Gene detail

Detailed information of CAB3984942.1 in Paramuricea clavata

Genomic Location: pcla8_s000831:11448...17247
NR annotation: CAB3984942.1, zinc finger ZIC 4 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A048512

GTCAAGCTGATAAAATGCTGGTCGCGTATAATAATATTCTGTGAAACGGATTGACTGAGGGAGTTATCTTTGGATTCTTAGCTACGGTTGGAATTAATAACAGCGACATAGCGATAGCCAAGGTACGAGATAAGTTTGTATACTTGTATGATGGTCGGGTGATCAGAATTCGGCAAACGTTTGATATCAGATGTGACGATAGATTAGCAACATTTGAACAGGCCTATTTAAAACGTTTCccatttgtttttcaaaatgatTTAGCCGTCGGTCTAAAATTTACGAATTGgaattacactaacacaaatcAAATGTTATTTCTCGCGATGGGTGGTAGAAAACAACGATTTCCTGTCAAAATTCTGCTATCTACGAAGAAAGTTGATACTCGCACatcatttgaagagtaaataatgCTTCAGATTTAATAGGAAAGGGTTTTTGATATATGTTGTCAGTGATGAGGGTTGTTATAGGCTAGCAATTTGAATATAGCtaattcaaacgaaactttaaaccttaaactctaactCTCTAAGCACGAAAAGCACAATGGTGGGAATGCATAGTCCGCCTTTAAGTATTTCACTGCGGgctaaaggcccatttccactcaggcaAATTTTCTGCAGAAGgaacattttttaaaatgtgattGACCGAcgcaaattttccgtcggaaaaatttgaagttgaaaatgttcaacttttaacaatgatatttgcagaaaattttccgtccGTGGAAATGTTTagttgagtggaaatgggccttaaccGTCTGCCACGCAGCTATTATTAATTGTGATTTTCGAGCTCCTTTTCTTGACTTATGTATATTTATACAGTTCAAGGGCTGGCTAGCACCATTATTTTAAATCTTGAAAAAGTGAATTATCCAACATTTCCAGTTAaattttgctcaattttttCAATCTTTCAATGTTACTGGTACGGTGCTGTCTTACGTGAATAGAGACCCTGCATACCTCAATTTTCTAAAGGCCCTTCAATCGCTTCGTTTGTTTTCTATAAACGGGTAAGTTTATTATATAAGTGTTAAAACGGCGTGATTTAGGTGCCTCTGTGTTTTTTTAGAAGTACAAAGCGGTTAGCCCTTATTCCCTAACAGTTGAAAGCCGGCTTTGTCAACTTATCGCGTAATTTGAATTCCCCCAATTTTGAGGGGTCTATGCAGGAATCAGAATTTCTTACCTATCCCTGGTTCGAGTATTTCGGATACATTTCCTACGCTCTACGACTGTCTCTGGAACGGGAAAATGCCAAGAACTGATTCTGACAAAAATTACGGTAAATGTCAAAACTAATATATAGTATCAATAATCACAATATTGTTATGAGTGTTATTTGTTATGACAGATTTATATTACTAGAATATTTCAATTGATAGTTTAAATTTGAATATAGTTACCGgcgttttagtttatgtataaTATCTTGTAGAAATTTTTGGGGCCCGTTTTTGATGTCTCTTTCCATCACTGCATCAGGGAAAAATTAGAATTTTGTCGGGGAAGAGCTATGTTTTATAGTATGCTGTAGCAAGACAATTGTATTTTGCTGCACAGTATCCTCAAGATGCAGGAAACGCCGTTTCAGATACTCAAACTCAGGCAGAACAAAAGTTTTAAAGGCTAAAGCCGTTGGCGTTGCAACTTAGTTAGATCAGTGCTTAGTCCCCCTGTCGTGATGCTGTTAGGTTTGCGGTAGGTTATTCAATGTCAATAATCCAGCTGTGTTTTCAAAAAAAGTCTTTAGAATTTCTTAAACTTGGTGGGGGTCCAACGTGAGCGTCCCGCGATTGCCTTATTCTGCCAACTGCACCGCATGCTGTTCTAGCACTGCGTTCACTGCGACGTTTACTACGTCCACGGCTAAATATGTGATCGGGGTATCGATGACCGTCTGCCATGCAGACGCAGGTTACATAAGCAATAActtttactggacctccagggagaacagtttgaaaATCCTGCAGTCTTTTGAAGATTgatgaaaaatatttcattcaGATTGCTTCATGAAAGAGGGAAATATTAAGTTGTGACTATAACCAATGACACGGCCGCTTTAAATTTTAGCTTAAAACAGTTATCTTACAGCAGCTATGGTTTTCTACATTGCATGCCATGGGGGAACGAAAAAAAGGCAATTCATAACAATTAGGTAATAGAgaataaacaattaaatgacCATGACCTCgcaattaataaaaagaaactttaatttataaatactgaAGTTTAATCTTGGACTAGGTTAAACAATCAATGGACAATTTTAAGAAACTTGAAAAAATCGCTACGCGGGAATAACCGGTCCCAGATCTTTAAAATTTATTGTCAAATCTGTGATGTTTATTAGGGTATACGCGTAAAAATGAACAAAACGAATATCCGGACAGGCTTGAACAAGATCAAGGTTGTGCTTCACCCTTTATAATTATAGAGAACATGTTGTCAGCAATGCCAATGttacagtattgttacaactggacaatgctgtaacaacattgtAATGTCGACAACTTGTTCTTAGGGTGAAGCACAACCGGCTTTTAGTTGATATATAGTGTGTAATATACTAGTTTCGATGTATGTTTAGAAACACAGTGTAACTAGATTGTTCCCGCAAAACAGTATGACAGCAACAGCCAATGCAAGATCTTTGTATAGTTTGTTAAACAGTCGTGTTATGAAATATCATACGTTAATTTCTTGCACGGGCATGTTAAATTATATGTAAGCAAAGTCAAGATAAAATGCTGGTCGAGTGTAATAATATTCCGTAAAACGGATTGACTGAGGGGGTTATCTTTGGATTCTTAGCTACGGTTGGAATTAATAACAGCGACATAGCGATAGTGAAGGTACGAGATAAGTTTGTATGGTCGAGTGATCAGAATTCGGCAAGCGTTTGATATCAGATGTGACGATAGATTAGCAACATTTGAACAGGCCTGTTTAAAACGTTTCATATTTGTTTGTTGAAAATGATTTTGCTGAACCGATAGTCTAAAATTTACGAATTACATTATTCATTAACACAAACCAAATGTTATTTCTCGCGATGGGTGGTAGAAAACAGCTATTTCCTGTCAAAATTCTGTTATCTACGGAGGAAGTTGAGCCGAGAAAAATAAACTTAACACACATTTGATACTCGAACATGatctgaagagtaaataatGCTTTGGATTAGGAAATGTTTTCTGATATAGCTTGTAACAGATAGGCaatttaaatataaccgaaaaCTATAACTGAGGTTTTTTCATGCTTCATCGTTCTCTTTTGTAGGTTGAGATATTTTAAAATACCAAAGATCATGCATGGTTTTATATTACATATGAGGTATCTCAACCACTGTCACAAAATTAAGTCTATAAATCAGAAATAAAACATATTTTGTTCGGAATTAGAATTCTTCAATGCCAGGCATCGCTAATTATAAATTTGTTACACTTGTGCATAAACAGTGTTGGGTAATTCAAATTCGGACCATCGGCAATTAAGCTTTAGCAATTTTGTCGCAGTGGGTTACCAAGTTCCGGTTAATTTCATTAAACTGTAAAACAAACGTCTGTCGCTTTGAAGCTGTCATTCAACGGCGATACCGTCCAATTAAATTGATCAATTCATACAAGTGTGAAAGCATTCGCGAAACATTTgccatttcaattttcaaacagTCAGTTTGGTGAGAGTTAGTGAACAATCTGTGTTGCCGGTGTCTAATTTACATATCATTGTTTGAACTTATTATTTATAGTCTTTCGCAAGAAACGGAAGGATGGCAAGGTTTGACTATATTACGCAGCAGAATGTTTATACAAATATGGCTTTTCAGCGCGTAGCAAGTGAAGCAGAAGAACAACAGACTTTAAGTTTTCATCCTACCCTGTTTGTTGATGGCGCAACAGCACATCTTCAAGGTTTAAACGTAGTTGGTAGCGGCCCAACAGCAGCGCACGGCTATCCTGTTGATTTGAATCATACAGCGAGCTCATCTCAAGTGGCATATACAAGCCCGCAGTCAAATTACGCAGGTATTCCTCCCTTTTCGTCGCTACTCACGGCAAGAGATCTACTCCTGAGGAGAGAACATCTCCCCGCAGCGCAACTTGCCAACAACACAGAACAAACATTTCATCATGGACTACAAGCTTCGGTTATCACATCACCATTTCAAAATCATGGCCTCAACCTCGCCATTGCAAGCCAACTGGCGAACAATTCAACACCACCAAACACACAGGAAGAGAACACTTCGTTCACAGCATTGCGTCCCGTGAATCAAGCAGAAAGACTCAACGGTACGGTCACAACAGATGCGACAACTCATGTCAACCTTCCTAGCCCAACAATCATGGTTTCAGCAGCGTCACATGCAACTAGCATCAACAATATGAAATCTGTGAACGTTGTAAACTCTCATGTCGATACTCTTACAACAGGCGCATTTACTCCCTACTTTAAACCACAAGAAATCAAACAAGAATTGGTCTGTCAGTGGTTGGTCACAAAAGGTAAAGTCGGTAGTTGTATTTGCGGGTGTAATTTCACTAACCTAGTTGATCTTGTCAAACATTTATCAAACGAACATGTAGCAAACCCCGAGAGTTCAAGCCATGTTTGTCGTTGGGATAAATGTAGTCGTGATGGTCGTGCATTTAAAGCGAAATATAAACTGATCAACCATCTTCGTGTGCACACAGGAGAGCGACCATTTTCATGTCCGTATCAAGAATGCGGGAAACTTTTTGCGCGCTCGGAAAACCTCAAGATACACAAAAGAATACACACGGGCGAGAAACCTTTTGTTTGCGAATTTGAAGGATGTAGTCGACGCTTTGCCAACTCGAGCGATCGCAAGAAACATTCACATGTCCATACTTCGGATAAACCGTACTCCTGTAAGATTGGTGGGTGCGAGAAAAGTTATACTCACCCAAGCTCGTTGCGCAAACATATGAAAGCTCACTTGGCCGTGAAGGAAGAGAATATGGTGGAAAATACATGTACGATACTTCGTGGCGAGACAGAGGGATTATGTACGTCTCTGGCAGCAGGAGGTGCTTGGTATTGCGCTGAGAAACCCGTGTCATTATCAGTTAGCGCAGCAGGAAACAAATCGAACGGCAATACATCGCCAAAGAACCAACTTAGTCCAATTGTAAAAAACAGAGTTTAGAGGGGACAAAGTCAACTGCGTTCAATTTACACACTGTGATTTGTCGGCCCGATTTCAGACACACTTTTATGATATTTGAGGTGAATTTAAAGTCATTTGActaaatcatgaaaatattcgtATTTAATATTCGAGTGTCCAATTGTGAAGTTGGTCCGAAAAATCGGAGTGGGCAAACGTAGCTTAGATATTTACAGTCATAGAGAGATAACATTCGTAAGTTATTTATTCTATACATGAGACAACGCTTCTTTCAGAGGGCGTTGTATTTTGACTCACTTCACGCGCATGTCATGTGTTTTACTAATACGTAGACTTAGTTGGCTCGAATTGCGAGAACATTTAATATCGTCTTATACATAATAAACACGGATCACccactttgaaatttttctagTTTTCACTTGCACGAATATTTTAGGGAAGACACAACATGATTTGTTATCATTTGGAAATGGTGTCATCGCAAGCATGCACGTAACATTAGACTCGTATTACaaagcaaaatatttgaaagatgAATGACTTGtatgatttatataaaacttACTAATGGATGTGAAAGACATTTGAAACATTATAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9IB89	Zinc finger protein ZIC 5 OS=Xenopus laevis OX=8355 GN=zic5 PE=2 SV=1
Q9YIB7	Zinc finger protein ZIC 2-B OS=Xenopus laevis OX=8355 GN=zic2-b PE=2 SV=1
Q8N9L1	Zinc finger protein ZIC 4 OS=Homo sapiens OX=9606 GN=ZIC4 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001009 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00096 all species →	zf-C2H2	Zinc finger, C2H2 type	Domain	Interproscan
PF18366 all species →	zf_ZIC	Zic proteins zinc finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR041643 all species →	Domain	ZIC protein, zinc finger domain	Interproscan
IPR050329 all species →	Family	GLI C2H2-type zinc-finger	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19818 all species →	ZINC FINGER PROTEIN ZIC AND GLI	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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 CAB3984942.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3984942.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

6TPM > 0

4Conditions

34.1Max TPM

5.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	2	5.68	34.06
apical branchlet · Temperature treatment at T0	6	2	7.37	32.73
apical branchlet · Temperature treatment at T25	5	1	1.50	7.51
apical branchlet · Control at T0	4	1	5.30	21.19

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	34.06
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.01
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	32.73
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.47
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.51
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	21.19
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.