bmp-like protein

Overview
Namebmp-like protein (AGX01006.1)
Smed IDSMED30009537
Length (bp)1163
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 bmp-like protein (SMED30009537) t-SNE clustered cells

Violin plots show distribution of expression levels for bmp-like protein (SMED30009537) 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 bmp-like protein (SMED30009537) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for bmp-like protein (SMED30009537) 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



SMED30009537

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30009537h1SMcG0017870 SmedASXL_014299SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30009537h1SMcG0017870 dd_Smed_v4_12035_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009537h1SMcG0017870 dd_Smed_v4_12035_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009537h1SMcG0017870 dd_Smed_v4_12035_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
dorsal-ventral muscle cellSMED30009537h1SMcG0017870 dd_Smed_v4_12035_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of bmp-like protein vs. TrEMBL
Match: U3RF22 (Bmp-like protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 559.681 bits (1441), Expect = 0.000e+0
Identity = 306/306 (100.00%), Postives = 306/306 (100.00%), Query Frame = 3 
Query:   66 MSTYKMVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMXXXXXXXXAKLSFLRYYKRFYFQLICTDCIDQSXXXXXXXXXXXXXXXXXXXXXXXXXXSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 983
            MSTYKMVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ
Sbjct:    1 MSTYKMVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 306
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BLAST of bmp-like protein vs. Planmine SMEST
Match: SMESG000063420.1 (SMESG000063420.1)

HSP 1 Score: 556.599 bits (1433), Expect = 0.000e+0
Identity = 305/306 (99.67%), Postives = 305/306 (99.67%), Query Frame = 3 
Query:   66 MSTYKMVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMXXXXXXXXAKLSFLRYYKRFYFQLICTDCIDQSXXXXXXXXXXXXXXXXXXXXXXXXXXSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 983
            MSTYKMVPEQVIIFFILSSL VMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ
Sbjct:    1 MSTYKMVPEQVIIFFILSSLSVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 306
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BLAST of bmp-like protein vs. Planmine SMEST
Match: SMESG000063420.1 (SMESG000063420.1)

HSP 1 Score: 545.428 bits (1404), Expect = 0.000e+0
Identity = 300/301 (99.67%), Postives = 300/301 (99.67%), Query Frame = 3 
Query:   81 MVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMXXXXXXXXAKLSFLRYYKRFYFQLICTDCIDQSXXXXXXXXXXXXXXXXXXXXXXXXXXSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 983
            MVPEQVIIFFILSSL VMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ
Sbjct:    1 MVPEQVIIFFILSSLSVMGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 301
[Close]
BLAST of bmp-like protein vs. Planmine SMEST
Match: SMESG000063420.1 (SMESG000063420.1)

