SMED30028012

Overview
NameSMED30028012
Smed IDSMED30028012
Length (bp)1622
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 SMED30028012 (SMED30028012) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028012 (SMED30028012) 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 SMED30028012 (SMED30028012) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028012 (SMED30028012) 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



SMED30028012

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
head regionSMED30028012SMESG000045022.1 SmedASXL_015985SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30028012SMESG000045022.1 SMESG000045023.1 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30028012SMESG000045022.1 SMESG000045023.1 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028012SMESG000045022.1 SMESG000045023.1 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30028012SMESG000045022.1 SMESG000045023.1 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
photoreceptor neuronSMED30028012SMESG000045023.1 SMED30001792smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30028012SMESG000045022.1 SMESG000045023.1 dd_Smed_v4_13675_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028012 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.028981:2066..8002 -5210
Homology
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BLAST of SMED30028012 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 683.33 bits (1762), Expect = 0.000e+0
Identity = 380/383 (99.22%), Postives = 383/383 (100.00%), Query Frame = 3 
Query:  264 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKMKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVIFFQSDLKLFTFLHQSLHLLLXXXXXXXXXXXXXXXXXLLVNSKIWKAFCAGQSIQILTKN 1412
            MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKK+KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVIFFQSDLKLFTFLHQSLH+LLIFGRISRIIPRIIQSTILLVNSKIWKAFCAGQSIQILTKN
Sbjct:    1 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKIKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVIFFQSDLKLFTFLHQSLHILLIFGRISRIIPRIIQSTILLVNSKIWKAFCAGQSIQILTKN 383
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BLAST of SMED30028012 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 602.053 bits (1551), Expect = 0.000e+0
Identity = 320/323 (99.07%), Postives = 323/323 (100.00%), Query Frame = 3 
Query:  264 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKMKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVI 1232
            MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKK+KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSV+
Sbjct:    1 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKIKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVV 323
[Close]
BLAST of SMED30028012 vs. Planmine SMEST
Match: SMESG000045022.1 (SMESG000045022.1)

HSP 1 Score: 602.053 bits (1551), Expect = 0.000e+0
Identity = 320/323 (99.07%), Postives = 323/323 (100.00%), Query Frame = 3 
Query:  264 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESXXXXXXXXXXXXXXXXXXXXXXXXXDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKMKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVI 1232
            MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMN+NKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKK+KDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSV+
Sbjct:    1 MKFNSLSNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYKDREKELEDGMNVNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESIIQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNSKMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKIKDFNQTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSESGKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRFFNTDSLNGYFIHFSSVV 323

