Gene detail

Detailed information of g10146.t1 in Montipora capitata

Genomic Location: Sc0000279:197881...219696
NR annotation: XP_029205115.1, lysine-specific histone demethylase 1A isoform X1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g10146.t1

atgtcgggttcttatccgccaccaattctcccaaagccgacaagtattcttccttttatagcaaccaagccaaacatgccaggtcagggtgtgaatgggaattactctgactctcataagatggaagaaaaaagagataatggatcatcttctgaatttttcgacgaggattcagacatgtccagaaggacaagccaacgcaaacgcccaaaagttgagtacacagaggtcgatgttaaactggcaaatttgacagatgatgaattatctgatgatgaagttattcagagaaacacaccacgaatatcaccaactaccacaccaatggaggctgaggaacaacgtgaaggagaagaggaagaagaagaagaagatgttcctgaaggacttgaaggtgcagcatttcaaagcagacttccatttgacaagatgacttcacaagaagtatcctgttttccagatgtatcgcaaggtcccccacaaattcagaaacacttcttatacctcaggaatagaatgctgcaattatggctggaaaatccaaggcaacagttaaccctggaacatatgttatcccaactagatccttctcaaaataatgaccctaagcttgcctccagggtccacgcctttctttccagatatggtttaatcaactttggagtgtacaagaccctccaaatgccaccagcattgaagaaagctccaaaagtgatagttgttggctctggaatctcaggccttacagcagcaagacagttgcagtcctttggcattgatgtaacaattgttgaagccagggagcgtgttggtggaagagttgccacattccgcaaaggacaatacatagcagatcttggggctatggttttgactggattaggtggaaaccctttgactgtgatggcaaatcaaatcagcatggagttacataaaatcagacagaaatgtcccctgtatgaaactcatgggaaatcgggccctattgaaaagaaagccaacagcagactctcggcagtgagggttccgaaagagaaggatgagatggttgaacgtgaattcaatagactgctagaagcgtcatcgttcctgtctcatcagctagatttcaattacatgcacagtaaacctgtatcattgggtcatgcattggagcttgttatcaaaatgcaagagagacaagtcaaggaacagcagattgaacatgctaaaaaaattctgaagattcaagaacaactgaagacaaacctgtcccagatggtgcaaataaaagaaaaagtcaagcaaacacataaagaatatcaagatgcactcaaagttaaggaaccaagggacatcacagcagagttcttagtaaaaagcaagttaagggacttgaatgccctttgcagggaatatgatgaaatggcagaggagcaactacggattgaagagagattggaggaacttgaagaaaaccctcccagtgacgtttatttatcatcaagagatcggcagatccttgactggcattttgccaacctggagtttgcaaatgccacacccttgacatcattatcattaaagcattgggatcaagatgatgactttgaattcagtggtagtcacatgactgtacgtaatggttactcatgcctgccaaaggccttggctgaaggactggatatcagactcaatacagctgtgcgacatgtccgctacaataggactggtgtggaattggtaacacagagtactagtaagtcatctattacgaccactcaaacattcaaaggagatgctgtacttataactcttcccctgggagtacttaaaagccatccacctagtgcgcagtttcacccacccctcccagagtggaagaccgctgctattcacagaatggggtttggaaatctcaacaaggtggtcttgtgttttgatcgagtgttctgggatccaaatacaaatctttttggtcatgttggaagtacaacagcaaatcggggtgagctgttccttttctggaatctgtacaagtcaccagtcctcattgctcttgttgctggagaagctgcaaacaagctggagaatgtttcagatgagattattgttggcagtgccattgctgtgttaaaagggatctttggaagcagtgcagttcctcagccaaaggaaacagtggtgacgcgctggaagtcggatgaatggtccagaggctcgtattcatttgtggcagctggctcttcaggaaatgactatgatctaatggcatccccagtggcccctcccccagtagcaggaatgccacctggaaacccctccccacccaatccccctagggttttctttgcgggagaacatactatcaggaattaccctgccacagtccatggtgcgctactgagtggtttgagagaggctgggagaattgctgatcagttcctaggactgccatatgaggttaatagagttgggcaggctcctgtatctcaaggctga

