Gene detail

Detailed information of XP_066919125.1 in Clytia hemisphaerica

Genomic Location: NW_027103286.1:1638569...1655817
NR annotation: XP_047141827.1, clathrin heavy chain 1 [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

XP_066919125.1

ATGGCGGGTCAACTTTTGCCCATACGATTTCAAGAGCATCTCCAGCTTCAAAATGTTGGTATCAATGCTTCAAACATTGGGTTTTCAACCCTTACCATGGAATCAGACAAGTATATCTGTGTTCGAGAAAAAGTTGGGGAACAATCACAAGTTGTTATTATTGATATGGCAGATGCCAACAATCCAACCAGGAGACCAATTTCCGCAGATTCTGCCATCATGAATCCCATCTCTAAAGTCATTGCTTTAAAAGCTGGCAAAACCTTGCAGATTTTCAATATTGAGATGAAAAGTAAAATGAAAGCACACAATTTGACAGAAGATGTTATCTTTTGGAAATGGATCAACGTCAACACATTAGGTTTAGTGTCAGAATCAGCTGTCTACCATTGGGGTATGGAAGGTGACTCAAGCCCAGTCAAGATGTTTGATAGACATCAGTCTTTGGCTGGATGCCAGATTATTAATTACAAGATTGACCACAGTGGACAGTGGCTTCTTCTGGTTGGTATCTCTGCACAACAGAACAGAGTTGTCGGAGCAATGCAATTATACTCTGTAGAAAGAAAAGTCAGTCAGCCTATTGAAGGGCATGCTGCTACCTTTACTCAATTCAAAGTTCCAGGAAATGCACAACCTTCCAACATATTTTGTTTTTCTGTACGTGGAGCTACTGCTTCTAAAATCCATGTCATTGAAGTAGGCACACCTCCAGCCGGAAACCAACCCTTTCCAAAAAAGGCAGAAAATATTTTATTTCCACCAGAAGCGGACAAGGATTTCCCAGTCGCTATGCAAGCCAGTCAAAAGTATGGAATAGCCTATCTTGTCACAAAGTATGGATACATCCACTTGTATGACATTGAAAGTGCTCAATGCATTTACTCAAATCGTATTAGCGGAGAAACCATTTTTGTAACTGCCTCATACGAACCTACAGAGGGGATTATCGGTGTCAACCGAAAAGGACAGGTTCTATCAGTCAGTGTTGATGAAGATAAGATGGTTCCATTTTTGATTCAAGTTAAACAAAACGGTGAGCTTGCACGGAAACTGGCTGAGCGTTGTAATCTTCCTGGTGCAGATAACTTGTTTGTTCAAGCTTTCAATGAAAAATTTGGGATGGCTCAATACCAAGAAGCGGCCAAGATTGCAGCTAAAGCACCAAAGGGTATTTTGAGAACTCCAGAGACAATACAAAGGTTTCAGCAACTCCCATCACAACCTGGGCAGACTTCTCCTTTACTTCAATATTTTGGAATTCTTCTCGACCAAGGACAATTGAACCGATATGAGTCAGTAGAATTGTGTCGTCCAGTACTCATGCAAAGCAGAAAACAATTGATGGAAAAATGGTTGAAAGAAGACAAGCTTGACTGCAGTGAAGAGCTTGGTGACTTGGCGAAACAGTTTGACAGCACATTAGCATTATCTGTTTATCTGAGAGCTAATGTTCCAGACAAGGTTATCATGTGTTTTGCTGAAACTGGGCAATTCCAAAAGATTGTCTTGTATGCCAAGAAAGTTGGACACACTCCTGATTATGTTATGCTTTTGAGAAATGTCATGCGATCCAACCCAGAGGCTGGAGCGCAATTTGCTGGCATGCTCATTCAAGATGATGAGCCTCTTGCTGAGCTCAATGCGATTGTTGATGTATTCATGGAATACAATATGATTCAACAATGTACCTCATTCTTGTTGGATGCCCTGAAGAACAACAGACCATCTGAAGGTCCTCTTCAAACTAGACTCTTGGAAATGAACCTTATGTCTGCTCCTCAAGTTGCTGATGCTATCCTTGGTAACCAAATGGTGACACACTACGACCGTGCACATATTGCTCAACTTTGTGAACAAGCTGGTCTTCTTCAAAGAGCCTTGGAACATTACACTGATATCTATGACATCAAACGAGCTATTGTTCATACACAAGTTTTGAATCCAGAGTGGCTTGTAAACTATTTTGGTACATTATCGGTTGAAGACTCAATTGAGTGCGTCAGGCAAATGTTGACCCATAACATCCGTCAAAACTTGCAAATCTGCGTACAAATTGCATCCAAATACCACGAACAACTTACCACTACAGCCCTCATTGAGATCTTTGAATCATTCAAAAGCTTCGAAGGATTATTCTATTTCCTTGGTTCCATTGTCAACTTTTCTCAAGAAGCAGATGTTCATTTCAAATATATCCAGGCTGCATGCAAGACAGGTCAGATGAAAGAAGTTGAAAGAATTTGCAGAGAAAGTAATTGTTACGATCCGGAACGAGTTAAAAACTTCTTGAAGGAAGCCAAACTGACTGATCAACTTCCATTGATCATTGTCTGTGATCGATTTGATTTTGTTCACGATTTGGTACTGTACCTTTACAAGAACAACTTGCAAAAATACATTGAGATCTACGTGCAAAAGGTAAACCCATCACGTCTGCCCATCGTTGCTGGTGGGCTGTTGGATGTTGACTGCACCGAAGATATCATCAAAAGTCTCATCCTCTCCGTCAAAGGACAATTCTCTACTGACGAACTTGTCGCAGAATGTGAAAAGAGAAACCGTCTTAAACTCCTCCTTCCATGGCTGGAGTCACGCATTCACGAGGGATCTGAAGAACCTGCTACCCATAATGCCTTGGCTAAGATCTACATTGACTCAAACAACAATCCAGAACGATTCCTCAGGGAGAACCAGTTTTACGACAGTGTGGTTGTTGGCAAATATTGTGAGAAACGAGATCCTCATTTGGCTTGTGTTGCTTACGAACGTGGACAGTGTGATGAAGAGCTTATTCAGGTTTGCAACGAGAACTCTTTGTTCAAGAGTTTAGCCAGATACTTGGTGCGTCGAAGGAATCCTGACTTGTGGGCTACAGTCCTCGTCGTTGAAAACCAATACCGAAGACAGCTCATCGATCAGGTGGTACAAACTGCCCTCTCAGAGACACAAGACCCTGAAGATGTGTCAGTCACCGTCAAAGCTTTCATGAGTTCTGATTTACCCAACGAACTCATCGAATTATTGGAGAAGATAGTCTTGGAAAACTCTGTCTTTAGCAACCACAGAAACTTACAAAACTTGTTGATCCTGACGGCCATAAAAGCCGATCGTACCCGCGTCATGGAGTACATCACTCGTTTGGATAACTACGATGCTCCCGACATCGCAAACATCGCTATCGGAAGTGAACTTTTCGAAGAAGCTTTCGCTATTTTCAAGAAATTCGACGTCAACACATCCGCTATCCAAGTCTTGATTGAAAACATCCAAAATCTTGACCGCGCGTACGAATTCGCTGAACGCTGCAACGTACCTGAAGTGTGGAGCATCCTTGGTAAAGCTCAGCTCGATCAAGGTTTGGTCAAAGAAGCCATAGACTCCTACATCAAAGCTGATGATCCTTCTTCGTACCAAGATGTCGTCGACGCCTCCAAGAATGCTGGCAACTACGAAGACTTGGTCAAATTCTTACAAATGGCTCGCAAGAAGGCCAAGGAAACCTTCATCGATACCGAACTTATTTTCGCTTTCGCACACACCGGACGACTTGCTGAACTGGAAGAATTCATTTCCACTCCCAACCACGCCAACATCGGACAAGTCGGTGAGCGTTGTTTTGAACAGAAAATGTTCGAGGCTGCTCGCATCCTGTTCAACAACATCTCCAACTTTGCACGATTGGCGTCCACTTTGGTTCACTTGGGTGAATACCAAGCGGCCGTTGATGGGGCGAGAAAAGCTAACAGTACTCGCACATGGAAAGAGGTCTGCTTTGCTTGTGTTGACGGTAAAGAATTCCGATTGGCTCAGATGTGTGGTTTGAACATCGTCGTTCACGCTGACGAGCTCGACGATCTCATCAAATATTATGAAAGTCGTGGTTACTTTGAAGAATTGATCACACTGATGGAAGCTGCTTTAGGTTTGGAACGCGCACACATGGGAATGTTTACAGAATTGTCCATCCTTTATTCTAAATATAAACCAAGCAAGATGAAGGAACATCTCGATCTTTTCTGGTCACGTGTCAATATTCCAAAGGTTCTGAGGGCATGCGAACAAGCTCACCTATGGTCAGAGCTCGTTTTCTTATACGACAAATACGAAGAGTACGACAACGCTATTGTTACCATGATGAAACACCCTACGGTCGCTTGGAAAGAAAATCTATTCAAAGATGTAGTTACCAAAGTCGCGAATATTGAACTCTATTACAAAGCATTACAATTCTATTTGGACAATAAACCATTATTAATTAACGATTTACTAGTCGTCTTAACACCAAGGATGGATCATACTCGCGCCGTCAACTTTTTCATCAAAGCTAAACATCTTATGCTGGTCAAACCTTATTTACGATCAGTTCAAAACCATAACAACAAAGCAATCAACGAAGCGCTAAATAATCTTTTAATCGAAGAGGAAGATTATAACGGGTTACGCGCCTCAATCGATGCTTTCGACAATTTCGATAATATTCAATTAGCTCAAACGATGGAGAAGCACGAGTTGATCGAGTTCCGTCGTATCGCTGCTTACCTTTACAAGGGAAATAACAGGTGGAAGCAATCTGTCGAACTTTGTAAGAAAGATCATCTCTACAAGGATGCCATGGCTTTCGCTTGTGACTCTCGAGACTCAGAGGTTGCAGAAGGTTTATTGCAATGGTTCTTGGAGATCAACAAGACGGAATGTTTTGCTGCCACTCTCTTCATGTGTTACGATCTCTTGAAGCCTGATGTCGTGTTAGAATTAGCCTGGAGACACAACCTGATCGATTTTGCGATGCCTTACATGATTCAAGTCATGAAAGAATACTTGAACAAGGTTGACAAATTAGCAGAAACGAGCGCCAAACGCGAAGAAGAAAAAGACACACCTGAGCAACCAATCATGGGTGTTGAACAATTGATGATCACTTCTGGACCAGCCTATCCGCAACAAAACATGTACGCACAACAACCCGGTATGGGAATGCCACCGCAGGGAATGCCACCACAAGGAATGCCAAATATGGGCATGCAACCGGGAATGGGTCAGCCAGGCATGCCACAGGGTGGAATGCAGCAAGGATTTTACTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q68FD5	Clathrin heavy chain 1 OS=Mus musculus OX=10090 GN=Cltc PE=1 SV=3
P49951	Clathrin heavy chain 1 OS=Bos taurus OX=9913 GN=CLTC PE=1 SV=1
Q00610	Clathrin heavy chain 1 OS=Homo sapiens OX=9606 GN=CLTC PE=1 SV=5

