Gene detail

Detailed information of Ppa0G076030 in Paragorgia papillata

Genomic Location: Contig00089:722649...781532
NR annotation: XP_028405527.1, collagen alpha-5(IV) chain-like [Dendronephthya gigantea]
Species Paragorgia papillata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Ppa0G076030

ATGAACGCTAAGCGACCAATGTTGCCTGGAAGGAGTGCACAACGCTTCTTTGAGACGATGTTCCCCGTCAACGAAAAGACTCGTTCAGAAGTAACAGAGGACGGTGGACAAGAAAGATATGAGAAAGCTAGACGCGTCAAAGCAGGCCATTCAATGAAGGCACATTTATGTACTGCAGCTACTGCTATTATTGATTCGTTTATTATCCAAAAAGGCGTTCAAGGTAGTCGTGGCCCCAAAGGATATCCAGGATTTCCTGGTTGTAAAGGAGAAGAGATCTTACAAGATTTTCCAAGATCACACAAGATCTTACAAGATCTTGACAAGATTCTCACAGTGGGGGAAGATGGCACTCTAATTGGTTCTACAGGTTTGCCTGGTTTGCCTGGTCCAAATGGAGATCGCGGTCCAAAAGGTCAAAAGGGCGAGCCAGTGTCTGGTGTAGCACCAGACTTGAAAGGTGAAACGGGAGCTCCTGGTCCGAAGGGTGCTCAAGGAATGCAGTGTTCCGAAGTATGGTATGGCAGCGCACGATTAACTGCATTCTGGGGTAATGTTGGTGATGAAGGACCTGGAGGACCCCGGGGTGACAAGGGAGAAGTTGGAGATAAAGGATTTCGTGGGCCAACAGGTGACGTGGGGACTATAGGAGACTCGGCAAAACCGGATGGGGAAAGTGGTCAACCAGGAGGCGAGGATGGTGAAAAAGGCGATCCTGGTGAAGATATAATTCTTTCTGGAAGAAAACCGGAGAACCTGGGTGAACCTGGTGATAGAGGAGATGAAGAAACTATTGGCTTTCCAGGCATAAAGGGGGTACCGGGTAACCGTGGATTCCCAGGACCTCGTGGCGATGAAGGTTCAGATGGAAAACAGGGATTCAGAGGTAATCCAGGAGATCGAGGACCGCAAGGCAATCCGGGCAATATTGGTTTAGAAGGCGAACGTGGCGATAAAGGAAGAAGGGGACCGCCGGTATGTTTCGGACCGCTCGACCGCTCTGCCCGCGTGGACAAAAACCCTAAAGGAAAACAAGGTAAACAAGGACAAAAAGGTGAAATTGGATCTCCTGGTGATCCAGGAGATCAAGGAGATAGTGGCGACCAGGGTAACCGTGGAGCTCTAGGAGGGCCAGGAGATCCAGGCGTAAATGGAATGCAAGGTGCTAAAGGAGTTACTGGTCCGAACGGTAGAAAAGGTCAGAAAGGTCGTATGGGAGATGATGCTAAATCTATTCCCGGACCGCCAGGCATGGATGGAAAACCTGGGCTAAAAGGATTTCGAGGAGGTATTGGAGATCCTGGACCTAAAGGAATTGTTGGTCTACCTGGCAAAGCACCAACTGCCAACTGTGATATACCTGAACAATGTCGTAAAGGTAAACAAGGTCAGCCTGGTCCTCGAGGTTCAATTGGAGACGAAGGAGGCACTGGAAATCAAGGACCGATTGGAGAGAAAGGTTTTCCTGGCGGCAATTGTCCTTCATGTCCACCTGGTGATAAAGGTGCTTCAGGTGAAAAAGGAGGTCCTGGTTTCCCTGGAGCGAAGGGGGATAAGGGTACCCCAGGAGCTAGTGGAAAACCTGGAGAGAGGGGCATGGCTGGATTCATGGGATCCAAAGGGAATCCAGGGGAAAAAGGTTATCAAGGTTTTCTTGGTGCACGTGGAGCAAAGGGTGCAAAAGGTGATCCTGCAATACTTGATAAACCTCTTACAGTTGGTGAAAGTGGCGATGTTGGGGGTTCTGGTGATCAAGGTCCCAAAGGTTTGAAAGGTTTGGAAGGACGAAATGGAGTAGCTGGTATCACTGGCGTTTTCGGTGAGCGAGGTGATCAAGGACAAAGAGGTGAAGATGGTATTCCGGGAAGAAATGGCGCTCAAGGAGACCCTGGAGATTTTGGATCAAAAGGTCCCAATGGGAAACCGACACCCGGAGATCCTGGACCCAAAGGAGAGACTGGAGACGAAGGCGAACGGGGTGATGATGCAGGTTTCATTGCACTAGAATCGCAAGGTCGTGGGTTTAATTCCTGCCAGAAGGCCTGTCAACCAGGAGACCCAGGAGATAATGGATCTGAAGGTGAAGGAGGTAAAAAGGGACCAAGAGGAGATAAAGGAGTGGAAGGATCACAAGGCAGCGTAGGTGATTCTAGTGTTGGGCCCCGGGGGCGCAATGGCTCTCCTGGAGATAACGGTGCAATGGGTGATCCTGGAAATAATACAATAGGACAACCAGGAGAACCTGGTGCAGACGGAAAGGTTGGAGATCAAGGGCCTCCTGGTGAGACGGGAGATCCAGGTAGTTCTAGTGATGCAGTTGGCAAGAAAGGTGATCCTGGTAAAATTGGAGATGGCCCCAGTGGTCCACAAGGACAAAAAGGAGAAAAGGGAGACCAAGGAACTAATGATTGTGGTGGCGTTCTCGATGTTGCCTTTATCGTTGATTCATCTGGTAGCGTTAAAGATAATTTTGACACAGTAAAAAAATTTGTGAAAAAGTTCATTGATGCCTTTGATATTGCTGAAAACAGAACACGTGCTGCATTGATAACTTTTCAAGACCGTGCCACCATTCAATTTGGCTTTGTAGATGAATTCGACCCCGAAGTTCTAAAATTATTTGTCGATAGAATTATCCATTCTGGTGGGCAGACGTTTATTGATAAGGCACTAATAAAAGCCAACGACGAAGTCTTTAATACAGCCAATGGGTGGAGGAATGAGAACTCGTTATTGATTGTTTTAACTGATGGTAACCAAACAACCACAAAAGGGAAGTATACTCCTCTAGACCAGGCTTCAGAGCCTCTAAAAAAGAAAGGTATCCGCTTGGTTACTGTTGACGTCGGCAACATCAATGAACAGCAGATGAGGATTCTTTCTCCTGCAGACAAAGATCGATTTTCCGTCAACAATTTTACTGAATTGTTACCTCTTGTACAGAAAATGATATCCAGTAATCTTTGCCCAGATGGAAAGCCTGGTGAACCTGGACCAAAGGGATCTGAAGGAAAACCTGGCGAGCGTGGAGATAATGGAAATCCTGGAATGGATGGCCAGCCTGGTGCAAAGGGCGTTACAGGTGCCCTAGGGACTGATGGGAGGCCAGGAAAGGATGGAAATAGGGGAGAAACTGGAGATCAGGGTCCAAAGGGGATGGTTGGACGTGCACCTCAACATGCTGGTCCAAAAGGTGAAAAAGGCGATACAGGGGACTTTCCGCCAGGTCCCCGAGGCGATGAAGGATTACCTGGCGTTGTTGGTGAAATTGGTTCACCAGGCGACAAAGGCATCGAGGGAGCATCAGGAAGCAAAGGCGAAGCCGGACCTCCCGGGAGCGACGGAGCAACAGGTTCAGAAGGTCCAGAAGGTCTAGTCGGTTCACTAGGTGAACAAGGATTTGGTGACCCTGGTAATCCTGGACAAGATGGCCAAGAAGGTCAAAAGGGGGAAAAGGGAAAAGTTGGAATACGTGGAGATTCGGGAGATAAGGGAACGGTTGGAAGAACAGGACATGTCGGTGCAGAGGGCGATAGAGGCATGCAAGGCGATGTGGGTCAAAACGGAGACTCTGGAGAGCCAGGTGATAAAGGTGCAGTTGGTGATGTAGGGGCGAGAGGACCACCAGGGGCTGATGGAAAACAAGGACCAGACGGAGACAACGGAGATCCTGGCAATGTAGGTGTATTTAGTGGGGGACGTGGATTTACTGGTGGACCTGGAGACCCAGGAAAACAAGGACCGAAAGGCACAGTGGGTGACTCTGGGGCGAAGGGACCACCAGGACAACTTGGCAATAAAGGTGATGCAAGTGATGTTGTTGGTCCACCTGGTGAGCAAGGAGATGATGGTGTCCTCGGGAGAAAAGGTGCTAAGGGACGTAAAGGTAGTGACGGTCATCCAGGGTCTGTTGGCGATTCAGGAGATGATGGAGCACAGGGTGACTCTGGGTCTCCTGGTGGTGGTGGTGATAAAGGTTTTGTAGGATCTCATGGTCTACCGGGGCGAAAAGGTATTAAAGGCGTGAAGGGACTCTCTGGTCCTGTTGGTGATAATGCACGACATGGATATAAAGGCAATGTTGGTGAATCTGTGATAATCAAGGGTCCACCAGGACAGAACGGATTTCAGGGAGAACGGGGACCAAAAGGAACAGATGGTGAAAATGGCAAGCCCGGTGTACCAGGTCCTGATGGCGAAGCTGGCTCGAAAGGAGATTCAGGCGCTATAGGGGAACCAGGTTTACCTGGAGATCCAGGAACACGTGGACCTCCTGGGCAGTTAGGTCCTCAAGGAGAACTTGGTCGGAAAGGAGAACCTGGACCCGCTGGATTTGTTGGAGATCAGGGTCCACCAGCAAGTGCTTCCGGATTTTATGTGACACGACATAGTCAAGATCAGACTCCACCTGTGTGTCCAGTTGGTTATGTCAAAATGTGGGATGGTTACAGTCTACTGTATGTCCAAGGTAACGACAAGTCGCATGGTCAAGACCTGGGACAGGCTGGTTCCTGCTTACGCCAGTTTTCCACAATGCCATATCTCTACTGTAACATCTTCAAGAGGTGCAATCTTGCCTCAAGAAACGACTATAGTTACTGGCTCTCATCTTCTAAGCGAATACCTATGATGCCTGTTGACAATGACGCTGTCGAACCTTATATTAGTCGCTGCTCGGTTTGTGAAACTCCCGGACCTGTCATGGCTGTTCATAGCCAAGAGCAATCACTTCCTTCGTGTCCAGCAGGATGGCACGGACTTTGGGATGGATATAGTTTCATCATGCATACTGGTGCTGGAGGTAGTGGCAGTGGCCAGAGTCTTTCTTCACCAGGATCGTGTCTTGAAGCATTCCGTCCTAATCCTTTCATTGAATGTCACGGTCGGGGAACGTGCCATTACTTTGCCAATAAATATAGTTTCTGGATGGCTACCGTGAAACTTGAAGAAATGTTTACTTCCCAATCTCCTGAAGTTTTAGCTGAGATTAAAGGACAAGATCTTCGTTCCCGTGTTAGCCGATGTCGTGTTTGCGTTCGTCCGCCAAAATCAACACGCCCTCAACCTCATCCTGGCTTTTGGGAAAATGTCAGCGAACCAACTACGCATTCGGAAGGCGCTACTGACGCGAAAAACTTGCTGAGACAAGCTGGATTCCAATAA

