RRM domain-containing protein

Overview
NameRRM domain-containing protein
Smed IDSMED30034887
Length (bp)660
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 RRM domain-containing protein (SMED30034887) t-SNE clustered cells

Violin plots show distribution of expression levels for RRM domain-containing protein (SMED30034887) 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 RRM domain-containing protein (SMED30034887) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for RRM domain-containing protein (SMED30034887) 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




SMED30034887

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30034887 dd_Smed_v4_391_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034887 dd_Smed_v4_391_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30034887 dd_Smed_v4_391_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034887 Contig42761uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034887 Contig42761newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30034887 dd_Smed_v4_391_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
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A0R3SG94 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS3907 PE=4 SV=1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.709e-17
Identity = 40/69 (57.97%), Postives = 54/69 (78.26%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSL 387
            CPGI+ +I+W LLVIFIAWP+AGF+A IYVFLLPFA C   L++ L+ LL +I+LP+ W++  V M S+
Sbjct:    5 CPGIIYSILWALLVIFIAWPVAGFVACIYVFLLPFAACITPLESGLDALLVVIKLPLTWSKKCVNMTSI 73          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A0R3T7K4 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS3041 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 3.277e-17
Identity = 39/69 (56.52%), Postives = 53/69 (76.81%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSL 387
            CPGI+ +I+W LL+IF+AWP+AGFLAGIYVFLLPF  C   L+  LE +L+ I+LP+ WA+  V+M  +
Sbjct:    5 CPGILYSILWALLIIFVAWPVAGFLAGIYVFLLPFGACITPLEQFLEQMLEFIKLPLIWAKKCVSMTPI 73          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A068Y4G0 (Expressed conserved protein OS=Echinococcus multilocularis OX=6211 GN=EmuJ_000722000 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 3.551e-17
Identity = 39/69 (56.52%), Postives = 53/69 (76.81%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSL 387
            CPG++ +IVWFLLV+F+AWP+AGFL  IY+FLLPFA C   L+  L+ L   ++LP+ W++  VAMKSL
Sbjct:    5 CPGLLYSIVWFLLVVFVAWPIAGFLGCIYIFLLPFAACVPPLEDFLDQLFIFVKLPLIWSKKGVAMKSL 73          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A068X0S6 (Expressed conserved protein OS=Echinococcus granulosus OX=6210 GN=EgrG_000722000 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 3.551e-17
Identity = 39/69 (56.52%), Postives = 53/69 (76.81%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSL 387
            CPG++ +IVWFLLV+F+AWP+AGFL  IY+FLLPFA C   L+  L+ L   ++LP+ W++  VAMKSL
Sbjct:    5 CPGLLYSIVWFLLVVFVAWPIAGFLGCIYIFLLPFAACVPPLEDFLDQLFIFVKLPLIWSKKGVAMKSL 73          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A183TJU6 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS16744 PE=4 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 2.062e-16
Identity = 37/69 (53.62%), Postives = 49/69 (71.01%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSL 387
            CPG+  A++WFLL IFI WP+ GFLAGIYV LLPFA C   L  ++E LL++++LP  W +  + M SL
Sbjct:    6 CPGLCYAVIWFLLAIFIGWPVGGFLAGIYVLLLPFAACIAPLNDLMEALLKVVKLPYYWMKKALRMASL 74          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO40799 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S654])

HSP 1 Score: 58.151 bits (139), Expect = 8.336e-12
Identity = 30/65 (46.15%), Postives = 44/65 (67.69%), Query Frame = 1
Query:  190 IVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKS 384
            I+ AI+WFL++ F+ WP+  F AG YV L PF  C  ALK + E L++ + LP++ A++MV  KS
Sbjct:    3 ILWAIIWFLVLWFVGWPIGFFCAGWYVCLSPFEACIDALKGLTELLMKGVMLPLEVAKHMVEGKS 67          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO30181 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S654])

HSP 1 Score: 58.151 bits (139), Expect = 8.336e-12
Identity = 30/65 (46.15%), Postives = 44/65 (67.69%), Query Frame = 1
Query:  190 IVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKS 384
            I+ AI+WFL++ F+ WP+  F AG YV L PF  C  ALK + E L++ + LP++ A++MV  KS
Sbjct:    3 ILWAIIWFLVLWFVGWPIGFFCAGWYVCLSPFEACIDALKGLTELLMKGVMLPLEVAKHMVEGKS 67          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO40535 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S6X0])

HSP 1 Score: 58.151 bits (139), Expect = 9.840e-12
Identity = 30/62 (48.39%), Postives = 42/62 (67.74%), Query Frame = 1
Query:  199 AIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKS 384
            AI+WFL++ FI WP+  F AG YV L PF  C  A+K V E L++ ++LP++ A +MV  KS
Sbjct:    6 AIIWFLVLWFIGWPIGFFCAGWYVCLSPFEACIDAIKQVTELLMRGVKLPLEVAVHMVEGKS 67          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000017203.1 (SMESG000017203.1)

