Gene detail

Detailed information of NY_Scal100_v1.47273.1 in Scolanthus callimorphus

Genomic Location: chr7:12901854...12907796
NR annotation: no NCBI-NR hit recorded
Species Scolanthus callimorphus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

NY_Scal100_v1.47273.1

CAGACTGTCCTTGCAAAAGCTAGATATGACAACATTGCTGACTCTACTGATGAGCTGACCTTCCGGAAAGGAGATATAATCACCGTCCTTGAGAAAGACATTGATGGCTTGCTAGGGTGGTGGCTATGCTCTCTACATGGCCGCCAAGGTATTGCCCCTGGCAACCGCTTGACGGAGATAGGGGCTGGGACACACCCTTCAATAACCACCCCTACCTCTCCCAAAAGCCTTCTTGATGAGTTGGATTATGCCGTCCCTAAACCATTTGAGGAGCAAGGAGAAGACTATGACGTCCCAAGGTCTGTTCTCAGTCCTCAAGATTATGACTTCCCCAAGGCGGATGACAAATTTAATTTTGAGACTGTAGAAAATGGGACTGAGAAGAAGACAGATAAGGATAAAGATGGAAATATTTACCAGGAAATCTATGATGTCCCTTATACCCCTAGCCCCAAGAAGGTCCCCCCTCCCCGCCCACCAGTGTCACCTGCTGTGAAAAGAAAGTTTGAGGAGAAAACTCAAGTGAAAACAGATGATGGTCCGGGTAAAGACAAGACGAATGATGAAGAACCTGTAGAACCATTACCCCCACGCTCACCCATCCCCAAGCCACACCCCAAACCACCAAGGGCAAGCAAACTGAACACAGATAAAAACAAAGCAGAACCGCCTGCAAGGCCACCTAAACCAGCGTCATTCAAAGCAAAGAGTAAGACAGAGGGGGTTGATGGGAAGGGTATAGCGAAAGAGGATAAAGGCATATATGCTGTGCCGTGTGGCCAGGAGATTTACGAGGTCCCTAAAACAGACTCTAAAGTGGCAGATGAATCGACAGCAGAGAAAAACAACAACTTGTCCTCAAAGGATAAAGTCAGCGATACGGTCAAAGCAGACGAGAAGGCTATTAACGTCGTTAGTTCTTCGGTACAGCCTGGCACTCCAAGTAGTGCTTCTAAAGATGCAGCAGTGAATGATAACAAGGCCTCGTCATACCCAGAGGACATCTATGACGTCCCTACCGCGGATTTGTCTAGCGGAGAAATCTATGACGTACCGGCTGCTATCAAAGCGCTACAAGACGAGGATATTTACGATACTCCACCTAGAATCCCAACGGGAACATTAGAGAGACAAACATCTCTGGGATCTAAACAGGACACCAACCATGGAGCGCACATGCTCAGTAAAACTGTGGATGTTAATCATAATAAAAGGAATGAGAAAGCCCCTGAAGGGCCTGCCTGGCTGGTGAAGGGGGATTCGGGAAGTTTTGGGCGGAAGGTCGATCCTGCTCTAAAGAGAAGCTCGGATGGAAGCACTGGAAAGAGGAGCTCGAACTCGAGTACGGGTAGCGGGAAACAGAGCTCTGATTCGGATGATTATGTGGATTATCAGGATATATATGGTGATGGGCATGACAAGCATGTGAATATTTATGACGTCCCTGTACAGCACGTCCAAGTGTCCGACATCGAAACCGCCCCCGTGGAGAAGAAAACCGCGGAGAGTATTCTACAGCGAATCAACATGTCTGCAGTTAAAGGACTCAAGTTAGACCCGCCTGGTGCGCTACAGAGACTCAGCAAACTGGAACAAGCAGTTGATGTGACGGTTTCTAAACTGCTTAGCTACGTCACCACAAAATGGCGGGACCCAGTCTTATTACGGCCTAAAATTGCGGATATCAGAGACATAGCCGGCAAAGGAAAGGTCGCACTAAGGTTGTTGACAGAATTCGGGCTCAGTACACTCGTAAATGCGCGAAGCCTTGCGAATGAAGAACTCGTTGGCAAGCTGAGTAGAGCAATAGAGCCGTTGTTAGAGACTTACTACTCGTTGAAGGTTGCGCTGCAGCGATTGGATGAGACGTACCCGAGGGATCAAAGAAACTTGCGAGTATTGTCAGGACCACAGCCACAGTGCTCTTTAATCGTCCGAAAAAGCCTCCAGTACTCCTTCCAACAAAAGAACAACAAACTGCCAAAGCCTGATGCTGTGAGCGAGGGGAAATCTCCAGCGGGTGAGCCAGTTTCTAAAGTTGAATCAAGCAGCAGAGGCACGAAACCACCCGCAACTAAACCTAAACCGGCATTGAATGGCAAGGATGCTAAGCCAGTTGTAAATGGCGATCATAAAGAAGACAAATCACAGGTTGAAAGAAAAGCGTCCATCGAAGAGGAGGGTGAACGTCCAAGAACTGGTACGGTAGCACAAGCTATAGCAAAGGTGGAAAAAATCGGTCTTTCCCCTTCGAAGGCGGACAGTGAAGAGATCAGCTCTACTGCTATGATGTTAGGTCTTATTAAGCAGTCAGTAGAAGAGAATATTAAGCCCTCGGGGCGAAAATTCAGTCCAGGTACCGTGCGAAGACTTTGTGGAATGGATGGGGAAATAATCGAGGACGGTGTAGAAGGGGCGAGGACGGAGGGAGAGGTTCCAGTCTTGCCTCCACGCAGGCCGAGTACCCCTTCTAAAGGCGCTCCTCCACCCCCCGCGAGACGCGACAGCGGGGAGAGACTACAACACGTGCGCCAAAAGAGCCTGGAGAGATTCGTCCCCGAGGGGGAATCCCCACCAGTCACTAACGGCCCCCCTAACCCTCCTCCTAAACCTAAACTGGATCGACACAAGACCATGCGTAAGAGTTATAAGTACCCCATGCGGCACGAAAAGGTCCGATTACGCGACAAAGTCGAGGTACCGGAGTCCCCTACGGGAAAACGCAAATGTAACTCGGACCCTACGGACTTAGAAATGAGCCCTGAGGAAGACGCTAAACAACACCGGGCATCGGACTCGTTAGAAGGTAAAGTCCCGGAGAATGGCATCACGATAAACACGAACTCTGTTCACATCTCGGATTCCGATCTACCGACTGGGTTACGAGGGCAATCTACTATGACTCCTTTGTCACCCAAACTTGATTCGCCGAGCTCTCCGAAAAAATCCATCGTTCAACGGAGTAAATCATTCTCAAGGACTAAACCTTCCTCGACTAAGACAACCATGGTAGAGGAATCCGGTCTTGGGGATTTTATTTTATCATTCAGTGATAAAGAACTTTTAGAATTTTATAAATACGAAATCGATGCTCAGCTTTTTGTACTCAACGAGGCCATGAAAGGGCTATTTACCTCCGTCGACACCAGCCAGCCACCCAAGACTTTTGTATCGAACAGTAAATTCGTGGTATTGAGCGCACATAAGTTTATTTACATCGGAGACACGCTACAACGAAAGATATCTCATGATAAACTCGGTATGGACGTCACTTCAGCGACGGCTAAGTTATCTGAATGTGTGAAGACGCTTGTCCACGCAACTAAGATGGCGGCGCTCCAGTACCCTGCTATGAACCCCATGAGGGACCTGACTACTGCGGCGGCAGAGGTGTCCGAGGCCTCTATAGCACTACATAAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGTTATACCATCAGTAGTCCAGCGCTCAACCATCAGGAGTCCAGCGCTATGCTATACCATCAGTAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGTAGTCCAGCGCTCAACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGAGGAGTCCAGCGGAGTCCAGCGCTATGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTGACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGAGGAGTCCAGCGTTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCACCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGA

