Gene detail

Detailed information of g16343.t1 in Montipora capitata

Genomic Location: Sc0000679:142803...153820
NR annotation: XP_029212158.1, uncharacterized protein LOC114975997 isoform X1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g16343.t1

atgcatagtccaagtgaagctataattgagcggtcgaagcatttgattgcgactaccccgggctctgttgacataacctctggaacacactcagaactacttcagtcttccgcgatcccgatatccttgaagactgctgcatctcctagttcagtggattgcgaggcagaggaaactgatggtccaaacgctggactcgagcaagcgcttaagtcttctgtcagcaaggaaattcaagaaaggattaaaaaaatattggaggaggtacagcagttgtcagacactgagaaattgttactttacctgcggcttccaggagagacagcatctgattccatagatgactttgaccaaaatcaaagtcttcctatttcaactaccagggctgaacaaacacaagcattccattggatccgctgtcatttggaggaatgtgacaataattctactttacccaagcatgaggtttatgatgaatacaaagctcactgtgaaagcatgaatgctgcccggacactcagcgcaccagactttgggaagataatcaagtgtgtgttccctagagtgaaagcaagaagactgggtacacgagggaattcgaaatactgttacagtggaatccaaagaaaaaagaacgttaaaccaccaactctcccatcattgcagatcccaccagcaagtgacaaggacaagagttcaacaaatacagcaaacagtttgagtggaggcgataaaatagaagaggaccagactctgtctgcagcttgtttacttgtgtgcgaatgggcaaacaaactgcttggaagggtattcagtaccctgattgagttggccaggtttcttgtaggaggaagttatgtttccagcaaatccatggcagcatttgttgtgatgtccagcaatgacctgaacacaccacagatcagtcattcaatggtgtctttgatgacacccctgaagcaagtagaggaacagatgttactaacacaaaaacgaaggcattcacagcagttagcaaaaaaattgtcatcacgacaacagcagaagcaaattcccactaattctatcattcagcagggcactggcttgtgtaacacaccaacacagttgttaggacacaagacactggtgagcatatcaagtccacaaaagcctcctcacaaacaaccattacacattcagccaaagccaatacaaccagcacttcaaagccctccagcacaagtaggaacattctaccaacaacaacaacaacctagtaaccctagcacgtcacctagtagctaccctcccaagattagacccataacaccatccatgatatcacctaccacccccatacagcccacagtaccacagacaccatcacctttccagtcatcgccaaagttcaatactccagggacacctcagaatcgtccagtcacaccaagctcagcaaatgctgctgcaaggcacacaccaaactcagctgagcctacacgcttcctgtttactccaatccccagtagctcacaagaacagagaatcaatagaggagaaacaagtccgctgacgttacgaccaacagcaacccatcctagccaaatcattaacagtgattggccacagcaaggatctcaacagttgggaattaatgatgtgccaatttcacccagtaaacaaccaagattgatgaatcaaaaccatccatcaactccaacttccaaccgcagacctggctcatttgcatatccattaccatcaccacggactccacaacgcattgcaccacagcagtatgttacatcacccacaatgggggcatcccctggggttggacatcagctaaatcctgtttctccaaatgttgcacaacacagccaagaatttatgatcccaattattacaaatgtggaaagcatggctccaaaaggatttacaccatctgtaaatataacaacgacaacatcgtcccttggcaatgtgcacatctcacagcagcattctaaacaagggtccccggtgattttgccaaaatcctgcagatacagcagtggtacagataatgcacacattcagctggctccagtcatacaccatcaggcaacagactactcatcagaacttgagtcaatctgcaaccagcccacaagctctgcaagccaaatccctccaccttcataccagcgcagccaatcagtgcctccgttaacacagcataatatggcagaccaaaggtttcatccattgacaccccaaaccacccctcgtcctcctcgtcctcaacatcttactccatctcccatggatacttcgagccaacatttaaatggtttaaaggagctgcgcaacagagttctttatggcgatgttaataacaatggatcacgaccaacacaggttgaaagtgctttttcagcacgacggaatctcacacctatgctcaatgctgaaaattcaaatgtaaatgtgtcaaactgggaagtgcaaccagttcgaacaaaccacccaaacagggaaggagagaatcatgaaatggcaatgctggaaaataacttgacttttgcagatctcggtaatgacaatgatgagacactttctgatttaaacacactggatgatgcaacaactgaggcagtactgaggaacatttgtaacaacacatcaggagtatggcccacaaatgatgttcatgcctggccaaactcccaagcattgcaaattatggattag

