCGAAGAATCAAACAATATAAATGAAATCTATTCGTGGAAGT
TTTTTGAACATTTTTTTATTAGTCACGGAAAAGACGAAGGATTTAATTTC
TATTACTTTTTCAACAATTATATCAAAAATAGATTTGGAAAACTTTCTTG
TCAATTGTGTGAAATAATAGGTCCGTTTTTATTAAACAATTGGTTTGACA
AATTAACTGTTTCACAACAACAAATTCTGATAAATCCGAAAACATGTAAA
GATTTTAGCAACATCAAAGAATGCTATAAAACAATAGAAATAATAATAAA
TTATTGGAAAGGCATAAGAAACAAGGATTCAGTGAGCATAGATTTTACTT
GCTGGTCTTTACTTAAGTGCAAAAAAAGAAATAATCTTATGACTCCTTTT
AATAATAAAATGACAACCGAAACAGTACAATGTACAGTCTGTAAAAGATT
CTCAGAAATTATCAGTGAAACTTCTAACGAGAAAAATTTTATCAAAGACG
CCTCTGATGCTTTTCGACTCATATTTTGTCCTTCAATTTTCAAAACTCAA
AAAGAATGTTCAGATTTTCTTTCAAAAGATTTCAAAAACCTTTTACAGAC
CTTAAGTTCTCGAATTCAACAATATTATTTATGTCGGATTGCTTGCCCAA
ATAAAATGACATCAATTAATAATAATAATAATAATAA
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protein sequence of SMED30000214-orf-1

>SMED30000214-orf-1 ID=SMED30000214-orf-1|Name=SMED30000214-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=453bp
MSTIGCLLIFLSSIVALQAFDLETVYYKQFCRQNLITGPLKTGFCEYFKS
FQNFKAKSFPTFQECSTCNAFIELLIWNNHTETALSNLMKYTQETYCNLV
KASKKQKCTIMINSKKSYILKFLRKMMTKELFCKIFLNCTNPSDQTLRNH
FYDFLLNSKDVYPTEFFEFFYQKHNYPWNFSEYSMFNSLSSRQKKSSHIY
EFFQGFIKNLKPNRNNSLISYWDYKYFFEESNNINEIYSWKFFEHFFISH
GKDEGFNFYYFFNNYIKNRFGKLSCQLCEIIGPFLLNNWFDKLTVSQQQI
LINPKTCKDFSNIKECYKTIEIIINYWKGIRNKDSVSIDFTCWSLLKCKK
RNNLMTPFNNKMTTETVQCTVCKRFSEIISETSNEKNFIKDASDAFRLIF
CPSIFKTQKECSDFLSKDFKNLLQTLSSRIQQYYLCRIACPNKMTSINNN
NNN
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000421tail
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR011001Saposin-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR11480SAPOSIN-RELATEDcoord: 61..437
NoneNo IPR availablePANTHERPTHR11480:SF3BCDNA.GH08312coord: 61..437
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.879
IPR011001Saposin-likeSUPERFAMILYSSF47862Saposincoord: 64..141