Contactin rig-6

Overview
NameContactin rig-6
Smed IDSMED30035414
Length (bp)324
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 Contactin rig-6 (SMED30035414) t-SNE clustered cells

Violin plots show distribution of expression levels for Contactin rig-6 (SMED30035414) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30035414

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30035414h1SMcG0000204 Contig4707newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30035414h1SMcG0000204 Contig4707newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30035414h1SMcG0006295 Contig4707newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30035414h1SMcG0006295 Contig4707newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30035414h1SMcG0006295 SmedASXL_010629SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30035414h1SMcG0006295 SmedASXL_015715SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
muscle cellSMED30035414h1SMcG0006295 dd_Smed_v4_14150_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30035414h1SMcG0006295 dd_Smed_v4_14150_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035414h1SMcG0006295 dd_Smed_v6_19912_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30035414h1SMcG0006295 dd_Smed_v6_14150_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
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BLAST of Contactin rig-6 vs. Ensembl Celegans
Match: rig-6 (Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:H2KZ60])

HSP 1 Score: 45.0542 bits (105), Expect = 1.956e-6
Identity = 21/42 (50.00%), Postives = 29/42 (69.05%), Query Frame = 1 
Query:  142 NWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKT 267
            N   + IT+ENL P+T YQF VRS  +  IG  S+P+++VKT
Sbjct:  378 NMEKDSITVENLLPNTEYQFRVRSVESAAIGEPSIPSDWVKT 419
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BLAST of Contactin rig-6 vs. Ensembl Celegans
Match: rig-6 (Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:H2KZ60])

HSP 1 Score: 45.0542 bits (105), Expect = 1.956e-6
Identity = 21/42 (50.00%), Postives = 29/42 (69.05%), Query Frame = 1 
Query:  142 NWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKT 267
            N   + IT+ENL P+T YQF VRS  +  IG  S+P+++VKT
Sbjct:  378 NMEKDSITVENLLPNTEYQFRVRSVESAAIGEPSIPSDWVKT 419
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BLAST of Contactin rig-6 vs. Ensembl Celegans
Match: rig-6 (Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:H2KZ60])

