Gene detail

Detailed information of CAB4004495.1 in Paramuricea clavata

Genomic Location: pcla8_s005022:3101...6269
NR annotation: CAB4004495.1, extended synaptotagmin-3-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A053465

ATGAAGCCACAGCAAGCAAGATTAGCAAAGAAACTGCAGAATAAACCGATATGGCGGAGATATATAAGTTATATAAATTTCCCTAAGCTGGGGCAATATGTAGGTCTGTCTCTAGGCCTCTGGTTTGCAGGGAAATATAATTTCAGCTCAGCATGGATTGCAATGGGTCTGTTAGTGTTCGTTTGGTGGGATTTTGAGACGCGCGAGAAGAAGCTACGGCGAAAACGAATCCAGAAATCAGTCAGTGTTGCCGGAGTCAAGATGGAGAATTTACCGTCGTGGGTGTTTGTTGAGAGCTCAGAACGTGTTGTCTGGATGAATAACATGATTCACCATATGTGGCCCTACATCGGAGCCATGGTCAAGAAAATCCTTAAAGAGAATGTCGAACCAGCCATGCAAGCAAGCCTACCCTGTTCGCTAAGTAGCCTCACTTTCGAGACAATCTCGTTTGGTCAAGTTGCGCCCAAAATCACCGGAATCAACTCGTACGCGCCCGAAGATGCCCCAGATGAATTCATCCTGGACCTTGACCTCCTGTACGAAGGCGATGCAAAAATCAAGCTCTCTGTGAAATCGGTCAACATGGGCGTGTCTGATATCCAACTTCGCGGAATGTTGCGAATTATTTTCAAACCGTTTGTCGGCGAACCCAACCCGATTGGCGGTTTAACTGTTTTCTTCCTAAACCGCCCGAAAATCAAATTTGATCTGATTAACTTATTGAATGTTCTGGATATTCCTGGTCTGAAAAGTAAACTCAGAAGCGTTGCAGAGGATGTTATTTGCTCTATTATGGTCTTACCCAATCGTATCGTTGTCCCAATGTCACCCGAGCTTGTTGCCGATGATAGTGACCTGCGTTACCCCATTCCTGAAGGTGTTGTCCGAATGAAAATAATCGAAGCAAAAGAATTGACGAAAATGGATTCGGCATTGAGAGGCGGCGCTGCTGACCCTTATATTGTCCTCGGAGTTGGTGCTCAGAAATTCCGTACAAAAACCTGTAAAAACACGCTTAAACCGGTTTGGAACGAGGTGTACGAAGCTTTTGTAGACAACGATGAGGGCCAGGAGATTGAGATGAGCATGTTCGATGAGGAGAAGACTTCAAAGGATGCAAAAATGGGAACACTCGAAGTTGATATTACCTCGGTTGCACAGCATGGTAGCCGGGATCTGTGGCTGCCCTTGGACGGCGTCAAAAGTGGAGTGGTACATCTTGATTTAGCTTGGTGTAAGCTTAGCTCGAAACCCAAAGATCTCAAACCTGCTGGTCAGTCGCTGTCAAGTGCACTTCTTATGGTGAAAATTAAGCAAGGAAAGAACTTACCCAACCCACTCAAACCTAAAGAAATCCCGGTCGTGTTGTGTAAGGTTATTGTGGGAGACTCAGAGAAGGAGACATACCATGTTGGTCTGAATGCGGAGACCCAAACCATCGATTGGAAACAAGCTTTACGATTTTTAGTGAAACAACCTGCTACCACCTCAATCAAGATTGAAGTTATCGAAAGCAAGGGTACCAAGAAGCTCGGAAATGTGGTCATTCCCTTGACAACGGTTGCGGATGCAAACGAAATGGTGCTGGAAAAGGAATTCAATCTTACCGACTCGGGTGGAAAAGGCAGTCTAGCATGTAAGTTCACCTTGCGAGCATTAGTCCCGGGTGCGAAGGAGATTTCAGAAGTTAAACGAAAGCGTGCAGTACGATACTCCGAGCGCCCATCCGTGTCCGATGTCCCTTCCCCCACCACTCCGAAAGTGATGGTTAACGATGCTGTCGAAGAGTTGTCCTCGTTTGATGAAGACCGACAATCGACAAGCTCATCTCCAAGAGGTAGTATGTACGAGGTGAGTAGCGGCGGGGGCTCTAGAGAGAACCTTGTCAACTACGGCAGTGTGGAGCTCTCGCTCAGTTACAGCCATGTCAGAAATTGTTTGGTCGTTGTTGTCCATGCCGCACATGGCCTGCCCACAAGAGATTCGAAAGCCAAGACCAGCCCCTATGTTCGGTTGTACCTCCTCCCCGAGCGCTCTAAGAAGTCCCGCCGCGAGACCACGCCCAAAGAAGGTACCCTGGATCCAGTGTATGACGAGAAGTTCGAGTACATCACCTCCCTTGAGGAACTTCGGGAATGCACACTTGATGTCGCTGTCAAGAACCACAAGTCCAAATTCACCTCCAGACGCAGGCGAAATTTCATTGGTCAAATCCGAATCCCATTGTCCTCCCTTGATCTGTCGAAGGAACAAAGAATGACATACAACCTGGTGAAGTGGACCCCACAGTGA

