Gene detail

Detailed information of CAB3988747.1 in Paramuricea clavata

Genomic Location: pcla8_s001403:27441...30221
NR annotation: CAB3988747.1, rho GTPase-activating 100F-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A025391

ATGGCTTCGCCAGGCTTGCAAAGTCAATCCCGGCGACGGCTACCTCGAGCTCCGAATATTGACGCAAGCGTTGAAAAAGTAGAGTGTCGTGACTCTGTTGACATTGAACAGCAACAAAATATGGCTTCAATCGCAAAGAAACGACTTACTCCAGAGGTTGTTGCTATGCTTTTATCGTTGGATTACGACAGCGAGACAACAGTGAATGCAAACAAAGTTGTAGGAAGTGGTATTTCCACAAAATCTGTTGGTGAAATATCCCAAACACCAAATACAAAAGTAATTTTACAAGGCGATGTTGGTTTGGTGAATATACTCAAGACCTCTGGACAACCTTTAGGGTTTTCATTACGGGAGTATAATGTTAATAAATGTGAAGAACCTGGAGGGATATTTGTCTCTAGACTAACTCCTGGTGGCGTTGTGGAACAGAATTCCTTACTTAGCACTGGAGATGAAATTTTAGAGATTAACCGTGTCGCCGTTAAAGACTATAAACTCAGTGATGTTGTAGCTATGATTCAAATTCCAAAGAAATTGACATTGAAAGTGAGATTTAAATGTAGAGGAGACAGCAGTGACGTTTCGAAAGAACATGGTACTGAGAAACCAAAACCAAGTGTCCGAAATGTGAATAATAACTACATTGAACCAAATCACAGATTTGAATGTCACAGAACTGGTCCGAAACAGGGCGCCCAAATTTCTGCAAAAGAAAGTATTATTACAGCACCAGGCGCCCTTAAATTCAGGCGTAGTTCTTCTGGCAGGTTATTACCCGCACCTCCCGAGTCAGAAGTAAGTATATCACATTTCAATACTCGCCATGAAAATCGCCCTAGTTCATATACTTCAAATATTGTTTCAAGTGATTTATCCCGGCTGAAACACGACAATAATACTATTAACCTGAATACCCGGTTGGGTTCAAACAGCAACTTTAGTGAAAACAATAGCTTAAGTCAACGAGCTTCACAAACACATTTAAATAAAGAAATTGTAAAAATTCACTCAAATCCAGAGATTTCTACAAGCAAGCAGAAAAATCAAAAGAGATCTACTGTTATGCCTGCGTCAATAAATGAAAGAAAACCTTCGCAAGGAACAGACAGTCAGGACGGCAGATATACTTCAAAGCGCTTAGACCCAGGTGATATAAAGTTCGATATTTTAGCTTCATATGATCCGAAGTATTCGAACTTTGATTCTGCGTCTAACATTATTTCTCGTACGTTGGACGAAATCAAAATTGAATCAAAAGATGATCTTTCCAAATCTACTTTACGTAAAACATCGGAGACGTTCGGCTCTAGTTCGTCATTATCAAGCAATGGTTCTCCAAAACCTCAAGTTAGGAAATCTAAAAACAGTTCATCAAGTCTCGGTAGTAGTGGCCTCTCTCGATCAGATATGTTAGCGCATTCCTCCCGACTTTCTGACAACAGCCCAGTGAGCTCGTCAGCTGAAAATGAAGACCAAATGTCTAAAGGTGTTTCTGAGAACTCGATTAAACAAAATCAGAAACCTCCGTTCACTCATTCTTTGTCTTCAGACGATTTAAACCGATCTCACAATAGCTGGTTTTCCAAGATCGGACACCCAAAACTGAAACACGTTCGGAAATTCTCGGAAGGCGCACGACCACTTTCAATACCTGCTGCTTTCGGAGAACCATATCGTGTGCAGGAATCAACAGATGTCTCATCTGATGACGCGGAACATGGCTACAGGTTATACCCAAGTACACCCCAGGAAACTGCTTCACGTGCTGTGACTGGAATGGTCACTTTGGATATCGTCAAAGGAGCTCAGATTGGCGAGTCTATCACGAGAGAGAAACGCAAAAAGACTAAAGTGCTCTGTAGTGTAGATTCTGACGGGGTCAGGCAAGCTTGTACAGTCTCGAAGAAAGGTATTAATGATTTCCAATGGAACGAGAGTTTTGAAATAGAGTTACAACGAACACGTGAAATTCGAATAACGGTTTGCTCTCATTCCAAAAAGGAGGATGTTAAGATTGCAGAAGGTTGTTTAAGCCTCGCTTCATTGTTAAACGAAGGTAATGAACACTTGCTTGCAGTTTGTTTAGAACCCTCCGGAATGCTTTGTATCAAATTAAAATTCACTGATATGAAATTTCTTCTTCAACGCACGCCGTCACAAAAGAAGGAAGGTGTTTTCGGTTTTCCGCTTGAGACAGTCTTACGACGTGAGGGTTCAAAAATCCCGAACTTGATTCGCAAGTGTGTGGAGGAGATTAATGAGCGAGGCCTGGAAACAACTGGAATTTATCGAATTTGCGGGAATGCCGCTAAGAAGAAAGTATTGCGAGCGCAATTTGACAACAATAGTGCGAGTGTTGACTTGAGTCAGACTGAGAATCCTGTTGATATTAACATTATAACTGGTTTGCTGAAAGATTACCTACGTGAATTACCTCGACCTCTTCTCTCTCAAGATATACGTGAGTTACTCTGCGAAACAGATGCGGTACCAGATAATCCTCGAGATAATCTAGTTTCTGCGATCATTAAAAAGTTCACTCGCACGTCCAAAGCGACCATTATGTACTTGTTAGATCATTTCGTCACTGTATTGATGAACTGTGATGCAAACAAAATGGATAGTCATAATTTAGCAGTATGTATTGGGCCTGTATTGCTGTGTCCATCACTTGGTGGAAGCACAACCAGTACTGTTAGTGATACAAAGAAAGATATCAGTGCCATTAAGTTATTGTTAGAAGTTTGGCCTAAACCAGAACAGATTTCAGCCTGTTAA

