Gonadotropin-releasing hormone like-1

Overview
NameGonadotropin-releasing hormone like-1
Smed IDSMED30034905
Length (bp)374
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 Gonadotropin-releasing hormone like-1 (SMED30034905) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Gonadotropin-releasing hormone like-1 (SMED30034905) 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.
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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



SMED30034905

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30034905SMESG000061019.1 SmedASXL_033159SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30034905SMESG000061019.1 dd_Smed_v6_8966_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30034905SMESG000061019.1 OX_Smed_1.0.09407ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30034905SMESG000061019.1 GU295185smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034905SMESG000061019.1 GU295185smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034905SMESG000061019.1 GU295185smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30034905SMESG000061019.1 GU295185.1smed_ncbi_20200123PMID:30485821
Tewari et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
reproductive organSMED30034905SMESG000061019.1 Contig10622newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30034905SMESG000061019.1 Contig10622uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. TrEMBL
Match: E3T7U7 (Gonadotropin-releasing hormone like-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 179.104 bits (453), Expect = 3.951e-56
Identity = 96/97 (98.97%), Postives = 97/97 (100.00%), Query Frame = 1 
Query:   43 MTKFVRXXXXXXXXXXXVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNIK 333
            MTKFVRFFIILFIFLQIVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNI+
Sbjct:    1 MTKFVRFFIILFIFLQIVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNIR 97
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BLAST of Gonadotropin-releasing hormone like-1 vs. TrEMBL
Match: A0A267HBD7 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig008027g1 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 3.159e-11
Identity = 39/85 (45.88%), Postives = 49/85 (57.65%), Query Frame = 1 
Query:  112 QSYHFS---NDWLPGKRY-----HTGHQMFRLKKGFHYFRLKKPSNCIFDNYFK---QDILKLARKHSGLCPSDLSFIEE-LQNI 330
            Q +HFS   N W PGKR      H GHQ+FRLKKG+H+FRLKK   C      +    DI+K A+  S LCP+D   I   +QN+
Sbjct:   58 QQFHFSHGVNGWKPGKRGLAEEGHAGHQIFRLKKGYHFFRLKKDQECAIGEEARALLADIVKSAQSGS-LCPADRQVISAFVQNL 141
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BLAST of Gonadotropin-releasing hormone like-1 vs. TrEMBL
Match: A0A1I8GSG1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 9.554e-11
Identity = 34/71 (47.89%), Postives = 43/71 (60.56%), Query Frame = 1 
Query:  112 QSYHFSNDWLPGKRY-----HTGHQMFRLKKGFHYFRLKKPSNCIFDNYFK---QDILKLARKHSGLCPSD 300
            Q +HFS+ W PGKR      H GHQ+FRLKKG+H+FRLKK   C      +    DI+K  +  S LCP+D
Sbjct: 3271 QQFHFSHGWKPGKRGLAEEGHAGHQIFRLKKGYHFFRLKKDQECAIGEEARALLADIVKSTQSGS-LCPAD 3340
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. TrEMBL
Match: A0A267F661 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig008027g2 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 4.633e-10
Identity = 38/85 (44.71%), Postives = 48/85 (56.47%), Query Frame = 1 
Query:  112 QSYHFS---NDWLPGKRY-----HTGHQMFRLKKGFHYFRLKKPSNCIFDNYFK---QDILKLARKHSGLCPSDLSFIEE-LQNI 330
            Q +HFS   N W PGKR      H GHQ+FRLKKG+H+FRLKK   C      +    DI+K  +  S LCP+D   I   +QN+
Sbjct:   68 QQFHFSHGVNGWKPGKRGLAEEGHAGHQIFRLKKGYHFFRLKKDQECAIGEEARALLADIVKSTQSGS-LCPADRQVIAAFVQNL 151
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. TrEMBL
Match: E3T7U8 (Secreted peptide prohormone 19 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 9.276e-10
Identity = 30/68 (44.12%), Postives = 40/68 (58.82%), Query Frame = 1 
Query:  127 SNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNI 330
             +D L  KR H GHQ+FRLK+G+H+FRL+K   C+     K  I       S LC SD SF+ EL ++
Sbjct:   21 GSDDLIVKRKHIGHQIFRLKRGYHFFRLRKDEKCLIPGELKSAIKNDLESGSNLCGSDKSFLAELASL 88
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BLAST of Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Match: SMESG000061019.1 (SMESG000061019.1)

HSP 1 Score: 179.874 bits (455), Expect = 5.815e-60
Identity = 97/97 (100.00%), Postives = 97/97 (100.00%), Query Frame = 1 
Query:   43 MTKFVRXXXXXXXXXXXVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNIK 333
            MTKFVRFFIILFIFLQIVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNIK
Sbjct:    1 MTKFVRFFIILFIFLQIVSEICPQSYHFSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNIK 97
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Match: SMESG000053016.1 (SMESG000053016.1)