Transcript

g16343.t1

ATGCATAgtccaagtgaagctataattGAGCGGTCGAAGCATTTGATTGCGACTACCCCGGGCTCTGTTGACATAACCTCTGGAACACACTCAGAACTACTTCAGTCTTCCGCGATCCCGATATCCTTGAAGACTGCTGCATCTCCTAGTTCAGTGGATTGCGAGGCAGAGGAAACTGATGGTCCAAACGCTGGACTCGAGCAAGCGCTTAAGTCTTCTGTCAGCAAGGAAATTCAAGAaaggattaaaaaaatattgGAGGAGGTACAGCAGTTGTCAGACACTGAGAAATTGTTACTTTACCTGCGGCTTCCAGGAGAGACAGCATCTGATTCCATAGATGACTTTGACCAAAATCAAAGTCTTCCTATTTCAACTACCAGGGCTGAACAAACACAAGCATTCCATTGGATCCGCTGTCATTTGGAGGAATGTGACAATAATTCTACTTTACCCAAGCATGAGGTTTATGATGAATACAAAGCTCACTGTGAAAGCATGAATGCTGCCCGGACACTCAGCGCACCAGACTTTGGGAAGATAATCAAGTGTGTGTTCCCTAGAGTGAAAGCAAGAAGACTGGGTACACGAGGGAATTCGAAATACTGTTACAGtggaatccaaagaaaaaagaacgtTAAACCACCAACTCTCCCATCATTGCAGATCCCACCAGCAAGTGACAAGGACAAGAGTTCAACAAATACAGCAAACAGTTTGAGTGGAGGCGATAAAATAGAAGAGGACCAGACTCTGTCTGCAGCTTGTTTACTTGTGTGCGAATGGGCAAACAAACTGCTTGGAAGGGTATTCAGTACCCTGATTGAGTTGGCCAGGTTTCTTGTAGGAGGAAGTTATGTTTCCAGCAAATCCATGGCAGCATTTGTTGTGATGTCCAGCAATGACCTGAACACACCACAGATCAGTCATTCAATGGTGTCTTTGATGACACCCCTGAAGCAAGTAGAGGAACAGATGTTACTAACACAAAAACGAAGGCATTCACAGCAGTTAGCAAAAAAATTGTCATCACGACAACAGCAGAAGCAAATTCCCACTAATTCTATCATTCAGCAGGGCACTGGCTTGTGTAACACACCAACACAGTTGTTAGGACACAAGACACTGGTGAGCATATCAAGTCCACAAAAGCCTCCTCACAAACAACCATTACACATTCAGCCAAAGCCAATACAACCAGCACTTCAAAGCCCTCCAGCACAAGTAGGAACATTctaccaacaacaacaacaacctagTAACCCTAGCACGTCACCTAGTAGCTACCCTCCCAAGATTAGACCCATAACACCATCCATGATATCACCTACCACCCCCATACAGCCCACAGTACCACAGACACCATCACCTTTCCAGTCATCGCCAAAGTTCAATACTCCAGGGACACCTCAGAATCGTCCAGTCACACCAAGCTCAGCAAATGCTGCTGCAAGGCACACACCAAACTCAGCTGAGCCTACACGCTTCCTGTTTACTCCAATCCCCAGTAGCTCACAAGAACAGAGAATCAATAGAGGAGAAACAAGTCCGCTGACGTTACGACCAACAGCAACCCATCCTAGCCAAATCATTAACAGTGATTGGCCACAGCAAGGATCTCAACAGTTGGGAATTAATGATGTGCCAATTTCACCCAGTAAACAACCAAGATTGATGAATCAAAACCATCCATCAACTCCAACTTCCAACCGCAGACCTGGCTCATTTGCATATCCATTACCATCACCACGGACTCCACAACGCATTGCACCACAGCAGTATGTTACATCACCCACAATGGGGGCATCCCCTGGGGTTGGACATCAGCTAAATCCTGTTTCTCCAAATGTTGCACAACACAGCCAAGAATTTATGATCCCAATTATTACAAATGTGGAAAGCATGGCTCCAAAAGGATTTACACCATCTGTAAATATAACAACGACAACATCGTCCCTTGGCAATGTGCACATCTCACAGCAGCATTCTAAACAAGGGTCCCCGGTGATTTTGCCAAAATCCTGCAGATACAGCAGTGGTACAGATAATGCACACATTCAGCTGGCTCCAGTCATACACCATCAGGCAACAGACTACTCATCAGAACTTGAGTCAATCTGCAACCAGCCCACAAGCTCTGCAAGCCAAATCCCTCCACCTTCATACCAGCGCAGCCAATCAGTGCCTCCGTTAACACAGCATAATATGGCAGACCAAAGGTTTCATCCATTGACACCCCAAACCACCCCTCGTCCTCCTCGTCCTCAACATCTTACTCCATCTCCCATGGATACTTCGAGCCAACATTTAAATGGTTTAAAGGAGCTGCGCAACAGAGTTCTTTATGGCGATGTTAATAACAATGGATCACGACCAACACAGGTTGAAAGTGCTTTTTCAGCACGACGGAATCTCACACCTATGCTCAATGCTgaaaattcaaatgtaaatgTGTCAAACTGGGAAGTGCAACCAGTTCGAACAAACCACCCAAACAGGGAAGGAGAGAATCATGAAATGGCAATGCTGGAAAATAACTTGACTTTTGCAGATCTCGGTAATGACAATGATGAGACACTTTCTGATTTAAACACACTGGATGATGCAACAACTGAGGCAGTACTGAGGAACATTTGTAACAACACATCAGGAGTATGGCCCACAAATGATGTTCATGCCTGGCCAAACTCCCAAGCATTGCAAATTATGGATTAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A0A1L8H0H2	DNA-binding protein RFX7 OS=Xenopus laevis OX=8355 GN=rfx7.L PE=2 SV=1
Q2KHR2	DNA-binding protein RFX7 OS=Homo sapiens OX=9606 GN=RFX7 PE=1 SV=2
F8VPJ6	DNA-binding protein RFX7 OS=Mus musculus OX=10090 GN=Rfx7 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006718 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02257 all species →	RFX_DNA_binding	RFX DNA-binding domain	Domain	Interproscan
PF18326 all species →	RFX5_N	RFX5 N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039779 all species →	Family	RFX-like DNA-binding protein	Interproscan
IPR003150 all species →	Domain	DNA-binding RFX-type winged-helix domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12619 all species →	RFX TRANSCRIPTION FACTOR FAMILY	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:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	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
K09175	RFX7; DNA-binding protein RFX7	-	Transcription factors	ko03000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g16343.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

219.2Max TPM

48.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	56.86	219.17
whole organisms · low pH treatment	15	15	44.27	208.74
whole organisms · extra low pH treatment pH treatment	12	12	40.47	185.88

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	219.17
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	172.61
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	171.01
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	161.77
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	144.52
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	99.47
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	82.78
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	30.88
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	30.63
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	28.85
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	6.66
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	5.82
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	5.81
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	5.58
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	5.35
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	5.21
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	5.16
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	4.46
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	3.24
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	2.89
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	2.23
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	208.74
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	176.18
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	169.06
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	24.54
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	22.72
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.07
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	7.68
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.01
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.18
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	4.87
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	4.02
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.87
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.86
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	2.93
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	2.34
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	185.88
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	172.59
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	31.67
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	29.88
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	29.69
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.28
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.10
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	6.04
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	5.60
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	4.55
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	3.88
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.50

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.