Transcript

rna-PACLA_8A025391

ATGGCTTCGCCAGGCTTGCAAAGTCAATCCCGGCGACGGCTACCTCGAGCTCCGAATATTGACGCAAGCGTTGAAAAAGTAGAGTGTCGTGACTCTGTTGACATTGAACAGCAACAAAATATGGCTTCAATCGCAAAGAAACGACTTACTCCAGAGGTTGTTGCTATGCTTTTATCGTTGGATTACGACAGCGAGACAACAGTGAATGCAAACAAAGTTGTAGGAAGTGGTATTTCCACAAAATCTGTTGGTGAAATATCCCAAACACCAAATACAAAAGTAATTTTACAAGGCGATGTTGGTTTGGTGAATATACTCAAGACCTCTGGACAACCTTTAGGGTTTTCATTACGGGAGTATAATGTTAATAAATGTGAAGAACCTGGAGGGATATTTGTCTCTAGACTAACTCCTGGTGGCGTTGTGGAACAGAATTCCTTACTTAGCACTGGAGATGAAATTTTAGAGATTAACCGTGTCGCCGTTAAAGACTATAAACTCAGTGATGTTGTAGCTATGATTCAAATTCCAAAGAAATTGACATTGAAAGTGAGATTTAAATGTAGAGGAGACAGCAGTGACGTTTCGAAAGAACATGGTACTGAGAAACCAAAACCAAGTGTCCGAAATGTGAATAATAACTACATTGAACCAAATCACAGATTTGAATGTCACAGAACTGGTCCGAAACAGGGCGCCCAAATTTCTGCAAAAGAAAGTATTATTACAGCACCAGGCGCCCTTAAATTCAGGCGTAGTTCTTCTGGCAGGTTATTACCCGCACCTCCCGAGTCAGAAGTAAGTATATCACATTTCAATACTCGCCATGAAAATCGCCCTAGTTCATAtacttcaaatattgtttcaaGTGATTTATCCCGGCTGAAACACGACAATAATACTATTAACCTGAATACCCGGTTGGGTTCAAACAGCAACTTTAGTGAAAACAATAGCTTAAGTCAACGAGCTTCACAAACACATTTAAATAAAGAAATTGTAAAAATTCACTCAAATCCAGAGATTTCTACAAGCAAGCAGAAAAATCAAAAGAGATCTACTGTTATGCCTGCGTCAATAAATGAAAGAAAACCTTCGCAAGGAACAGACAGTCAGGACGGCAGATATACTTCAAAGCGCTTAGACCCAGGTGATATAAAGTTCGATATTTTAGCTTCATATGATCCGAAGTATTCGAACTTTGATTCTGCGTCTAACATTATTTCTCGTACGTTGGACGAAATCAAAATTGAATCAAAAGATGATCTTTCCAAATCTACTTTACGTAAAACATCGGAGACGTTCGGCTCTAGTTCGTCATTATCAAGCAATGGTTCTCCAAAACCTCAAGTTAGGAAATCTAAAAACAGTTCATCAAGTCTCGGTAGTAGTGGCCTCTCTCGATCAGATATGTTAGCGCATTCCTCCCGACTTTCTGACAACAGCCCAGTGAGCTCGTCAGCTGAAAATGAAGACCAAATGTCTAAAGGTGTTTCTGAGAACTCGATTAAACAAAATCAGAAACCTCCGTTCACTCATTCTTTGTCTTCAGACGATTTAAACCGATCTCACAATAGCTGGTTTTCCAAGATCGGACACCCAAAACTGAAACACGTTCGGAAATTCTCGGAAGGCGCACGACCACTTTCAATACCTGCTGCTTTCGGAGAACCATATCGTGTGCAGGAATCAACAGATGTCTCATCTGATGACGCGGAACATGGCTACAGGTTATACCCAAGTACACCCCAGGAAACTGCTTCACGTGCTGTGACTGGAATGGTCACTTTGGATATCGTCAAAGGAGCTCAGATTGGCGAGTCTATCACGAGAGAGAAACGCAAAAAGACTAAAGTGCTCTGTAGTGTAGATTCTGACGGGGTCAGGCAAGCTTGTACAGTCTCGAAGAAAGGTATTAATGATTTCCAATGGAACGAGAGTTTTGAAATAGAGTTACAACGAACACGTGAAATTCGAATAACGGTTTGCTCTCATTCCAAAAAGGAGGATGTTAAGATTGCAGAAGGTTGTTTAAGCCTCGCTTCATTGTTAAACGAAGGTAATGAACACTTGCTTGCAGTTTGTTTAGAACCCTCCGGAATGCTTTGTATCAAATTAAAATTCACTGATATGAAATTTCTTCTTCAACGCACGCCGTCACAAAAGAAGGAAGGTGTTTTCGGTTTTCCGCTTGAGACAGTCTTACGACGTGAGGGTTCAAAAATCCCGAACTTGATTCGCAAGTGTGTGGAGGAGATTAATGAGCGAGGCCTGGAAACAACTGGAATTTATCGAATTTGCGGGAATGCCGCTAAGAAGAAAGTATTGCGAGCGcaatttgacaacaatagtGCGAGTGTTGACTTGAGTCAGACTGAGAATCCTGTTGATATTAACATTATAACTGGTTTGCTGAAAGATTACCTACGTGAATTACCTCGACCTCTTCTCTCTCAAGATATACGTGAGTTACTCTGCGAAACAGATGCGGTACCAGATAATCCTCGAGATAATCTAGTTTCTGCGATCATTAAAAAGTTCACTCGCACGTCCAAAGCGACCATTATGTACTTGTTAGATCATTTCGTCACTGTATTGATGAACTGTGATGCAAACAAAATGGATAGTCATAATTTAGCAGTATGTATTGGGCCTGTATTGCTGTGTCCATCACTTGGTGGAAGCACAACCAGTACTGTTAGTGATACAAAGAAAGATATCAGTGCCATTAAGTTATTGTTAGAAGTTTGGCCTAAACCAGAACAGATTTCAGCCTGTTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9V9S7	Rho GTPase-activating protein 100F OS=Drosophila melanogaster OX=7227 GN=RhoGAP100F PE=1 SV=2