HSP 1 Score: 60.077 bits (144), Expect = 6.740e-13
Identity = 30/67 (44.78%), Postives = 40/67 (59.70%), Query Frame = 1 
Query:  130 NDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNI 330
            +D L  KR H GHQ+FRLK+G+H+FRL+K   C+     K  I       S LC SD SF+ EL ++
Sbjct:   22 SDDLIVKRKHIGHQIFRLKRGYHFFRLRKDEKCLIPVELKSAIKNDLESGSNLCGSDKSFLAELVSL 88
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Match: SMESG000073636.1 (SMESG000073636.1)

HSP 1 Score: 50.447 bits (119), Expect = 2.974e-9
Identity = 24/66 (36.36%), Postives = 38/66 (57.58%), Query Frame = 1 
Query:  124 FSNDWLPGKRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEEL 321
             S  +   KR  TGH+MFRLKKGFH+ +LK+   C+  +  K++I+     +  +C  D  F+ +L
Sbjct:   20 ISLSYSENKRALTGHRMFRLKKGFHFIKLKRNFECVIPDSVKEEIM-----NGNICLEDQEFLRKL 80
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Match: SMESG000030647.1 (SMESG000030647.1)

HSP 1 Score: 43.5134 bits (101), Expect = 1.153e-6
Identity = 18/49 (36.73%), Postives = 29/49 (59.18%), Query Frame = 1 
Query:  184 KKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLSFIEELQNI 330
            K+G+H+FRLKK  +C+  +  K  I    + H  LC +D  FIE + ++
Sbjct:   27 KRGYHFFRLKKSGDCVIPDVMKAMIETKIQNHEQLCAADKKFIEMISSV 75
[Close]
BLAST of Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Match: SMESG000024831.1 (SMESG000024831.1)

HSP 1 Score: 41.5874 bits (96), Expect = 6.709e-6
Identity = 21/53 (39.62%), Postives = 31/53 (58.49%), Query Frame = 1 
Query:  148 KRYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSDLS 306
            KRY TGH +FRLKK +HYFRL++  + +  +    D++    KH    P  L+
Sbjct:   18 KRYDTGHDIFRLKKSYHYFRLRRALDQMKCSRNTNDLVNFIEKHCMEKPDFLA 70
The following BLAST results are available for this feature:
BLAST of Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
E3T7U73.951e-5698.97Gonadotropin-releasing hormone like-1 OS=Schmidtea... [more]
A0A267HBD73.159e-1145.88Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8GSG19.554e-1147.89Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267F6614.633e-1044.71Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
E3T7U89.276e-1044.12Secreted peptide prohormone 19 OS=Schmidtea medite... [more]
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BLAST of Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 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 Gonadotropin-releasing hormone like-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000061019.15.815e-60100.00SMESG000061019.1[more]
SMESG000053016.16.740e-1344.78SMESG000053016.1[more]
SMESG000073636.12.974e-936.36SMESG000073636.1[more]
SMESG000030647.11.153e-636.73SMESG000030647.1[more]
SMESG000024831.16.709e-639.62SMESG000024831.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034905 ID=SMED30034905|Name=Gonadotropin-releasing hormone like-1|organism=Schmidtea mediterranea sexual|type=transcript|length=374bp
CATATAAAGGAGGCAGGGAAAGCATCCCAAACATTAGAAAATATGACAAA
ATTTGTTCGTTTCTTTATTATTTTATTCATTTTCCTGCAGATTGTCAGTG
AAATATGTCCACAGTCTTATCATTTTAGTAACGACTGGCTTCCAGGGAAA
CGATATCACACAGGTCATCAAATGTTTCGGTTAAAAAAAGGCTTTCATTA
TTTTAGATTAAAAAAGCCATCGAATTGCATTTTTGACAACTATTTCAAAC
AAGATATTCTGAAATTAGCCAGAAAGCATTCGGGACTTTGCCCAAGCGAT
TTAAGTTTCATAGAAGAACTTCAAAACATAAAATAATTTGTAATGTTTAT
GGTTATAAATAAACTATGTCGGTG
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protein sequence of SMED30034905-orf-1

>SMED30034905-orf-1 ID=SMED30034905-orf-1|Name=SMED30034905-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
HIKEAGKASQTLENMTKFVRFFIILFIFLQIVSEICPQSYHFSNDWLPGK
RYHTGHQMFRLKKGFHYFRLKKPSNCIFDNYFKQDILKLARKHSGLCPSD
LSFIEELQNIK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 21..43