Neur_chan_LBD domain-containing protein

Overview
NameNeur_chan_LBD domain-containing protein
Smed IDSMED30013175
Length (bp)401
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




SMED30013175

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30013175SMESG000041818.1 SmedASXL_005028SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
headSMED30013175SMESG000041818.1 dd_Smed_v6_50434_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Neur_chan_LBD domain-containing protein vs. TrEMBL
Match: A0A5K4FCR6 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 119.013 bits (297), Expect = 2.106e-28
Identity = 63/141 (44.68%), Postives = 79/141 (56.03%), Query Frame = 3
Query:   69 SKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLD-------------------------DRTDMKDINL-----STFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            SK  V L  +F+K+ +VDT+NE Y  DIFLQA+WREPLLD                         D T  + +N        FWNP+L+I+N   E    + HEV F E  ++AY+ EKRRIK  F ETLEL+HFPFDCQD
Sbjct:  272 SKARVELVLIFVKVGQVDTVNERYQADIFLQARWREPLLDAMWNKSSLKSKSSWQTNPSIENPFTDLTSKRQLNTLKLQDDEFWNPRLLIDNAEGEPIEIISHEVEFIEPDFEAYLVEKRRIKGIFHETLELRHFPFDCQD 412          
BLAST of Neur_chan_LBD domain-containing protein vs. TrEMBL
Match: A0A5K4F965 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 118.627 bits (296), Expect = 2.707e-28
Identity = 63/141 (44.68%), Postives = 79/141 (56.03%), Query Frame = 3
Query:   69 SKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLD-------------------------DRTDMKDINL-----STFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            SK  V L  +F+K+ +VDT+NE Y  DIFLQA+WREPLLD                         D T  + +N        FWNP+L+I+N   E    + HEV F E  ++AY+ EKRRIK  F ETLEL+HFPFDCQD
Sbjct:  272 SKARVELVLIFVKVGQVDTVNERYQADIFLQARWREPLLDAMWNKSSLKSKSSWQTNPSIENPFTDLTSKRQLNTLKLQDDEFWNPRLLIDNAEGEPIEIISHEVEFIEPDFEAYLVEKRRIKGIFHETLELRHFPFDCQD 412          
BLAST of Neur_chan_LBD domain-containing protein vs. TrEMBL
Match: A0A4Z2CPI1 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_008605 PE=4 SV=1)

HSP 1 Score: 116.316 bits (290), Expect = 3.219e-28
Identity = 61/137 (44.53%), Postives = 77/137 (56.20%), Query Frame = 3
Query:   81 VYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLD-------------------------DRTDMKDINL-----STFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            V L  +F+K+ +VDT+NE Y  DIFLQA+WREPLLD                         D T  + +N        FWNP+L+I+N   E    + HEV F E  ++AY+ EKRRIK  F ETLEL+HFPFDCQD
Sbjct:   17 VELVLIFVKVGQVDTVNERYQADIFLQARWREPLLDAMWNKSSLKSKSSWQTNPSIENPFTDLTSKRQLNTLKLQDDEFWNPRLLIDNAEGEPIEIISHEVEFMEPDFEAYLVEKRRIKGIFHETLELRHFPFDCQD 153          
BLAST of Neur_chan_LBD domain-containing protein vs. TrEMBL
Match: A0A3R7CFX9 (Neuronal acetylcholine receptor subunit alpha-7 OS=Clonorchis sinensis OX=79923 GN=CHRNA7 PE=4 SV=1)

HSP 1 Score: 115.931 bits (289), Expect = 6.158e-28
Identity = 60/135 (44.44%), Postives = 76/135 (56.30%), Query Frame = 3
Query:   81 VYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLD-------DRTDMKDINL---------------------STFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            V L  +F+KI +VDT+NE Y  DIFLQA+WREPLLD        R + +   +                       FWNP+L+++N   E    V HEV F E  ++AY+ EKRRIK  F ETLEL+HFPFDCQD
Sbjct:   39 VELMLIFVKIGQVDTVNERYQADIFLQARWREPLLDATWNTSRPRNNFRTFKMVENPVMELAPKRHLHTLKLQDDEFWNPRLLLDNAQGEPIEIVSHEVEFVEPDFEAYLVEKRRIKGVFHETLELKHFPFDCQD 173          
BLAST of Neur_chan_LBD domain-containing protein vs. TrEMBL
Match: A0A4S2MHH5 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_001259 PE=4 SV=1)