D3ZZN9	Rho GTPase-activating protein SYDE1 OS=Rattus norvegicus OX=10116 GN=Syde1 PE=1 SV=1
Q9DBZ9	Rho GTPase-activating protein SYDE1 OS=Mus musculus OX=10090 GN=Syde1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007735 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00168 all species →	C2	C2 domain	Domain	Interproscan
PF00620 all species →	RhoGAP	RhoGAP domain	Domain	Interproscan
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR000008 all species →	Domain	C2 domain	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR035892 all species →	Homologous_superfamily	C2 domain superfamily	Interproscan
IPR000198 all species →	Domain	Rho GTPase-activating protein domain	Interproscan
IPR008936 all species →	Homologous_superfamily	Rho GTPase activation protein	Interproscan
IPR052118 all species →	Family	Rho GTPase-activating regulator	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46150 all species →	RHO GTPASE-ACTIVATING PROTEIN 100F	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0046578 all species →	Biological Process	regulation of Ras protein signal transduction	Interproscan
GO:0097060 all species →	Cellular Component	synaptic membrane	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
K20655	SYDE; Rho GTPase-activating protein SYDE	-	Membrane trafficking	ko04131	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3988747.1 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

16TPM > 0

4Conditions

25.7Max TPM

5.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	6.75	11.69
apical branchlet · Temperature treatment at T0	6	6	9.72	25.70
apical branchlet · Temperature treatment at T25	5	2	1.41	5.64
apical branchlet · Control at T0	4	2	1.99	4.44

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.69
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.66
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.55
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	4.88
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.31
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.41
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	25.70
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	13.76
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.17
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.53
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.61
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.57
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.64
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.42
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
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	4.44
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	3.53
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.