Transcript

NY_Scal100_v1.47273.1

ATGCAGACTGTCCTTGCAAAAGCTAGATATGACAACATTGCTGACTCTACTGATGAGCTGACCTTCCGGAAAGGAGATATAATCACCGTCCTTGAGAAAGACATTGATGGCTTGCTAGGGTGGTGGCTATGCTCTCTACATGGCCGCCAAGGTATTGCCCCTGGCAACCGCTTGACGGAGATAGGGGCTGGGACACACCCTTCAATAACCACCCCTACCTCTCCCAAAAGCCTTCTTGATGAGTTGGATTATGCCGTCCCTAAACCATTTGAGGAGCAAGGAGAAGACTATGACGTCCCAAGGTCTGTTCTCAGTCCTCAAGATTATGACTTCCCCAAGGCGGATGACAAATTTAATTTTGAGACTGTAGAAAATGGGACTGAGAAGAAGACAGATAAGGATAAAGATGGAAATATTTACCAGGAAATCTATGATGTCCCTTATACCCCTAGCCCCAAGAAGGTCCCCCCTCCCCGCCCACCAGTGTCACCTGCTGTGAAAAGAAAGTTTGAGGAGAAAACTCAAGTGAAAACAGATGATGGTCCGGGTAAAGACAAGACGAATGATGAAGAACCTGTAGAACCATTACCCCCACGCTCACCCATCCCCAAGCCACACCCCAAACCACCAAGGGCAAGCAAACTGAACACAGATAAAAACAAAGCAGAACCGCCTGCAAGGCCACCTAAACCAGCGTCATTCAAAGCAAAGAGTAAGACAGAGGGGGTTGATGGGAAGGGTATAGCGAAAGAGGATAAAGGCATATATGCTGTGCCGTGTGGCCAGGAGATTTACGAGGTCCCTAAAACAGACTCTAAAGTGGCAGATGAATCGACAGCAGAGAAAAACAACAACTTGTCCTCAAAGGATAAAGTCAGCGATACGGTCAAAGCAGACGAGAAGGCTATTAACGTCGTTAGTTCTTCGGTACAGCCTGGCACTCCAAGTAGTGCTTCTAAAGATGCAGCAGTGAATGATAACAAGGCCTCGTCATACCCAGAGGACATCTATGACGTCCCTACCGCGGATTTGTCTAGCGGAGAAATCTATGACGTACCGGCTGCTATCAAAGCGCTACAAGACGAGGATATTTACGATACTCCACCTAGAATCCCAACGGGAACATTAGAGAGACAAACATCTCTGGGATCTAAACAGGACACCAACCATGGAGCGCACATGCTCAGTAAAACTGTGGATGTTAATCATAATAAAAGGAATGAGAAAGCCCCTGAAGGGCCTGCCTGGCTGGTGAAGGGGGATTCGGGAAGTTTTGGGCGGAAGGTCGATCCTGCTCTAAAGAGAAGCTCGGATGGAAGCACTGGAAAGAGGAGCTCGAACTCGAGTACGGGTAGCGGGAAACAGAGCTCTGATTCGGATGATTATGTGGATTATCAGGATATATATGGTGATGGGCATGACAAGCATGTGAATATTTATGACGTCCCTGTACAGCACGTCCAAGTGTCCGACATCGAAACCGCCCCCGTGGAGAAGAAAACCGCGGAGAGTATTCTACAGCGAATCAACATGTCTGCAGTTAAAGGACTCAAGTTAGACCCGCCTGGTGCGCTACAGAGACTCAGCAAACTGGAACAAGCAGTTGATGTGACGGTTTCTAAACTGCTTAGCTACGTCACCACAAAATGGCGGGACCCAGTCTTATTACGGCCTAAAATTGCGGATATCAGAGACATAGCCGGCAAAGGAAAGGTCGCACTAAGGTTGTTGACAGAATTCGGGCTCAGTACACTCGTAAATGCGCGAAGCCTTGCGAATGAAGAACTCGTTGGCAAGCTGAGTAGAGCAATAGAGCCGTTGTTAGAGACTTACTACTCGTTGAAGGTTGCGCTGCAGCGATTGGATGAGACGTACCCGAGGGATCAAAGAAACTTGCGAGTATTGTCAGGACCACAGCCACAGTGCTCTTTAATCGTCCGAAAAAGCCTCCAGTACTCCTTCCAACAAAAGAACAACAAACTGCCAAAGCCTGATGCTGTGAGCGAGGGGAAATCTCCAGCGGGTGAGCCAGTTTCTAAAGTTGAATCAAGCAGCAGAGGCACGAAACCACCCGCAACTAAACCTAAACCGGCATTGAATGGCAAGGATGCTAAGCCAGTTGTAAATGGCGATCATAAAGAAGACAAATCACAGGTTGAAAGAAAAGCGTCCATCGAAGAGGAGGGTGAACGTCCAAGAACTGGTACGGTAGCACAAGCTATAGCAAAGGTGGAAAAAATCGGTCTTTCCCCTTCGAAGGCGGACAGTGAAGAGATCAGCTCTACTGCTATGATGTTAGGTCTTATTAAGCAGTCAGTAGAAGAGAATATTAAGCCCTCGGGGCGAAAATTCAGTCCAGGTACCGTGCGAAGACTTTGTGGAATGGATGGGGAAATAATCGAGGACGGTGTAGAAGGGGCGAGGACGGAGGGAGAGGTTCCAGTCTTGCCTCCACGCAGGCCGAGTACCCCTTCTAAAGGCGCTCCTCCACCCCCCGCGAGACGCGACAGCGGGGAGAGACTACAACACGTGCGCCAAAAGAGCCTGGAGAGATTCGTCCCCGAGGGGGAATCCCCACCAGTCACTAACGGCCCCCCTAACCCTCCTCCTAAACCTAAACTGGATCGACACAAGACCATGCGTAAGAGTTATAAGTACCCCATGCGGCACGAAAAGGTCCGATTACGCGACAAAGTCGAGGTACCGGAGTCCCCTACGGGAAAACGCAAATGTAACTCGGACCCTACGGACTTAGAAATGAGCCCTGAGGAAGACGCTAAACAACACCGGGCATCGGACTCGTTAGAAGGTAAAGTCCCGGAGAATGGCATCACGATAAACACGAACTCTGTTCACATCTCGGATTCCGATCTACCGACTGGGTTACGAGGGCAATCTACTATGACTCCTTTGTCACCCAAACTTGATTCGCCGAGCTCTCCGAAAAAATCCATCGTTCAACGGAGTAAATCATTCTCAAGGACTAAACCTTCCTCGACTAAGACAACCATGGTAGAGGAATCCGGTCTTGGGGATTTTATTTTATCATTCAGTGATAAAGAACTTTTAGAATTTTATAAATACGAAATCGATGCTCAGCTTTTTGTACTCAACGAGGCCATGAAAGGGCTATTTACCTCCGTCGACACCAGCCAGCCACCCAAGACTTTTGTATCGAACAGTAAATTCGTGGTATTGAGCGCACATAAGTTTATTTACATCGGAGACACGCTACAACGAAAGATATCTCATGATAAACTCGGTATGGACGTCACTTCAGCGACGGCTAAGTTATCTGAATGTGTGAAGACGCTTGTCCACGCAACTAAGATGGCGGCGCTCCAGTACCCTGCTATGAACCCCATGAGGGACCTGACTACTGCGGCGGCAGAGGTGTCCGAGGCCTCTATAGCACTACATAAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGTTATACCATCAGTAGTCCAGCGCTCAACCATCAGGAGTCCAGCGCTATGCTATACCATCAGTAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGTAGTCCAGCGCTCAACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGAGGAGTCCAGCGGAGTCCAGCGCTATGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTGACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGAGGAGTCCAGCGTTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCGCTATACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCCAGCGCTATACCACCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCTGTACCATCAGGAGTCCAGCGCTATACCATCACTGA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003882 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|SH3 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12026 all species →	CAS_C	Crk-Associated Substrate C-terminal domain	Domain	Interproscan
PF08824 all species →	Serine_rich	Serine rich protein interaction domain	Domain	Interproscan
PF00018 all species →	SH3_1	SH3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan
IPR038319 all species →	Homologous_superfamily	CAS, serine rich four helix bundle domain superfamily	Interproscan
IPR037362 all species →	Family	CAS family	Interproscan
IPR021901 all species →	Domain	CAS family, C-terminal	Interproscan
IPR014928 all species →	Domain	Serine rich protein interaction domain	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10654 all species →	CAS SCAFFOLDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007169 all species →	Biological Process	cell surface receptor protein tyrosine kinase signaling pathway	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0090527 all species →	Biological Process	obsolete actin filament reorganization	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for NY_Scal100_v1.47273.1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Scolanthus callimorphus tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Scolanthus callimorphus, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →