GCR156

Overview
NameGCR156
Smed IDSMED30032279
Length (bp)1472
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 GCR156 (SMED30032279) t-SNE clustered cells

Violin plots show distribution of expression levels for GCR156 (SMED30032279) 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 GCR156 (SMED30032279) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for GCR156 (SMED30032279) 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




SMED30032279

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30032279SMESG000022837.1 Contig31295newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032279SMESG000022837.1 Contig31295uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
oviductSMED30032279 GCR156smed_ncbi_20200123PMID:27163480
Saberi et al., 2016
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of GCR156 vs. TrEMBL
Match: A0A193KUR6 (GCR156 OS=Schmidtea mediterranea OX=79327 GN=gcr156 PE=2 SV=1)

HSP 1 Score: 352.443 bits (903), Expect = 1.446e-156
Identity = 209/210 (99.52%), Postives = 209/210 (99.52%), Query Frame = 2
Query:  227 MLNITNCGKNASDYQKPVQWYFYPSYFAXXXXXXXXXXXXXXXXXKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVXXXXXXXXXXXENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS 856
            MLNITNCGKNAS YQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVLLIDILLIMIMENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS
Sbjct:    1 MLNITNCGKNASYYQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVLLIDILLIMIMENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS 210          

HSP 2 Score: 231.876 bits (590), Expect = 1.446e-156
Identity = 112/112 (100.00%), Postives = 112/112 (100.00%), Query Frame = 1
Query:  856 KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT 1191
            KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT
Sbjct:  211 KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT 322          
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000062328.1 (SMESG000062328.1)

HSP 1 Score: 65.0846 bits (157), Expect = 3.705e-21
Identity = 26/65 (40.00%), Postives = 45/65 (69.23%), Query Frame = 1
Query:  949 SVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIR 1143
            S+KF +VLF + +LM+ISY P  L N   I++P  ++YYLF+L  LGDP++  ++R ++   +++
Sbjct:  272 SIKFVKVLFGVNLLMIISYLPAILYNAECIQFPSFSVYYLFFLHALGDPILFFMTRRELLNSLLK 336          

HSP 2 Score: 55.8398 bits (133), Expect = 3.705e-21
Identity = 45/155 (29.03%), Postives = 85/155 (54.84%), Query Frame = 2
Query:  485 ENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPR-SVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCR------------NFPSTSNRREISVKST-RIRMKEN 907
            ++    I+L+G+L++R+  IS   I L+ +A +R  A   P + N  R   ++K+++I ++   + + +RF L+    +C + + ID+ +K+ IGI   +++++ + IY +LF LLC R            NF S  N +E+  KS  +I  K+N
Sbjct:   93 KDHDTFIVLDGYLAIRDFAISSQMIILVLIAIDRLLAFLLP-LSNFWRIGRVLKVFKIFFILTLLFYSIRFTLLTVNINCDIKKSIDSDVKLFIGIFGGILMVINLIIYCILFALLCRRQIFNHKDSLLSANFKSL-NVKELESKSIPKIENKKN 245          
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000077660.1 (SMESG000077660.1)

HSP 1 Score: 62.3882 bits (150), Expect = 1.374e-19
Identity = 30/90 (33.33%), Postives = 53/90 (58.89%), Query Frame = 1
Query:  895 NERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTS 1164
            N ++S+   K        S++FA+ LF+I +LM+ISY P  L NV  + +   ++YYLF+L  LGDP++   +R +++  ++R   +  S
Sbjct:  242 NNKRSSLKNKFKSNKKSASIRFAKPLFAINLLMIISYLPAILYNVRFVGFHSYSVYYLFFLHALGDPILFFSTRPELKLALLRCLCIKKS 331          

HSP 2 Score: 53.1434 bits (126), Expect = 1.374e-19
Identity = 33/113 (29.20%), Postives = 59/113 (52.21%), Query Frame = 2
Query:  503 ILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRN 841
            I ++G+L++R+  IS      + +A +R   + HPQ+     + +IK+ +     I + +L+RF  +     C     +D  +K+ IGI   +++   + IY VLFGLLC R 
Sbjct:   91 IAVDGYLAVRDFSISSQMTIFVAIAIDRLLTLTHPQITKRRTNTIIKVLQTAVFFIGLFYLLRFIFLTIDIKCNSKVLLDKYMKLFIGIVGGVLMTTNLIIYLVLFGLLCHRQ 203          
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000062349.1 (SMESG000062349.1)