HSP 1 Score: 514.998 bits (1325), Expect = 0.000e+0
Identity = 284/284 (100.00%), Postives = 284/284 (100.00%), Query Frame = 3 
Query:  132 MGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMXXXXXXXXAKLSFLRYYKRFYFQLICTDCIDQSXXXXXXXXXXXXXXXXXXXXXXXXXXSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 983
            MGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ
Sbjct:    1 MGSWLPKFVDQQLNNQVNEAVSSVMLPLQAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIVFDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQLICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTAHCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLIRYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLVDLCKCQ 284
The following BLAST results are available for this feature:
BLAST of bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
U3RF220.000e+0100.00Bmp-like protein OS=Schmidtea mediterranea OX=7932... [more]
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BLAST of bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein 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 bmp-like protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000063420.10.000e+099.67SMESG000063420.1[more]
SMESG000063420.10.000e+099.67SMESG000063420.1[more]
SMESG000063420.10.000e+0100.00SMESG000063420.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30009537
GenBankAGX01006.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009537 ID=SMED30009537|Name=bmp-like protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1163bp
CAGTCTATCGACGATTTCGTATAAATTATCATTGAGATTCTGAAACAGGC
CGATTTCAAAATTAAATGAGCACCTACAAAATGGTCCCGGAGCAAGTTAT
AATTTTCTTTATTCTCTCTTCACTCTGTGTCATGGGGTCTTGGTTGCCGA
AATTTGTTGACCAACAGCTGAACAATCAAGTCAACGAGGCCGTGTCTAGC
GTCATGTTACCGTTGCAAGCAATACCATGCTCTTCAGGAGACTTCGTTAC
GAACTGCTTTATGATTGAAAGATTTCCTCAACCTCGTCTTCATGAATGGC
AGTTTCTGGAATTTCAAGTCAGTGCTCATAGTTCTACCGTTATGCGCACA
TTCAAGCTGATTGTGTTTGATGAGAAACCGGATTCGGAAAGAAAAAATGT
GATATTTGAATCTGCGTCTGTCGAGCCTGATCCAATCCTCATGGACATCA
TAATTGATATTACAACTGCTAAATTAAGCTTTCTTCGGTATTATAAGAGA
TTTTACTTTCAATTAATTTGCACCGACTGCATTGATCAATCCATACGAAT
TGCGAATGATAATGCCATTGCATTTATTATTATAAAACAAACCCGAATCA
TTCAGAGGCGATTAAGGAGATCAGTTGAGGATAGGAACAAATGTTTATCC
GATTCCAATACTGCACATTGCTGTATTCAAACAGTTTTTACCGAAAAACA
TGTTGCGTTTGAAAACGGAAGTCACATAATTGCGCCTCATACAATTCCCA
TAACGTATTGTCGAGGCCAGTGTTACTCAAATACGTATGAAGGTAACAAC
AATTACGTTCTGATACGCTATTTGAATTCCCTAGCAGACAGAGCGAAGAT
AAAAATGTATAAGCAGCTTCCTTGTTGTTCTGCTAGAAAATTCAGAGACT
TAATGATCCTCTATAGAACTCCAGATGGCAATAACAGAATGGAGGCTTCA
AGTAACCTTCTTGTCGACTTATGCAAGTGCCAATAATTAAACCAAACTTC
TAATTCCAATTATTTGTCAATGTGATATTTCCAGAATATTTCATTCATTT
ATTTTTATTGACAATCTCACCAATCATTTTTATCATTTTGAACCGGGCGT
CTTCATTTGTCATGACCAATTCTGTTTGATTCGGTTTTAGAAATATATTC
GATTGGCTCTTGG
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protein sequence of SMED30009537-orf-1

>SMED30009537-orf-1 ID=SMED30009537-orf-1|Name=SMED30009537-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=307bp
MSTYKMVPEQVIIFFILSSLCVMGSWLPKFVDQQLNNQVNEAVSSVMLPL
QAIPCSSGDFVTNCFMIERFPQPRLHEWQFLEFQVSAHSSTVMRTFKLIV
FDEKPDSERKNVIFESASVEPDPILMDIIIDITTAKLSFLRYYKRFYFQL
ICTDCIDQSIRIANDNAIAFIIIKQTRIIQRRLRRSVEDRNKCLSDSNTA
HCCIQTVFTEKHVAFENGSHIIAPHTIPITYCRGQCYSNTYEGNNNYVLI
RYLNSLADRAKIKMYKQLPCCSARKFRDLMILYRTPDGNNRMEASSNLLV
DLCKCQ*
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Aliases
The feature 'bmp-like protein' has the following synonyms
Synonym
bmp-like
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
PLANA:0002028dorsal-ventral muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR015615TGF-beta-rel
IPR001839TGF-b_C
IPR029034Cystine-knot_cytokine
Vocabulary: molecular function
TermDefinition
GO:0008083growth factor activity
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001839Transforming growth factor-beta, C-terminalSMARTSM00204TGFB_2coord: 202..306
e-value: 1.6E-5
score: 6.4
IPR001839Transforming growth factor-beta, C-terminalPFAMPF00019TGF_betacoord: 211..305
e-value: 1.7E-12
score: 48.2
IPR001839Transforming growth factor-beta, C-terminalPROSITEPS51362TGF_BETA_2coord: 182..306
score: 14.703
IPR029034Cystine-knot cytokineGENE3DG3DSA:2.10.90.10coord: 189..306
e-value: 4.2E-16
score: 61.5
IPR029034Cystine-knot cytokineSUPERFAMILYSSF57501Cystine-knot cytokinescoord: 193..305
NoneNo IPR availablePANTHERPTHR11848:SF256TRANSFORMING GROWTH FACTOR BETA FAMILYcoord: 97..306
IPR015615Transforming growth factor-beta-relatedPANTHERPTHR11848TGF-BETA FAMILYcoord: 97..306