Transcript

rna-PACLA_8A053465

atTGAGCACAGAGGATTGGGCACATTTTCGTGTGTACAAGTATTTGCGCTCTGCTTTCAAGCGCAAGGGAAAAAGGTATACGCTTTAACTGTTCAGCATATAAACTTAAACTTCATATTTAATATTGTCGATTTTAATACTCCGAAGTTTGCTGTATGCTATTGATAACATCAGGCATTTATACTGAATATTTGCATAATTTGTTGTTCAGATTTATTTGTGGTCAGCTTATAAATTCCTGCACGGCGAAGGAACATAATCTCAATTATTTTGGTCGAAAGTACAAGACTACATCGGGTTTTCTTTGAAGACTTTTGCTTTAAAGGTACAGTTCATTTTACATAACGTTTTGTTTTGTACAGATGAGTAAATACTAAAAGCACAGCGTATCCAATATTTGAGTGCCTAATTTATAAATTTCCGTTTTGAATTTGCACAGGTGAAATTATGAAGCCACAGCAAGCAAGATTAGCAAAGAAACTGCAGAATAAACCGATATGGCGGAGATATATAAGTTATATAAATTTCCCTAAGCTGGGGCAATATGTAGGTCTGTCTCTAGGCCTCTGGTTTGCAGGGAAATATAATTTCAGCTCAGCATGGATTGCAATGGGTCTGTTAGTGTTCGTTTGGTGGGATTTTGAGACGCGCGAGAAGAAGCTACGGCGAAAACGAATCCAGAAATCAGTCAGTGTTGCCGGAGTCAAGATGGAGAATTTACCGTCGTGGGTGTTTGTTGAGAGCTCAGAACGTGTTGTCTGGATGAATAACATGATTCACCATATGTGGCCCTACATCGGAGCCATGGTCAAGAAAATCCTTAAAGAGAATGTCGAACCAGCCATGCAAGCAAGCCTACCCTGTTCGCTAAGTAGCCTCACTTTCGAGACAATCTCGTTTGGTCAAGTTGCGCCCAAAATCACCGGAATCAACTCGTACGCGCCCGAAGATGCCCCAGATGAATTCATCCTGGACCTTGACCTCCTGTACGAAGGCGATGCAAAAATCAAGCTCTCTGTGAAATCGGTCAACATGGGCGTGTCTGATATCCAACTTCGCGGAATGTTGCGAATTATTTTCAAACCGTTTGTCGGCGAACCCAACCCGATTGGCGGTTTAACTGTTTTCTTCCTAAACCGCCCGAAAATCAAATTTGATCTGATTAACTTATTGAATGTTCTGGATATTCCTGGTCTGAAAAGTAAACTCAGAAGCGTTGCAGAGGATGTTATTTGCTCTATTATGGTCTTACCCAATCGTATCGTTGTCCCAATGTCACCCGAGCTTGTTGCCGATGATAGTGACCTGCGTTACCCCATTCCTGAAGGTGTTGTCCGAATGAAAATAATCGAAGCAAAAGAATTGACGAAAATGGATTCGGCATTGAGAGGCGGCGCTGCTGACCCTTATATTGTCCTCGGAGTTGGTGCTCAGAAATTCCGTACAAAAACCTGTAAAAACACGCTTAAACCGGTTTGGAACGAGGTGTACGAAGCTTTTGTAGACAACGATGAGGGCCAGGAGATTGAGATGAGCATGTTCGATGAGGAGAAGACTTCAAAGGATGCAAAAATGGGAACACTCGAAGTTGATATTACCTCGGTTGCACAGCATGGTAGCCGGGATCTGTGGCTGCCCTTGGACGGCGTCAAAAGTGGAGTGGTACATCTTGATTTAGCTTGGTGTAAGCTTAGCTCGAAACCCAAAGATCTCAAACCTGCTGGTCAGTCGCTGTCAAGTGCACTTCTTATGGTGAAAATTAAGCAAGGAAAGAACTTACCCAACCCACTCAAACCTAAAGAAATCCCGGTCGTGTTGTGTAAGGTTATTGTGGGAGACTCAGAGAAGGAGACATACCATGTTGGTCTGAATGCGGAGACCCAAACCATCGATTGGAAACAAGCTTTACGATTTTTAGTGAAACAACCTGCTACCACCTCAATCAAGATTGAAGTTATCGAAAGCAAGGGTACCAAGAAGCTCGGAAATGTGGTCATTCCCTTGACAACGGTTGCGGATGCAAACGAAATGGTGCTGGAAAAGGAATTCAATCTTACCGACTCGGGTGGAAAAGGCAGTCTAGCATGTAAGTTCACCTTGCGAGCATTAGTCCCGGGTGCGAAGGAGATTTCAGAAGTTAAACGAAAGCGTGCAGTACGATACTCCGAGCGCCCATCCGTGTCCGATGTCCCTTCCCCCACCACTCCGAAAGTGATGGTTAACGATGCTGTCGAAGAGTTGTCCTCGTTTGATGAAGACCGACAATCGACAAGCTCATCTCCAAGAGGTAGTATGTACGAGGTGAGTAGCGGCGGGGGCTCTAGAGAGAACCTTGTCAACTACGGCAGTGTGGAGCTCTCGCTCAGTTACAGCCATGTCAGAAATTGTTTGGTCGTTGTTGTCCATGCCGCACATGGCCTGCCCACAAGAGATTCGAAAGCCAAGACCAGCCCCTATGTTCGGTTGTACCTCCTCCCCGAGCGCTCTAAGAAGTCCCGCCGCGAGACCACGCCCAAAGAAGGTACCCTGGATCCAGTGTATGACGAGAAGTTCGAGTACATCACCTCCCTTGAGGAACTTCGGGAATGCACACTTGATGTCGCTGTCAAGAACCACAAGTCCAAATTCACCTCCAGACGCAGGCGAAATTTCATTGGTCAAATCCGAATCCCATTGTCCTCCCTTGATCTGTCGAAGGAACAAAGAATGACATACAACCTGGTGAAGTGGACCCCACAGTGATTCAGGACACCAGCACTAAAACAAGACACTAGACACTGTTAAGCACGAGAAAACTTATTTACTTTAGTCAAGCTAGAACATTTTTTTCATTGAATTATTCCTAGGAACATAACCGAACATTAAACCTTATTGAAATACTATAGTTGTCAATTTAGGTATGTAAAACTTATTGTATCTCATGATTGATAATACTGCGTGGTTGCACTTTATTGGCTACTACTTACTAGTGTGAAATAAAATCACAAAGTTAACATACCCGTGTACTTGAAACCATTGTTGTTTGCCACGCTTCTCTACTCGGCCTGAAAATTATAAATGGAAGTTTCCGACGTTTTGGAGCGAAGCTCCTTCATCAAGGGTTAGTGACAACTACTTACTAAACTTCAACTACACAACTAATCTATGTTGGTAACATGTGGAAAACCAC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3TZZ7	Extended synaptotagmin-2 OS=Mus musculus OX=10090 GN=Esyt2 PE=1 SV=1