Transcript

g10146.t1

ATGTCGGGTTCTTATCCGCCACCAATTCTCCCAAAGCCGACAAGTATTCTTCCTTTTATAGCAACCAAGCCAAACATGCCAGGTCAGGGTGTGAATGGGAATTACTCTGACTCTCATAAGATGGAAGAAAAAAGAGATAATGGATCATCTTCTGAATTTTTCGACGAGGATTCAGACATGTCCAGAAGGACAAGCCAACGCAAACGCCCAAAAGTTGAGTACACAGAGGTCGATGTTAAACTGGCAAATTTGACAGATGATGAATTATCTGATGATGAAGTTATTCAGAGAAACACACCACGAATATCACCAACTACCACACCAATGGAGGCTGAGGAACAACGTGAAggagaagaggaagaagaagaagaagatgttCCTGAAGGACTTGAAGGTGCAGCATTTCAAAGCAGACTTCCATTTGACAAGATGACTTCACAAGAAGTATCCTGTTTTCCAGATGTATCGCAAGGTCCCCCACAAATTCAGAAACACTTCTTATACCTCAGGAATAGAATGCTGCAATTATGGCTGGAAAATCCAAGGCAACAGTTAACCCTGGAACATATGTTATCCCAACTAGATCCTTCTCAAAATAATGACCCTAAGCTTGCCTCCAGGGTCCACGCCTTTCTTTCCAGATATGGTTTAATCAACTTTGGAGTGTACAAGACCCTCCAAATGCCACCAGCATtgaAGAAAGCTCCAAAAGTGATAGTTGTTGGCTCTGGAATCTCAGGCCTTACAGCAGCAAGACAGTTGCAGTCCTTTGGCATTGATGTAACAATTGTTGAAGCCAggGAGCGTGTTGGTGGAAGAGTTGCCACATTCCGCAAAGGACAATACATAGCAGATCTTGGGGCTATGGTTTTGACTGGATTAGGTGGAAACCCTTTGACTGTGATGGCAAATCAAATCAGCATGGAGTTACATAAAATCAGACAGAAATGTCCCCTGTATGAAACTCATGGGAAATCGGGCCCTATTGAAAAGAAAGCCAACAGCAGACTCTCGGCAGTGAGGGTTCCGAAAGAGAAGGATGAGATGGTTGAACGTGAATTCAATAGACTGCTAGAAGCGTCATCGTTCCTGTCTCATCAGCTAGATTtcaattacatgcacagtaaacCTGTATCATTGGGTCATGCATTGGAGCTTGTTATCAAAATGCAAGAGAGACAAGTCAAGGAACAGCAGATTGAACATGCTAAAAAAATTCTGAAGATTCAAGAACAACTGAAGACAAACCTGTCCCAGATGgtgcaaataaaagaaaaagtcaAGCAAACACATAAAGAATATCAAGATGCACTCAAAGTTAAGGAACCAAGGGACATCACAGCAGAGTTCTTAGTAAAAAGCAAGTTAAGGGACTTGAATGCCCTTTGCAGGGAATATGATGAAATGGCAGAGGAGCAACTACGGATTGAAGAGAGATTGGAGGAACTTGAAGAAAACCCTCCCAGTGacgtttatttatcatcaaGAGATCGGCAGATCCTTGACTGGCATTTTGCCAACCTGGAGTTTGCAAATGCCACACCCTtgacatcattatcattaaaGCATTGGGATCAAGATGATGACTTTGAATTCAGTGGTAGTCACATGACTGTACGTAATGGTTACTCATGCCTGCCAAAGGCCTTGGCTGAAGGACTGGATATCAGACTCAATACAGCTGTGCGACATGTCCGCTACAATAGGACTGGTGTGGAATTGGTAACACAGAGTACTAGTAAGTCATCTATTACGACCACTCAAACATTCAAAGGAGATGCTGTACTTATAACTCTTCCCCTGGGAGTACTTAAAAGCCATCCACCTAGTGCGCAGTTTCACCCACCCCTCCCAGAGTGGAAGACCGCTGCTATTCACAGAATGGGGTTTGGAAATCTCAACAAGGTGGTCTTGTGTTTTGATCGAGTGTTCTGGGATCCAAATACAAATCTTTTTGGTCATGTTGGAAGTACAACAGCAAATCGGGGTGAGCTGTTCCTTTTCTGGAATCTGTACAAGTCACCAGTCCTCATTGCTCTTGTTGCTGGAGAAGCTGCAAACAAGCTGGAGAATGTTTCAGATGAGATTATTGTTGGCAGTGCCATTGCTGTGTTAAAAGGGATCTTTGGAAGCAGTGCAGTTCCTCAGCCAAAGGAAACAGTGGTGACGCGCTGGAAGTCGGATGAATGGTCCAGAGGCTCGTATTCATTTGTGGCAGCTGGCTCTTCAGGAAATGACTATGATCTAATGGCATCCCCAGTGGCCCCTCCCCCAGTAGCAGGAATGCCACCTGGAAACCCCTCCCCACCCAATCCCCCTAGGGTTTTCTTTGCGGGAGAACATACTATCAGGAATTACCCTGCCACAGTCCATGGTGCGCTACTGAGTGGTTTGAGAGAGGCTGGGAGAATTGCTGATCAGTTCCTAGGACTGCCATATGAGGTTAATAGAGTTGGGCAGGCTCCTGTATCTCAAGGCTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6ZQ88	Lysine-specific histone demethylase 1A OS=Mus musculus OX=10090 GN=Kdm1a PE=1 SV=2
O60341	Lysine-specific histone demethylase 1A OS=Homo sapiens OX=9606 GN=KDM1A PE=1 SV=2
Q9VW97	Possible lysine-specific histone demethylase 1 OS=Drosophila melanogaster OX=7227 GN=Su(var)3-3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002920 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01593 all species →	Amino_oxidase	Flavin containing amine oxidoreductase	Domain	Interproscan
PF04433 all species →	SWIRM	SWIRM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR017366 all species →	Family	Lysine-specific histone demethylase	Interproscan
IPR050281 all species →	Family	Flavin monoamine oxidase and related enzymes	Interproscan
IPR007526 all species →	Domain	SWIRM domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR002937 all species →	Domain	Amine oxidase	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10742 all species →	FLAVIN MONOAMINE OXIDASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0008134 all species →	Molecular Function	transcription factor binding	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	Interproscan
GO:0005515 all species →	Molecular Function	protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11450	KDM1A, AOF2, LSD1; [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase	EC:1.14.99.66	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g10146.t1 across 48 RNA-seq samples of Montipora capitata. 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

48TPM > 0

3Conditions

217.1Max TPM

105.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	113.79	217.15
whole organisms · low pH treatment	15	15	99.54	132.19
whole organisms · extra low pH treatment pH treatment	12	12	96.50	116.69

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	217.15
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	191.08
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	154.90
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	143.50
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	126.59
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	125.13
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	118.93
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	118.38
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	118.07
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	117.92
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	113.39
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	112.80
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	111.95
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	91.87
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	90.91
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	90.21
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	81.54
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	77.22
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	66.30
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	61.62
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	60.18
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	132.19
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	126.18
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	125.42
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	122.50
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	119.78
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	115.73
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	106.04
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	100.24
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	95.62
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	92.45
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	77.22
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	73.19
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	71.78
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	71.69
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	63.12
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	116.69
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	115.95
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	115.48
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	114.08
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	112.23
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	112.17
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	106.81
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	80.74
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	78.02
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	77.69
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	66.83
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	61.34

Source: CnidoSite RNA-seq expression matrices (MCAPI_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.