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004973 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13838 all species →	Clathrin_H_link	Clathrin-H-link	Repeat	Interproscan
PF00637 all species →	Clathrin	Region in Clathrin and VPS	Repeat	Interproscan
PF01394 all species →	Clathrin_propel	Clathrin propeller repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000547 all species →	Repeat	Clathrin, heavy chain/VPS, 7-fold repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR016025 all species →	Homologous_superfamily	Clathrin heavy chain, N-terminal	Interproscan
IPR016341 all species →	Family	Clathrin, heavy chain	Interproscan
IPR022365 all species →	Repeat	Clathrin, heavy chain, propeller repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10292 all species →	CLATHRIN HEAVY CHAIN RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0030130 all species →	Cellular Component	clathrin coat of trans-Golgi network vesicle	Interproscan
GO:0030132 all species →	Cellular Component	clathrin coat of coated pit	Interproscan
GO:0032051 all species →	Molecular Function	clathrin light chain binding	Interproscan
GO:0071439 all species →	Cellular Component	clathrin complex	Interproscan
GO:0006898 all species →	Biological Process	receptor-mediated endocytosis	Interproscan
GO:0045334 all species →	Cellular Component	clathrin-coated endocytic vesicle	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K04646	CLTC; clathrin heavy chain	-	Exosome	ko04147	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066919125.1 across 40 RNA-seq samples of Clytia hemisphaerica. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