HSP 1 Score: 116.701 bits (291), Expect = 8.923e-28
Identity = 61/135 (45.19%), Postives = 77/135 (57.04%), Query Frame = 3
Query:   81 VYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLD-------DRTDMKDINL---------------------STFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            V L  +F+KI +VDT+NE Y  DIFLQA+WREPLLD        R + +  N+                       FWNP+L+++N   E    V HEV F E  ++AY+ EKRRIK  F ETLEL+HFPFDCQD
Sbjct:  234 VELMLIFVKIGQVDTVNERYQADIFLQARWREPLLDATWNTSRPRNNFRTFNMVENPVMELAPKRHLHTLKLQDDEFWNPRLLLDNAQGEPIEIVSHEVEFVEPDFEAYLVEKRRIKGVFHETLELKHFPFDCQD 368          
BLAST of Neur_chan_LBD domain-containing protein vs. Ensembl Nematostella
Match: EDO32790 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SU26])

HSP 1 Score: 47.3654 bits (111), Expect = 2.895e-7
Identity = 26/110 (23.64%), Postives = 51/110 (46.36%), Query Frame = 3
Query:   72 KKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            K  V +RC    +  +D I + ++ ++++ A WREP L  + + +++     W+PK+   N     +      + + E        E  +I+  F+E   L+ FP D Q+
Sbjct:   15 KVTVLIRCGISFLGDIDVIRQQFTCELWMTASWREPKLAGKKN-EEVKWDNEWSPKISFSNSLLLDRVYKGRRLYYEENSTVPLAQEVYKIRGTFKEQFSLEQFPVDLQE 123          
BLAST of Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Match: SMESG000041818.1 (SMESG000041818.1)

HSP 1 Score: 249.595 bits (636), Expect = 7.687e-84
Identity = 118/122 (96.72%), Postives = 121/122 (99.18%), Query Frame = 3
Query:   36 MEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            MEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKL+IENMFQESKSSVVHEVSFSEK ++AYITEKRRIKACFRETLELQHFPFDCQD
Sbjct:    1 MEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLVIENMFQESKSSVVHEVSFSEKRHEAYITEKRRIKACFRETLELQHFPFDCQD 122          
BLAST of Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Match: SMESG000041829.1 (SMESG000041829.1)

HSP 1 Score: 191.045 bits (484), Expect = 6.910e-61
Identity = 87/122 (71.31%), Postives = 105/122 (86.07%), Query Frame = 3
Query:   36 MEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            ME  SKS +K   +LVYLRCVFIKI+KVDT+NEFYS +IFLQ+KWREPLLD+R+D+KDI+LS+FWNPK+ IEN+F E+KSS+ HEVS+S K  +AYITEKRR+   FRE LELQHFPFDCQD
Sbjct:    1 MENNSKSVNKPVARLVYLRCVFIKIFKVDTVNEFYSAEIFLQSKWREPLLDNRSDIKDISLSSFWNPKISIENIFMETKSSISHEVSYSGKAREAYITEKRRVSGGFREVLELQHFPFDCQD 122          
BLAST of Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Match: SMESG000041796.1 (SMESG000041796.1)

HSP 1 Score: 187.578 bits (475), Expect = 6.451e-59
Identity = 89/125 (71.20%), Postives = 105/125 (84.00%), Query Frame = 3
Query:   30 FAMEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYK-AYITEKRRIKACFRETLELQHFPFDCQD 401
            + ME  SKSN  ++K+ VYLRCVFIKIYKVDT+NEFYSG+IFL AKWREPLLD+++D+KDI+LSTFWNPKL IEN+FQ +KS+   EVSF E   K A++ EK RIKA FRETLELQHFPFDCQD
Sbjct:   52 YLMENNSKSNQIKTKRKVYLRCVFIKIYKVDTVNEFYSGEIFLHAKWREPLLDNKSDLKDISLSTFWNPKLSIENIFQITKSTTSLEVSFDEGNNKRAFVVEKTRIKAAFRETLELQHFPFDCQD 176          
BLAST of Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Match: SMESG000064433.1 (SMESG000064433.1)

HSP 1 Score: 179.489 bits (454), Expect = 2.568e-56
Identity = 82/107 (76.64%), Postives = 98/107 (91.59%), Query Frame = 3
Query:   81 VYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            VYLRCVF+KIYKVDT+NEFYSG+IFLQ+KWREPLLD + ++KD+NL +FWNPKLIIEN+F E+KSSV  EV+F+EK Y+A+I EKRR+KA FRETLELQHFPFDCQD
Sbjct:   16 VYLRCVFVKIYKVDTVNEFYSGEIFLQSKWREPLLDHKPNLKDVNLFSFWNPKLIIENIFTENKSSVSLEVTFTEK-YEAFIIEKRRVKASFRETLELQHFPFDCQD 121          
BLAST of Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Match: SMESG000064435.1 (SMESG000064435.1)