Q5M7N9	Extended synaptotagmin-3 OS=Xenopus tropicalis OX=8364 GN=esyt3 PE=2 SV=1
A0FGR8	Extended synaptotagmin-2 OS=Homo sapiens OX=9606 GN=ESYT2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001220 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00168 all species →	C2	C2 domain	Domain	Interproscan
PF17047 all species →	SMP_LBD	Synaptotagmin-like mitochondrial-lipid-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035892 all species →	Homologous_superfamily	C2 domain superfamily	Interproscan
IPR000008 all species →	Domain	C2 domain	Interproscan
IPR051634 all species →	Family	Extended Synaptotagmin	Interproscan
IPR031468 all species →	Domain	Synaptotagmin-like mitochondrial-lipid-binding domain	Interproscan
IPR039010 all species →	Domain	Synaptotagmin, SMP domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45761 all species →	EXTENDED SYNAPTOTAGMIN-LIKE PROTEIN 2, ISOFORM C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005544 all species →	Molecular Function	calcium-dependent phospholipid binding	Interproscan
GO:0008429 all species →	Molecular Function	phosphatidylethanolamine binding	Interproscan
GO:0031210 all species →	Molecular Function	phosphatidylcholine binding	Interproscan
GO:0031227 all species →	Cellular Component	obsolete intrinsic component of endoplasmic reticulum membrane	Interproscan
GO:0031234 all species →	Cellular Component	extrinsic component of cytoplasmic side of plasma membrane	Interproscan
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0008289 all species →	Molecular Function	lipid binding	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 CAB4004495.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4004495.1 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

8TPM > 0

4Conditions

109.6Max TPM

13.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	31.70	109.60
apical branchlet · Temperature treatment at T0	6	2	11.83	49.07
apical branchlet · Temperature treatment at T25	5	1	0.62	3.10
apical branchlet · Control at T0	4	1	3.76	15.05

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	109.60
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	61.68
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	15.41
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.49
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
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	49.07
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	21.93
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
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	3.10
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
SRR19977435	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	15.05
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.