40Samples

40TPM > 0

16Conditions

291.9Max TPM

162.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mature medusa	5	5	135.37	169.81
medusa · Experiment Condition A1	4	4	152.71	161.24
medusa · Experiment Condition A2	4	4	177.57	179.77
medusa · Experiment Condition A3	4	4	89.62	91.29
Early gastrula	2	2	265.39	283.23
Planula 24hpf	2	2	272.48	291.94
Planula 48hpf	2	2	184.17	207.26
Planula 72hpf	2	2	153.04	162.80
Primary polyp	2	2	164.99	165.53
Gastrozooid	2	2	129.64	143.91
Gonozooid	2	2	185.26	191.73
Stolon	2	2	184.22	206.63
Baby medusa	2	2	158.30	163.20
medusa · Experiment Condition B1	2	2	130.53	145.73
medusa · Experiment Condition B2	2	2	155.90	159.82
Mixed	1	1	178.30	178.30

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR2816251	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	169.81
ERR2816250	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	161.29
ERR2816249	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	138.07
ERR2816248	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	115.11
ERR2862245	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	92.55
ERR3299475	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	161.24
ERR3299476	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	159.75
ERR3299478	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	146.94
ERR3299477	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	142.90
ERR3299482	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	179.77
ERR3299481	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	178.66
ERR3299479	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	176.85
ERR3299480	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	175.01
ERR3299486	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	91.29
ERR3299483	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	90.80
ERR3299484	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	88.65
ERR3299485	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	87.74
ERR2816230	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	283.23
ERR2816231	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	247.55
ERR2816233	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	291.94
ERR2816232	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	253.01
ERR2816235	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	207.26
ERR2816234	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	161.09
ERR2816236	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	162.80
ERR2816237	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	143.29
ERR2816238	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	165.53
ERR2816239	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	164.45
ERR2816241	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	143.91
ERR2816240	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	115.37
ERR2816242	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	191.73
ERR2816243	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	178.79
ERR2816245	Stolon	not recorded	Stolon	not recorded	ERP110164	206.63
ERR2816244	Stolon	not recorded	Stolon	not recorded	ERP110164	161.80
ERR2816247	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	163.20
ERR2816246	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	153.41
ERR3299472	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	145.73
ERR3299471	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	115.33
ERR3299473	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	159.82
ERR3299474	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	151.98
ERR2862244	Mixed	not recorded	Mixed	not recorded	ERP110164	178.30

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Clytia hemisphaerica 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	13	XP_066916521.1	0.910413636012795
Negatively correlated	11	XP_066912068.1	-0.825657777509252

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Clytia hemisphaerica, 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.	ready	open →
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 →