HSP 2 Score: 54.299 bits (129), Expect = 1.014e-7
Identity = 24/24 (100.00%), Postives = 24/24 (100.00%), Query Frame = 2 
Query: 1346 TCQFEDLESILCRTIDPNINKKLK 1417
            TCQFEDLESILCRTIDPNINKKLK
Sbjct:  330 TCQFEDLESILCRTIDPNINKKLK 353
The following BLAST results are available for this feature:
BLAST of SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 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 SMED30028012 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000045022.10.000e+099.22SMESG000045022.1[more]
SMESG000045022.10.000e+099.07SMESG000045022.1[more]
SMESG000045022.11.014e-799.07SMESG000045022.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028012 ID=SMED30028012|Name=SMED30028012|organism=Schmidtea mediterranea sexual|type=transcript|length=1622bp
AGAAACATTTCAAGATGTGATTAAGCACAAATTCAACAATTACTTCAAAG
TTATCACAGTTTGATAATTCTAATAAAGTTGTTATTCTCGTGAATTAATT
TTGAATACTTAATAACGTAAATTAAACGAAGATGAATGCAAAAGAAACAA
TGGAATTCGAGAATAATAAGATAATTAATGACAAAATAAACCAATTGTTA
GTAGAAAACAAAGTTTTAAAATCGAATTTACAAGCAATTGAAAAACAATA
TCAGGACCAGTTAATGAAATTTAACAGTTTATCCAATCAGTATTCAACAC
TAAAGGAAAAATCGGAAGAATACAAAACGCAATTGGAAGGTCTTCGAAAA
ACTATTGACATTCTACAATTTGAATCTAAAGAACAACTTCTAAAAGGCGC
GGAATTAGAAGAAAAATTAAAAAAGTATAAAGATCGAGAAAAAGAGCTGG
AAGATGGTATGAATATGAACAAAGCAAATGAACAGAAGGTTTATGAAATG
AAAATTTTATTAAAAGACTCAAGAAAGCAAAATATAAATTATTCCAATCA
AATTAAAGAATTGAGAAAAGACGAGTCTATAATTCAACAATTGAGAGAGG
AAATGTCATATTTACAACAGGAAAATATGACATTGAAAGCTTATATAGTT
TCCCAAAATAAAATGAGCCATTATGGAAATGCTTTTAAAAATTTCAAACT
TGAACAATTTTGTCCAATTTGCTCCAATTCAAAGATGGAATTATGCCAAA
GACATTATTTGGAAAATTTTTCATCCGAAAATCCAGAAAAAGAAACCCAG
GTTCCGGAGAGAAGCAGTTTTAATAGACTTGATATTGTCACTGACAAAGA
AACTAGTCAAAAGAAAATGAAAGATTTCAATCAAACAAATGCGCCGCTGC
CGAAATCCAACAAACAGCGAATAAAGCAATTAATGGATAAGTGTGATTTA
TCCAATGATGCGATTGAAGCGGCTGTGAAAACCATTTTCCATTTGGGAGA
CCAAGTGGAAATAGTTGTTGATTCGGAATCAGGAAAGATATGCGCAAAAG
CCACAGTGAAATATATGGGAAATCTTGATGATAGATATCACAGCAGCTTT
TTCTTAGGAGTGAAATTACATCAAATTGGTAATGAGAGATTAGTTAATTA
CTGCAATGGGAGTTTCAGAAAAAAACGTTTTTTCAATACAGATTCTTTAA
ATGGATATTTTATACACTTTTCAAGCGTTATATTTTTTCAATCAGACCTA
AAACTATTTACCTTCCTTCACCAATCACTACACCTATTGTTGATATTTGG
CCGCATTTCAAGAATCATACCAAGAATCATACAAAGTACAATTTTACTTG
TCAATTCGAAGATCTGGAAAGCATTTTGTGCCGGACAATCGATCCAAATA
TTAACAAAAAACTGAAATAGTATATTTGATAAGTTATGAAAAATGTAATC
CATTAAAACAAACAAATTATATTTGAAATTCTTTGTGATTTATATAAATT
TTGGATCGTATTGTAAATACTCCTATATTGCATTCTTTGCCAAGCGATTC
TTTTTTGTCTATTTTTTTATTATTTAAACGACATCAAATCTGCCATTGTT
AGTTATTTTTTAAACGTTTGGG
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protein sequence of SMED30028012-orf-1

>SMED30028012-orf-1 ID=SMED30028012-orf-1|Name=SMED30028012-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=428bp
MNAKETMEFENNKIINDKINQLLVENKVLKSNLQAIEKQYQDQLMKFNSL
SNQYSTLKEKSEEYKTQLEGLRKTIDILQFESKEQLLKGAELEEKLKKYK
DREKELEDGMNMNKANEQKVYEMKILLKDSRKQNINYSNQIKELRKDESI
IQQLREEMSYLQQENMTLKAYIVSQNKMSHYGNAFKNFKLEQFCPICSNS
KMELCQRHYLENFSSENPEKETQVPERSSFNRLDIVTDKETSQKKMKDFN
QTNAPLPKSNKQRIKQLMDKCDLSNDAIEAAVKTIFHLGDQVEIVVDSES
GKICAKATVKYMGNLDDRYHSSFFLGVKLHQIGNERLVNYCNGSFRKKRF
FNTDSLNGYFIHFSSVIFFQSDLKLFTFLHQSLHLLLIFGRISRIIPRII
QSTILLVNSKIWKAFCAGQSIQILTKN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR036859CAP-Gly_dom_sf
IPR000938CAP-Gly_domain
IPR013809ENTH
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 19..109
NoneNo IPR availableCOILSCoilCoilcoord: 127..171
IPR036859CAP Gly-rich domain superfamilyGENE3DG3DSA:2.30.30.190coord: 281..374
e-value: 1.3E-9
score: 39.3
IPR036859CAP Gly-rich domain superfamilySUPERFAMILYSSF74924Cap-Gly domaincoord: 268..368