HSP 1 Score: 166.392 bits (420), Expect = 3.371e-51
Identity = 80/122 (65.57%), Postives = 97/122 (79.51%), Query Frame = 3
Query:   36 MEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDIFLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFSEKGYKAYITEKRRIKACFRETLELQHFPFDCQD 401
            ME +S+SN +  +K +YLRCVFIKI+KVDT+NE Y  +IFLQAKWREPLLD+  D K+I+L  FWNPKL IEN+F E+K SV  EVS+SEK   AY+ EKRR+KA F E LEL+HFPFDCQD
Sbjct:    1 MEEDSESNQEPVQKKIYLRCVFIKIFKVDTVNENYYAEIFLQAKWREPLLDNECDYKNIDLKNFWNPKLRIENIFTENKVSVSLEVSYSEKEGVAYLMEKRRVKASFHEILELKHFPFDCQD 122          
The following BLAST results are available for this feature:
BLAST of Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5K4FCR62.106e-2844.68Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A5K4F9652.707e-2844.68Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A4Z2CPI13.219e-2844.53Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A3R7CFX96.158e-2844.44Neuronal acetylcholine receptor subunit alpha-7 OS... [more]
A0A4S2MHH58.923e-2845.19Uncharacterized protein OS=Opisthorchis felineus O... [more]
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BLAST of Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD 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 Neur_chan_LBD domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO327902.895e-723.64Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Neur_chan_LBD 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 Neur_chan_LBD domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000041818.17.687e-8496.72SMESG000041818.1[more]
SMESG000041829.16.910e-6171.31SMESG000041829.1[more]
SMESG000041796.16.451e-5971.20SMESG000041796.1[more]
SMESG000064433.12.568e-5676.64SMESG000064433.1[more]
SMESG000064435.13.371e-5165.57SMESG000064435.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013175 ID=SMED30013175|Name=Neur_chan_LBD domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=401bp
TGGAATGCAAACGTTTCAGCATCCAGAGTTTTGCAATGGAAGTCGAATCT
AAATCAAACCATAAACAGTCTAAGAAACTGGTATACCTGAGATGTGTTTT
TATCAAAATTTACAAAGTGGATACGATAAATGAATTTTACTCTGGAGATA
TTTTTCTTCAAGCAAAATGGAGGGAGCCTCTGCTTGATGATAGAACAGAT
ATGAAAGATATAAATCTGTCAACATTTTGGAATCCTAAGTTAATAATTGA
AAATATGTTTCAAGAATCAAAATCATCTGTAGTCCACGAAGTTTCGTTTT
CAGAGAAAGGATATAAAGCCTACATAACAGAAAAAAGGCGAATTAAAGCT
TGTTTTCGGGAAACACTTGAATTGCAACATTTCCCTTTTGACTGTCAAGA
T
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protein sequence of SMED30013175-orf-1

>SMED30013175-orf-1 ID=SMED30013175-orf-1|Name=SMED30013175-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=133bp
ECKRFSIQSFAMEVESKSNHKQSKKLVYLRCVFIKIYKVDTINEFYSGDI
FLQAKWREPLLDDRTDMKDINLSTFWNPKLIIENMFQESKSSVVHEVSFS
EKGYKAYITEKRRIKACFRETLELQHFPFDCQD
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004888transmembrane signaling receptor activity
GO:0005216ion channel activity
GO:0005230extracellular ligand-gated ion channel activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR036734Neur_chan_lig-bd_sf
IPR006202Neur_chan_lig-bd
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0006810transport
GO:0006811ion transport
GO:0034220ion transmembrane transport
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006202Neurotransmitter-gated ion-channel ligand-binding domainPFAMPF02931Neur_chan_LBDcoord: 17..128
e-value: 4.9E-6
score: 26.1
IPR036734Neurotransmitter-gated ion-channel ligand-binding domain superfamilyGENE3DG3DSA:2.70.170.10coord: 10..128
e-value: 4.2E-11
score: 44.7
IPR036734Neurotransmitter-gated ion-channel ligand-binding domain superfamilySUPERFAMILYSSF63712Nicotinic receptor ligand binding domain-likecoord: 20..128
NoneNo IPR availableCDDcd18988LGIC_ECD_bactcoord: 29..128
e-value: 2.65139E-8
score: 47.6726