HSP 1 Score: 44.669 bits (104), Expect = 2.299e-6
Identity = 21/42 (50.00%), Postives = 29/42 (69.05%), Query Frame = 1 
Query:  142 NWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKT 267
            N   + IT+ENL P+T YQF VRS  +  IG  S+P+++VKT
Sbjct:  800 NMEKDSITVENLLPNTEYQFRVRSVESAAIGEPSIPSDWVKT 841
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BLAST of Contactin rig-6 vs. TrEMBL
Match: A0A5J4P2K6 (Roundabout, axon guidance receptor 2 OS=Paragonimus westermani OX=34504 GN=DEA37_0014480 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.430e-7
Identity = 29/75 (38.67%), Postives = 43/75 (57.33%), Query Frame = 1 
Query:   31 TSLDLIWSSNNNPDLKVLYWIEYVHFGSK-NGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIG-IGRASVP 249
            ++LDL   + N P  +V YW+E+  F    +GW +   NWP   + I  L+P+T Y FL+R + N G +G AS P
Sbjct:  642 SALDLGHRAENQPR-QVAYWVEFYRFDRPLDGWTVVESNWPATTVKIGGLQPNTAYHFLIRPRWNFGRVGWASAP 715
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BLAST of Contactin rig-6 vs. TrEMBL
Match: A0A504YEM6 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_06134 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.768e-7
Identity = 36/102 (35.29%), Postives = 51/102 (50.00%), Query Frame = 1 
Query:   16 KNIKSTSLDLIWSS--------NNNPDLKVLYWIEYVHF-GSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSK-TNIGIGRASVPTEYVKTKNFMSDEP 291
            KN+ +TS+ LIW          ++     + Y +EY+   G  N W     NWP N I +  L P+T Y FLVRS+  N  IGR+S P   V+T   + + P
Sbjct:  610 KNVTATSVTLIWEPLQTFAAEISSTDHRTIAYRVEYLSLTGPSNSWVTVEHNWPMNTIYLTGLMPNTVYYFLVRSRWVNGRIGRSSDPLGPVRTSRNLINHP 711
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BLAST of Contactin rig-6 vs. TrEMBL
Match: A0A0R3TL61 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS7954 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 7.852e-7
Identity = 30/81 (37.04%), Postives = 49/81 (60.49%), Query Frame = 1 
Query:   16 KNIKSTSLDLIWSSNNNPDL-KVLYWIEYVHFGSKN-GWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIG-IGRASVP 249
            +N  + S+ L+W+  N  D  +V YWIE  H    + GW++ +++WP N I +E L+P++ Y FL+R +   G +G AS P
Sbjct:  556 QNQTAKSVTLMWNPPNVHDTNQVSYWIEMFHTAEADLGWQVLQESWPRNAIRLEPLQPNSAYYFLIRPRWIDGRVGWASAP 636
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BLAST of Contactin rig-6 vs. TrEMBL
Match: A0A0R3SPT7 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7009 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 9.084e-7
Identity = 30/81 (37.04%), Postives = 49/81 (60.49%), Query Frame = 1 
Query:   16 KNIKSTSLDLIWSSNNNPDL-KVLYWIEYVHFGSKN-GWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIG-IGRASVP 249
            +N  + S+ L+W+  N  D  +V YWIE  H    + GW++ +++WP N I +E L+P++ Y FL+R +   G +G AS P
Sbjct:  554 QNQTANSVTLMWNPPNIHDTNQVSYWIEMFHTAEADFGWQVLQESWPRNAIRLEPLQPNSAYYFLIRPRWIDGRVGWASAP 634
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BLAST of Contactin rig-6 vs. TrEMBL
Match: A0A564ZDU8 (Uncharacterized protein (Fragment) OS=Hymenolepis diminuta OX=6216 GN=WMSIL1_LOCUS15068 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 9.447e-7
Identity = 30/81 (37.04%), Postives = 49/81 (60.49%), Query Frame = 1 
Query:   16 KNIKSTSLDLIWSSNNNPDL-KVLYWIEYVHFGSKN-GWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIG-IGRASVP 249
            +N  + S+ L+W+  N  D  +V YWIE  H    + GW++ +++WP N I +E L+P++ Y FL+R +   G +G AS P
Sbjct:  554 QNQTANSVTLMWNPPNIHDTNQVSYWIEMFHTAEADFGWQVLQESWPRNAIRLEPLQPNSAYYFLIRPRWIDGRVGWASAP 634
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BLAST of Contactin rig-6 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000002245.1 (pep scaffold:Pmarinus_7.0:GL476603:2572:131951:1 gene:ENSPMAG00000001992.1 transcript:ENSPMAT00000002245.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.1282 bits (100), Expect = 2.825e-6
Identity = 31/96 (32.29%), Postives = 49/96 (51.04%), Query Frame = 1 
Query:    1 VVEIPKN-IKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEI----YRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKN 273
            ++++ +N I   ++ L WS   +P+  +L +   + F  K   EI     +  W  N ITI  LKP T Y F VR++T  G G+ S P  + +T N
Sbjct:  407 ILDVRQNRISKDAIALSWSEPKHPNSVILDY--EITFSEKEQTEISYTTVKSKW--NTITINGLKPSTIYTFQVRTRTTAGYGQYSKPFHF-QTSN 497
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BLAST of Contactin rig-6 vs. Planmine SMEST
Match: SMESG000001429.1 (SMESG000001429.1)

HSP 1 Score: 227.639 bits (579), Expect = 2.383e-70
Identity = 108/108 (100.00%), Postives = 108/108 (100.00%), Query Frame = 1 
Query:    1 VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEPYSGNVGFQFTK 324
            VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEPYSGNVGFQFTK
Sbjct:  541 VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEPYSGNVGFQFTK 648
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BLAST of Contactin rig-6 vs. Planmine SMEST
Match: SMESG000066973.1 (SMESG000066973.1)

HSP 1 Score: 106.301 bits (264), Expect = 6.586e-28
Identity = 51/97 (52.58%), Postives = 67/97 (69.07%), Query Frame = 1 
Query:    1 VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEP 291
            V++ P    + S+ L WSS      +V YWIEYV FGS+ GW IY+K+WP   IT+ENL P++WYQFLVRS+ + G+ RASVPTEYVKT +  +  P
Sbjct:  500 VLDPPTEKTADSVTLTWSSTG----QVTYWIEYVRFGSREGWVIYKKDWPDTKITVENLSPNSWYQFLVRSRNHKGLSRASVPTEYVKTLSRENSRP 592
[Close]
BLAST of Contactin rig-6 vs. Planmine SMEST
Match: SMESG000066973.1 (SMESG000066973.1)