HSP 1 Score: 140.198 bits (352), Expect = 3.768e-43
Identity = 72/72 (100.00%), Postives = 72/72 (100.00%), Query Frame = 1
Query:  175 MGCPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSLC 390
            MGCPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSLC
Sbjct:    1 MGCPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSLC 72          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000017955.1 (SMESG000017955.1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.541e-11
Identity = 26/70 (37.14%), Postives = 44/70 (62.86%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSLC 390
            CPG++ +++WFL +IF+ +P AGF AG Y+  LP   C     A+ + L + +Q P+  A+N++ M+  C
Sbjct:    5 CPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 74          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000016070.1 (SMESG000016070.1)

HSP 1 Score: 51.2174 bits (121), Expect = 1.287e-8
Identity = 32/82 (39.02%), Postives = 47/82 (57.32%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQ-LPMQWAENMVAMKSLC*IWFWLDNSSG 423
            CP I+ +I+WF L IF A+PL+  +A I V  +PF  CF   K + E L ++ + +  Q  ENM+ MK    ++  L NSS 
Sbjct:    6 CPNILYSILWFTLWIFFAFPLSFIVAFIEVLFVPFCACFEKAKQICEVLDRMFKIMAYQPIENMLNMKP---VFTKLSNSSQ 84          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000065952.1 (SMESG000065952.1)

HSP 1 Score: 44.2838 bits (103), Expect = 4.768e-6
Identity = 25/71 (35.21%), Postives = 40/71 (56.34%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQ-LPMQWAENMVAMKSLC 390
            CP ++ + +WFL+     WPLA FLA + V ++PF  C    K + E L ++ + L  Q  ENM+  + +C
Sbjct:    4 CPDLLWSFLWFLIWFCFTWPLAFFLALVEVAVIPFCACLEPAKQICEVLDRIFKVLAYQPMENMIYGRPIC 74          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000065952.1 (SMESG000065952.1)

HSP 1 Score: 44.2838 bits (103), Expect = 4.918e-6
Identity = 25/71 (35.21%), Postives = 40/71 (56.34%), Query Frame = 1
Query:  181 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQ-LPMQWAENMVAMKSLC 390
            CP ++ + +WFL+     WPLA FLA + V ++PF  C    K + E L ++ + L  Q  ENM+  + +C
Sbjct:    5 CPDLLWSFLWFLIWFCFTWPLAFFLALVEVAVIPFCACLEPAKQICEVLDRIFKVLAYQPMENMIYGRPIC 75          
The following BLAST results are available for this feature:
BLAST of RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3SG941.709e-1757.97Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A0R3T7K43.277e-1756.52Uncharacterized protein OS=Rodentolepis nana OX=10... [more]
A0A068Y4G03.551e-1756.52Expressed conserved protein OS=Echinococcus multil... [more]
A0A068X0S63.551e-1756.52Expressed conserved protein OS=Echinococcus granul... [more]
A0A183TJU62.062e-1653.62Uncharacterized protein OS=Schistocephalus solidus... [more]
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BLAST of RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing 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 RRM domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 3
Match NameE-valueIdentityDescription
EDO407998.336e-1246.15Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO301818.336e-1246.15Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO405359.840e-1248.39Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of RRM domain-containing 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 RRM domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017203.13.768e-43100.00SMESG000017203.1[more]
SMESG000017955.11.541e-1137.14SMESG000017955.1[more]
SMESG000016070.11.287e-839.02SMESG000016070.1[more]
SMESG000065952.14.768e-635.21SMESG000065952.1[more]
SMESG000065952.14.918e-635.21SMESG000065952.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034887 ID=SMED30034887|Name=RRM domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=660bp
AATTTATTAATTGGATTTAAATTTTGAATTATTTATTTTAGCAGCATGTG
ATTTGTGCAACTTGATAAGTTATTCCGTATTTTGCATTTTACGATTAGTT
TTATTTTTAGTGAGTTGATAAGATTTATTAAATTAAATTTTATTAGTATT
TTATTTTATTCTTTAGATTTCTGAATGGGTTGCCCTGGCATTGTCAATGC
GATCGTTTGGTTTTTATTGGTAATTTTTATTGCGTGGCCACTCGCGGGCT
TTCTCGCGGGGATTTACGTTTTTCTTTTACCGTTTGCCGGCTGTTTTGGT
GCTTTGAAAGCTGTTCTGGAACCTTTGCTGCAATTGATACAGTTGCCGAT
GCAATGGGCCGAGAACATGGTGGCCATGAAATCTTTGTGTTGAATTTGGT
TTTGGTTGGATAACTCAAGTGGACGTTATTAGCCTTTATTTGTTAAATAT
AATTGGTTTTTTTTGTTTATATTTTATTTTCATATTTTAACAGTTGCGGC
TGAGATCACAATTTTCAGGTCCATCGAGTTGCCATGGTTACAGAAGGTCC
TTCAACCCCCTCACTTTTATCCCAATGTTTTTCTTTAGGGAAATTTTTAA
ATATTGACATTTAATCATGGGGAATATTTACATAAATCTGTTGATTTGTG
CTTATGAATA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0003723RNA binding
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000240body wall musculature
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR39948FAMILY NOT NAMEDcoord: 6..71
NoneNo IPR availableTMHMMTMhelixcoord: 13..35