Gene detail

Detailed information of agem_s0076.g86.t1 in Acropora gemmifera

Genomic Location: sc0000076_pilon:1174763...1177942
NR annotation: XP_015769491.1, PREDICTED: putative inactive cadmium/zinc-transporting ATPase HMA3 [Acropora digitifera]
Species Acropora gemmifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

agem_s0076.g86.t1

ATGTGTCAGGAGTATCACTGTGACTGCTGCTCAGAAGAAATACCAGCAGACATTTGCGAGTGCGTCGTGTGTTACCATGGGAAGGTTAGAGGAAATTCCGCTTTGCGCAACATAGTAAAGAGCCTCCAAGAAGAGCCCAAGAAAGACCTTTGCTGTAAAAAGGCTAACTCGAACTCAAATCCAACAAAGTGGATCCAGTTACCAGAATGTTGTCTTAAGAATAAAACCTTGCGTGATGATACAACTGATCTCCCAAGTCAAACCACACCCAAATGTGGTAAAGAAACGCCTTCAGGCAAACCAAACGCAGAGAGCAGCAACGACTCTGAAGCTGTAACACCGGTACGCCACACCACAACAAAGCTGCGAGTACAGAATATATGTTGTGCAGGAGAAATCAAACTCGTCAAAGATTCACTTGAACCGCTGAAGGGCGTTACATCCATAACAGTCAACGTGATAGGTCGTGTAGTGTATGTCCGACACGATCCAGAGAGGATGTCACCCTCAGAGCTCGTCAGTTCCTTAAACCGAGTTCACCTGGGAGCAAGCATCATGGAAAGTGGCTCCCAACAGGCCGAAAGCAAGATCAACCGTCTTTCTCCCACCCTTTTATCATTTTTTATATATCTCTTAGCGCAAACCATAATTTTTATGGTAGCTGTTATAGCGCTCTTTGCTAAGGCATCTTGGTACCAGTGGATAGCCATTGCGGAGATAATATTTGGTATTGCACCAGTTTTGAGAAAAGCGTTGATGTCTTTCAAGACTTTCTCAGTCGACATAAATATGCTTATGCTTATTGCCATTTCAGGAACTCTGGCAATTCGACAATGGTTAGAGGGGGCAGCTGTAGTTTACGTATTCTCTCTAGCAGAAGGATTGCAGGAGCTTTGCATGCACAAAGTTCAGCAAACAATCTCTGGGTTAATAGTCGAGGCACCTCAAGTAGCGATAATGGCGATTACAGGCCAGAGTGTTCCGGTTGAACAGGTAACTATAGGAACAGCCATTGCAATCAGACCCGGTGAACTCATTCCCTTGGACGGTAAGGTAGTGAAAGGCAAAGCCGCTGTCGATGAAAGTTCTGTTTCTGGAGAATCTGTACCTGTTGAGAAAACTGTGGGCTCGAAGGTGTTTAGTGGAACTGTCAATCAAAATGGCTACTTGGAAGTTGAGACCACATCCGACTCCACTTCCTCTACAGTCGTCAAAATTGCACAGCTCGTTCAAGAAGCCAAGACTGGTTCCGCGAGCACTGAACTGTGTGTAAACCAGTTTGCCAAGTACTATACACCTGCAGTGGTCGTTAGCGCGACTCTAGTATTTGCTATTCCCGCCATACTTGGTGCAACTGGTGTGGGTACGTATTCAGAAGAGATAACAGAGTGGGGCCGAAGAGCACTTGCACTTTTAGTTATAGCTTGCCCCTGCGCTTTGGTCATGTCAACCCCGATTGCAGTGGTTTGTGGTATCACTGCGGCTGCACGGAAAGGAGCTCTAATTAAACGGGGGGCTAGTCTTGAGACGCTAGCGGAATTAGAAGTTTTAGCTTTTGACAAAACGGGAACTCTGACTGAAGGAAAGTTTCAAGTTGTTGGCATGGAATGTTCGTTTGGTGTGCAAGAACAAATTGTCCTGCGTTTAGCTGCGGCGCTTGAAAGCAAGTCTAGTCACCCTCTCGCAGCAGCTATAGTGAGTGAGTTCACTGGTTGTGTCACGGAAATGGCCACTTCGCAAATCTTAACTTTACCAGAAGTCTCACATTTGGAGCTTCATGAAGGTCAAGATATACTCAGACCCAACAGTCTGGCTACGCTTGATTGGCTGAGAAATCTTCGTGTCCACTCAGCTATGATCACTGGTGACAATACACGGACAGCCATGGCTGTCAAAGATAAACTAGGCCTTGACGAGTGCATTGCCGAAATGAAACCACAGGACAAGCTGGCGTGGGTCAAACAAAGACAAATTGGAATAAAGGACACTGATGATGGGAACTATGACAATGATCAACCAACTGGTCATCTATTCTGCTTATCTACCTGCTGTTTACATCGTGGCTGCCATTCCTTGAGATGCCGTGAAAACAAGAAAAGTACTGTGGGAATGGTCGGGGATGGTGTTAACGATGGTCCAGCGCTAGCGTCGGCGAATGTTGGAATTGCGATGGGCGCAGGAGGTACAGCTTTGGCAGTGGAAGCTGCAGACGTCGCACTGATGACCAATAACCTTGCCAAAATACCGGAAATAGTTGAACTTGGGCGTTTCTGTCGCCGCATTGTTTTTCAGAATATTGGTCTTTCGGTTATTCTTAAGCTTGCTATGGTGATAGCGGCGCTTGCTGGAAAGGCTTCCCTCGTGATAGCTGTCATGGCGGATGTACTTGGTTTATTGTTCGTGCTACTAAACGGCATAAGACCTCTTTGGTGGAAGGTCACTGACAAACACAAGAACTTGGATATTCAGCGTTTGGGCTAA

Transcript

agem_s0076.g86.t1

GGGGACCTCAACACATAGCAAAACTCCTTTTTGCGCGCACATGGTCGCGTGTGAAAAATGTAAGGGAACAAATGCTGTATATTAAATTTTCTATTTCCTGACTCGTTTTTTTAAATTTAAATTTACCCTTTTCGTCGTTTTGATAGACCACCTCAATCATGTGTCAGGAGTATCACTGTGACTGCTGCTCAGAAGAAATACCAGCAGACATTTGCGAGTGCGTCGTGTGTTACCATGGGAAGGTTAGAGGAAATTCCGCTTTGCGCAACATAGTAAAGAGCCTCCAAGAAGAGCCCAAGAAAGACCTTTGCTGTAAAAAGGCTAACTCGAACTCAAATCCAACAAAGTGGATCCAGTTACCAGAATGTTGTCTTAAGAATAAAACCTTGCGTGATGATACAACTGATCTCCCAAGTCAAACCACACCCAAATGTGGTAAAGAAACGCCTTCAGGCAAACCAAACGCAGAGAGCAGCAACGACTCTGAAGCTGTAACACCGGTACGCCACACCACAACAAAGCTGCGAGTACAGAATATATGTTGTGCAGGAGAAATCAAACTCGTCAAAGATTCACTTGAACCGCTGAAGGGCGTTACATCCATAACAGTCAACGTGATAGGTCGTGTAGTGTATGTCCGACACGATCCAGAGAGGATGTCACCCTCAGAGCTCGTCAGTTCCTTAAACCGAGTTCACCTGGGAGCAAGCATCATGGAAAGTGGCTCCCAACAGGCCGAAAGCAAGATCAACCGTCTTTCTCCCACCCTTTTATCATTTTTTATATATCTCTTAGCGCAAACCATAATTTTTATGGTAGCTGTTATAGCGCTCTTTGCTAAGGCATCTTGGTACCAGTGGATAGCCATTGCGGAGATAATATTTGGTATTGCACCAGTTTTGAGAAAAGCGTTGATGTCTTTCAAGACTTTCTCAGTCGACATAAATATGCTTATGCTTATTGCCATTTCAGGAACTCTGGCAATTCGACAATGGTTAGAGGGGGCAGCTGTAGTTTACGTATTCTCTCTAGCAGAAGGATTGCAGGAGCTTTGCATGCACAAAGTTCAGCAAACAATCTCTGGGTTAATAGTCGAGGCACCTCAAGTAGCGATAATGGCGATTACAGGCCAGAGTGTTCCGGTTGAACAGGTAACTATAGGAACAGCCATTGCAATCAGACCCGGTGAACTCATTCCCTTGGACGGTAAGGTAGTGAAAGGCAAAGCCGCTGTCGATGAAAGTTCTGTTTCTGGAGAATCTGTACCTGTTGAGAAAACTGTGGGCTCGAAGGTGTTTAGTGGAACTGTCAATCAAAATGGCTACTTGGAAGTTGAGACCACATCCGACTCCACTTCCTCTACAGTCGTCAAAATTGCACAGCTCGTTCAAGAAGCCAAGACTGGTTCCGCGAGCACTGAACTGTGTGTAAACCAGTTTGCCAAGTACTATACACCTGCAGTGGTCGTTAGCGCGACTCTAGTATTTGCTATTCCCGCCATACTTGGTGCAACTGGTGTGGGTACGTATTCAGAAGAGATAACAGAGTGGGGCCGAAGAGCACTTGCACTTTTAGTTATAGCTTGCCCCTGCGCTTTGGTCATGTCAACCCCGATTGCAGTGGTTTGTGGTATCACTGCGGCTGCACGGAAAGGAGCTCTAATTAAACGGGGGGCTAGTCTTGAGACGCTAGCGGAATTAGAAGTTTTAGCTTTTGACAAAACGGGAACTCTGACTGAAGGAAAGTTTCAAGTTGTTGGCATGGAATGTTCGTTTGGTGTGCAAGAACAAATTGTCCTGCGTTTAGCTGCGGCGCTTGAAAGCAAGTCTAGTCACCCTCTCGCAGCAGCTATAGTGAGTGAGTTCACTGGTTGTGTCACGGAAATGGCCACTTCGCAAATCTTAACTTTACCAGAAGTCTCACATTTGGAGCTTCATGAAGGTCAAGATATACTCAGACCCAACAGTCTGGCTACGCTTGATTGGCTGAGAAATCTTCGTGTCCACTCAGCTATGATCACTGGTGACAATACACGGACAGCCATGGCTGTCAAAGATAAACTAGGCCTTGACGAGTGCATTGCCGAAATGAAACCACAGGACAAGCTGGCGTGGGTCAAACAAAGACAAATTGGAATAAAGGACACTGATGATGGGAACTATGACAATGATCAACCAACTGGTCATCTATTCTGCTTATCTACCTGCTGTTTACATCGTGGCTGCCATTCCTTGAGATGCCGTGAAAACAAGAAAAGTACTGTGGGAATGGTCGGGGATGGTGTTAACGATGGTCCAGCGCTAGCGTCGGCGAATGTTGGAATTGCGATGGGCGCAGGAGGTACAGCTTTGGCAGTGGAAGCTGCAGACGTCGCACTGATGACCAATAACCTTGCCAAAATACCGGAAATAGTTGAACTTGGGCGTTTCTGTCGCCGCATTGTTTTTCAGAATATTGGTCTTTCGGTTATTCTTAAGCTTGCTATGGTGATAGCGGCGCTTGCTGGAAAGGCTTCCCTCGTGATAGCTGTCATGGCGGATGTACTTGGTTTATTGTTCGTGCTACTAAACGGCATAAGACCTCTTTGGTGGAAGGTCACTGACAAACACAAGAACTTGGATATTCAGCGTTTGGGCTAATTGAAAACACTACTGAAAGTTATGATTGAAACTAATCCATTGAGGAAACGGAATGGAGACGGCCTCATTTCGTCGGCTTGTTTGACCTCCAGTTTCCAATCATGTAATTTCGGTATATATTGTTCCTGCTCGCTCGCTACGCTCGCTCCACAGCAACATAAACCAATCATGGGTATATCGTGACAAAGCTAGAAACAAACACCGCTACATATATACTAGGGCCAGCCACACCAATCCCCCCTGTAGATTTTATATTTATACCAACGCTAGTCATCATGATACACAAAGAACACGGCTGATACGAAAACCCTGAATGGAAAAACGGAAACGTGTTACCCAATCAAGTGCAGGTGAATCA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A3BF39	Cadmium/zinc-transporting ATPase HMA2 OS=Oryza sativa subsp. japonica OX=39947 GN=HMA2 PE=1 SV=1
Q9SZW4	Cadmium/zinc-transporting ATPase HMA2 OS=Arabidopsis thaliana OX=3702 GN=HMA2 PE=2 SV=1
Q8H384	Cadmium/zinc-transporting ATPase HMA3 OS=Oryza sativa subsp. japonica OX=39947 GN=HMA3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001597 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00122 all species →	E1-E2_ATPase	E1-E2 ATPase	Family	Interproscan
PF00702 all species →	Hydrolase	haloacid dehalogenase-like hydrolase	Domain	Interproscan
PF00403 all species →	HMA	Heavy-metal-associated domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008250 all species →	Homologous_superfamily	P-type ATPase, A domain superfamily	Interproscan
IPR023299 all species →	Homologous_superfamily	P-type ATPase, cytoplasmic domain N	Interproscan
IPR036412 all species →	Homologous_superfamily	HAD-like superfamily	Interproscan
IPR018303 all species →	PTM	P-type ATPase, phosphorylation site	Interproscan
IPR006121 all species →	Domain	Heavy metal-associated domain, HMA	Interproscan
IPR051014 all species →	Family	Cation Transport ATPase Type IB	Interproscan
IPR036163 all species →	Homologous_superfamily	Heavy metal-associated domain superfamily	Interproscan
IPR023298 all species →	Homologous_superfamily	P-type ATPase, transmembrane domain superfamily	Interproscan
IPR001757 all species →	Family	P-type ATPase	Interproscan
IPR023214 all species →	Homologous_superfamily	HAD superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48085 all species →	CADMIUM/ZINC-TRANSPORTING ATPASE HMA2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005215 all species →	Molecular Function	transporter activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	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
K01534	zntA; Zn2+/Cd2+-exporting ATPase	EC:7.2.2.12 EC:7.2.2.21	Enzymes with EC numbers	-	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of agem_s0076.g86.t1 across 48 RNA-seq samples of Acropora gemmifera. 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.

48Samples

2TPM > 0

1Conditions

1.4Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
branch tip	48	2	0.05	1.42

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR3223317	branch tip	branch tip	not recorded	not recorded	SRP062488	1.42
SRR3223319	branch tip	branch tip	not recorded	not recorded	SRP062488	0.75
SRR2169558	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169421	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169422	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169423	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169425	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169426	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169518	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169527	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169528	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169529	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169530	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169531	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169532	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169533	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169534	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169535	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169536	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169537	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169538	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169539	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169540	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3169541	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182410	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182448	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182557	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182684	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182685	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182686	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182775	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182776	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182777	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182778	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182779	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182780	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182781	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182784	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182785	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182786	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182787	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182788	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182789	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182790	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182791	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182792	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182793	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00
SRR3182794	branch tip	branch tip	not recorded	not recorded	SRP062488	0.00

Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM, StringTie quantification over 48 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.