HSP 1 Score: 68.1662 bits (165), Expect = 3.278e-19
Identity = 36/95 (37.89%), Postives = 56/95 (58.95%), Query Frame = 1
Query:  883 HPYPNERKSTTVGKV---------FKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMI 1140
            +P  NE   T   ++         F+R  G S+KFA+VL  I ILM++SY P  L N   I +P  ++YYLF+L  LGDP+I +L+R +++  ++
Sbjct:  228 NPEENETSITKSRRISSLNSRKLRFRRRIG-SIKFAKVLLGINILMIVSYLPGVLYNNKFIPFPSYSVYYLFFLHALGDPIIFLLTRRELKNGLL 321          

HSP 2 Score: 46.2098 bits (108), Expect = 3.278e-19
Identity = 36/125 (28.80%), Postives = 67/125 (53.60%), Query Frame = 2
Query:  485 ENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTSN 859
            E+   NI L+ FL++R+  IS   ITL+ +A +R  A  +P       + ++ + +++ + +S+ ++ R  L+     CL  ++ID   K+ IGI+  + +++ + IY  LF LLC R      N
Sbjct:   85 EDTDTNIFLDVFLAIRDLSISAQMITLVLIAIDRLFAFVNPLSNYWVLNTVMWILKVLMLFLSLSYITRLILLSIGISCLNKKKIDKYGKIIIGISGGVFMLINLVIYVSLFSLLCQRQLVRQRN 209          
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000000172.1 (SMESG000000172.1)

HSP 1 Score: 62.003 bits (149), Expect = 2.250e-10
Identity = 30/69 (43.48%), Postives = 44/69 (63.77%), Query Frame = 1
Query:  931 KRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEM 1137
            K  F  S KFA V    T ++++S+ PVFL+N  ++K+PG  +YY FYL  L DP+ILI S+  +R  +
Sbjct:  214 KSKFNHSYKFAVVFSFATFILVVSFLPVFLSNTKMVKWPGYILYYGFYLHSLSDPIILIASKATLRNRI 282          
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000012028.1 (SMESG000012028.1)