HSP 1 Score: 106.301 bits (264), Expect = 6.787e-28
Identity = 51/97 (52.58%), Postives = 67/97 (69.07%), Query Frame = 1 
Query:    1 VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWPHNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEP 291
            V++ P    + S+ L WSS      +V YWIEYV FGS+ GW IY+K+WP   IT+ENL P++WYQFLVRS+ + G+ RASVPTEYVKT +  +  P
Sbjct:  528 VLDPPTEKTADSVTLTWSSTG----QVTYWIEYVRFGSREGWVIYKKDWPDTKITVENLSPNSWYQFLVRSRNHKGLSRASVPTEYVKTLSRENSRP 620
The following BLAST results are available for this feature:
BLAST of Contactin rig-6 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 Contactin rig-6 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 3
Match NameE-valueIdentityDescription
rig-61.956e-650.00Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:... [more]
rig-61.956e-650.00Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:... [more]
rig-62.299e-650.00Contactin rig-6 [Source:UniProtKB/Swiss-Prot;Acc:... [more]
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BLAST of Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5J4P2K64.430e-738.67Roundabout, axon guidance receptor 2 OS=Paragonimu... [more]
A0A504YEM64.768e-735.29Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A0R3TL617.852e-737.04Uncharacterized protein OS=Rodentolepis nana OX=10... [more]
A0A0R3SPT79.084e-737.04Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A564ZDU89.447e-737.04Uncharacterized protein (Fragment) OS=Hymenolepis ... [more]
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BLAST of Contactin rig-6 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 Contactin rig-6 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSPMAT00000002245.12.825e-632.29pep scaffold:Pmarinus_7.0:GL476603:2572:131951:1 g... [more]
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BLAST of Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 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 Contactin rig-6 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000001429.12.383e-70100.00SMESG000001429.1[more]
SMESG000066973.16.586e-2852.58SMESG000066973.1[more]
SMESG000066973.16.787e-2852.58SMESG000066973.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035414 ID=SMED30035414|Name=Contactin rig-6|organism=Schmidtea mediterranea sexual|type=transcript|length=324bp
GTTGTAGAAATACCGAAAAATATCAAATCTACGTCCTTAGACTTGATTTG
GTCTTCAAACAACAATCCAGATCTGAAAGTTTTGTATTGGATTGAATACG
TTCATTTCGGCTCTAAAAACGGTTGGGAAATCTATAGAAAAAATTGGCCA
CATAATTTCATTACAATTGAAAATCTAAAACCGGATACATGGTACCAATT
CTTGGTCAGATCAAAAACAAATATCGGCATCGGTAGAGCAAGCGTGCCAA
CGGAATATGTTAAAACAAAGAATTTCATGAGCGATGAACCGTATTCAGGA
AATGTCGGATTTCAATTCACAAAA
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protein sequence of SMED30035414-orf-1

>SMED30035414-orf-1 ID=SMED30035414-orf-1|Name=SMED30035414-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
VVEIPKNIKSTSLDLIWSSNNNPDLKVLYWIEYVHFGSKNGWEIYRKNWP
HNFITIENLKPDTWYQFLVRSKTNIGIGRASVPTEYVKTKNFMSDEPYSG
NVGFQFTK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR036116FN3_sf
IPR013783Ig-like_fold
IPR003961FN3_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: biological process
TermDefinition
GO:0007411axon guidance
GO:0035385Roundabout signaling pathway
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
GO:0030424axon
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013783Immunoglobulin-like foldGENE3DG3DSA:2.60.40.10coord: 2..93
e-value: 1.4E-13
score: 52.9
IPR003961Fibronectin type IIIPFAMPF00041fn3coord: 6..81
e-value: 1.1E-6
score: 28.8
IPR003961Fibronectin type IIIPROSITEPS50853FN3coord: 1..92
score: 13.192
IPR003961Fibronectin type IIICDDcd00063FN3coord: 6..87
e-value: 3.14135E-9
score: 47.8763
IPR036116Fibronectin type III superfamilySUPERFAMILYSSF49265Fibronectin type IIIcoord: 7..91