Transcript

Ppa0G076030

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7SIB3	Collagen alpha-2(IV) chain (Fragment) OS=Bos taurus OX=9913 GN=COL4A2 PE=1 SV=1
P27393	Collagen alpha-2(IV) chain OS=Ascaris suum OX=6253 PE=2 SV=1
P02463	Collagen alpha-1(IV) chain OS=Mus musculus OX=10090 GN=Col4a1 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001701 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01413 all species →	C4	C-terminal tandem repeated domain in type 4 procollagen	Domain	Interproscan
PF00092 all species →	VWA	von Willebrand factor type A domain	Domain	Interproscan
PF01391 all species →	Collagen	Collagen triple helix repeat (20 copies)	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR001442 all species →	Domain	Collagen IV, non-collagenous	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan
IPR050149 all species →	Family	Collagen superfamily	Interproscan
IPR036954 all species →	Homologous_superfamily	Collagen IV, non-collagenous domain superfamily	Interproscan
IPR008160 all species →	Repeat	Collagen triple helix repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24023 all species →	COLLAGEN ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005201 all species →	Molecular Function	extracellular matrix structural constituent	Interproscan
GO:0005581 all species →	Cellular Component	collagen trimer	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	Interproscan
GO:0030020 all species →	Molecular Function	extracellular matrix structural constituent conferring tensile strength	Interproscan
GO:0030198 all species →	Biological Process	extracellular matrix organization	Interproscan
GO:0031012 all species →	Cellular Component	extracellular matrix	Interproscan
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	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 Ppa0G076030.

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 Paragorgia papillata 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 Paragorgia papillata, 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 →