HSP 1 Score: 50.8322 bits (120), Expect = 9.852e-7
Identity = 28/77 (36.36%), Postives = 47/77 (61.04%), Query Frame = 1
Query:  937 HFGKSV---KFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIY-YLFYLPVLGDPLILILSREDIRQEMIRPFSL 1155
            +FGK +   KF +VLF + +LM++S+ P  L N  L+K+     + YLFY+  LGD +I +  R D+R+++ +   L
Sbjct:  243 NFGKRIIHMKFVKVLFWVNLLMIVSFLPGCLYNSGLLKFKAYNWFIYLFYVHSLGDAIIFLFIRLDLRKDLTKLLRL 319          
The following BLAST results are available for this feature:
BLAST of GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUR61.446e-15699.52GCR156 OS=Schmidtea mediterranea OX=79327 GN=gcr15... [more]
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BLAST of GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 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 GCR156 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000062328.13.705e-2140.00SMESG000062328.1[more]
SMESG000077660.11.374e-1933.33SMESG000077660.1[more]
SMESG000062349.13.278e-1937.89SMESG000062349.1[more]
SMESG000000172.12.250e-1043.48SMESG000000172.1[more]
SMESG000012028.19.852e-736.36SMESG000012028.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032279 ID=SMED30032279|Name=GCR156|organism=Schmidtea mediterranea sexual|type=transcript|length=1472bp
TAAAATTATGTAGTAAAACGCCTACTGGAAGTGTGAGGGAGTTTTGTCTG
ACAATCACACTCGATCACAGCAACTCGTCAACTATAACGCAGCCAATCAA
AACGGACCAATCAAATTTAAAGAAAAATTATTGGTCATTCATTAGTCAAC
ATTTTTTCTCTCATTTATATATTACATAATCGACATTGGAAATTTATTCA
TCGGAAAATCACCTGCTTTCTATTCAATGTTAAATATCACAAATTGCGGA
AAAAATGCTTCAGATTATCAGAAACCTGTCCAATGGTATTTTTATCCCAG
CTATTTTGCACTGTTTTTCTTGAGTTTACTGTTGAATTTTGTGTTCATCA
ATTCATTCATCAAGTACAGAAGGCGATTAACTTTCAAATTCAATATTTTC
AATTATCTCACTTTCAATCTGATCATCATCGACTTTACTCAATCGATTGT
TCTGTTAATTGATATTTTATTGATTATGATTATGGAAAATCGATCCGAAA
ACATTCTATTAGAAGGATTTTTGTCCCTGAGAAATTGTCTGATTTCCTGT
CATGCAATAACCCTTCTGTTCATGGCAACCAATCGATATCGGGCCATCAA
GCACCCTCAGATGGTAAATGATCCCAGATCAGTGTTAATAAAATTATACC
GAATTATATATGTAACAATTTCCATTCCATTTCTAGTTCGATTTGCGTTG
GTTTTCTGTTTGAGAGATTGTCTATTGTTACAAGAAATAGATAATGCTCT
GAAAATGTCTATTGGAATTGCAACAGCCCTCGTTGTCATGGTGATCATAT
GCATTTATTCGGTGTTGTTTGGTTTATTGTGTTGTCGAAACTTTCCGTCC
ACTTCAAACCGACGGGAAATTTCAGTAAAATCCACCCGTATCCGAATGAA
AGAAAATCTACAACTGTGGGGAAAGTTTTCAAAAGACATTTTGGAAAGTC
TGTAAAATTTGCTCAAGTTTTATTTTCTATTACGATTTTAATGATGATTT
CTTATGCGCCGGTTTTTTTAACAAATGTCAATTTGATCAAATATCCCGGA
CAGGCGATTTATTATTTGTTTTATTTACCGGTTCTCGGAGATCCGTTGAT
TTTGATTCTGTCTAGGGAGGATATCCGACAAGAAATGATCCGACCATTCA
GCCTGACAACATCACAGAGTGTGACAAATATTTATTTTACGTAACGATAT
TTAAGTGTTTACTTGCGATGAAATGCATTCCGGAAATCTCAATAATCACT
TCCTGCACACATTCCTTTCAGCTGAAATAAAATTTTCCAACAGTTATTTG
ATGTGGTTTAAAAGTAAAGATTTCCCAAAAACTACTAGAGGCAAATGTAT
CTCTCATAAATGTTACACATGTTGTTTTTTTGTTTAAATGACTGCAGAAA
TTTATCTTTCACTCACGCGATTTTGTTTGAAATTGCACACGTAACATTTA
TACACGTTTTTTTCTCACTGAC
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protein sequence of SMED30032279-orf-1

>SMED30032279-orf-1 ID=SMED30032279-orf-1|Name=SMED30032279-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
MHLFGVVWFIVLSKLSVHFKPTGNFSKIHPYPNERKSTTVGKVFKRHFGK
SVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPL
ILILSREDIRQEMIRPFSLTTSQSVTNIYFT*
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protein sequence of SMED30032279-orf-2

>SMED30032279-orf-2 ID=SMED30032279-orf-2|Name=SMED30032279-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=243bp
MLNITNCGKNASDYQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRR
LTFKFNIFNYLTFNLIIIDFTQSIVLLIDILLIMIMENRSENILLEGFLS
LRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISI
PFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGL
LCCRNFPSTSNRREISVKSTRIRMKENLQLWGKFSKDILESL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000205oviduct
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 8..235
e-value: 1.4E-8
score: 36.1
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 13..206
NoneNo IPR availableTMHMMTMhelixcoord: 61..83
NoneNo IPR availableTMHMMTMhelixcoord: 20..41
NoneNo IPR availableTMHMMTMhelixcoord: 179..201
NoneNo IPR availableTMHMMTMhelixcoord: 137..159
NoneNo IPR availableTMHMMTMhelixcoord: 98..117