Gene detail

Detailed information of g5439.t1 in Montipora capitata

Genomic Location: Sc0000107:606969...616766
NR annotation: XP_015777254.1, PREDICTED: transcriptional regulator prz1-like isoform X1 [Acropora digitifera]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g5439.t1

atgttgcagggaaatgcggagggccaagacaacactgaaattgatttgaaagattatacagccactgttagatatcttgagcagctacaagaaacgagcatcaagactttcacagcagaacttcagaaaagcggtgctgaaattttagagcagaagtccagtatgtacgagtctggacgaggcctctacggacaaacgccggcaggtttgaaaatatgcaatctggaggcgagtgtaagagcatcgcgattgcggggatacagtcaatataattcatttaatcaaggagaaatagactctggtgctgaggacgagccaaggatgatttcagccgtgtcaaagagagctgctcagttcgattaccattacgcggatcacaaaacgcacagtggaatgtccacaaaggaaagtgtcaactttataaacgccaacaacacgcaaaatggatttacggcgaaaaattccgcaggaccgttccctccagctgttgtcagcaactgtttatcgccgtcacttcagaattgctcgacgtcgcttggaatgaatccgttagctggcttaacggagctggcagagaaggccaacttcgtgtctgaactctcgcagaatggcgtcgctgtgtctcgctttagctctcaaccgagccgcggtcaattaaatggccaggccgttcagtacggcttcccagaagcaccaagaagccgaagctggtcaggttcgactcctgaaccagcagctaatttcttcagtggaagacagcaggcgtttcaaggcggcgacaacttctcgccttcgctctcgacgggcagctcagtgttttcagactccgatcttggaagcccttgtcctccgacaagagcgcgacaacatttctttcctcaaagtgttaacgagtcagattctgagctaagagatcttagccccacgaccgaaacaaatccatttgagcgatcgagtggagggttttcaaactacagccaaagatcatttgcaaattaccggctttggagtaaccaagctgaatcagcctcaccaaatgtcactttggtgccaaacccgaggggtaaactatcgcagcttttcaagtctggcagtcgcacaaaatcagaggaaattcttaaagatcatttacaaaatttcggcaagtttttgccttcggaaggagggaaagaacaggagaaaacacctcaaaatgacatcgaagatagctggagtagcgaagaagaaatcaaggagacgaaaaagacagcagtgaaatcgagcgcaaaggaatccagcgccagtgcgagcgaagagaacacattattcccttgtaaatggattggatgtgatggagtttattcggaaagagatgatttggttcggcatatcgaaaaggtccacatcgaccagagaaaagcggacgatttgtatatttgctattggaaagattgtagcaggcagagacgagcatttaacgcgagatacaagcttgttatacacatgagagttcactctggggagaagccaaatcggtgtacgttcccaggatgtaacaaggcattttcgaggctggagaacctaaaaatccatatgagatcccatactggtgagaagccatatctttgccagcatcttggctgtccaaaagctttcagcaattcctcagatagagcaaagcatcaaaggacacatcaggatactaaaccatatgcttgtcaagttccaggctgtccaaaaagatacacagatccaagttccctaagaaagcactttaaacagcatgcaaatggaaagatgcctcaagcaaatgcaagtggaaagcccaaacagaaacccagaggaaacaggtcatcaaagagagacctcctgagtgcaggagtgacaagacccctctctgagttcacttacattgatgagtatcaggcaagaaagcggcagaagacattagacactctccgacaaacaacagagaaaaaacttgcccttgaacgtagctttagtccttttgaaactcagagggcatggtatggagaggcactctatggtccattcagcccaccccctttgcaaccagtggcaagggccagcacaccgacacttgaagaggaacaaggctcctttcgatacacccaaatgttgagtacgatggaaataccaacctttgaagacactttaaaacctctcacaagtggatattcaacatga

Transcript

g5439.t1

ATGTTGCAGGGAAATGCGGAGGGCCAAGACAACACTGAAATTGATTTGAAAGATTATACAGCCACTGTTAGATATCTTGAGCAGCTACAAGAAACGAGCATCAAGACTTTCACAGCAGAACTTCAGAAAAGCGGTGCTGAAATTTTAGAGCAGAAGTCCAGTATGTACGAGTCTGGACGAGGCCTCTACGGACAAACGCCGGCAGGTTTGAAAATATGCAATCTGGAGGCGAGTGTAAGAGCATCGCGATTGCGGGGATACAGTCAATATAATTCATTTAATCAAGGAGAAATAGACTCTGGTGCTGAGGACGAGCCAAGGATGATTTCAGCCGTGTCAAAGAGAGCTGCTCAGTTCGATTACCATTACGCGGATCACAAAACGCACAGTGGAATGTCCACAAAGGAAAGTGTCAACTTTATAAACGCCAACAACACGCAAAATGGATTTACGGCGAAAAATTCCGCAGGACCGTTCCCTCCAGCTGTTGTCAGCAACTGTTTATCGCCGTCACTTCAGAATTGCTCGACGTCGCTTGGAATGAATCCGTTAGCTGGCTTAACGGAGCTGGCAGAGAAGGCCAACTTCGTGTCTGAACTCTCGCAGAATGGCGTCGCTGTGTCTCGCTTTAGCTCTCAACCGAGCCGCGGTCAATTAAATGGCCAGGCCGTTCAGTACGGCTTCCCAGAAGCACCAAGAAGCCGAAGCTGGTCAGGTTCGACTCCTGAACCAGCAGCTAATTTCTTCAGTGGAAGACAGCAGGCGTTTCAAGGCGGCGACAACTTCTCGCCTTCGCTCTCGACGGGCAGCTCAGTGTTTTCAGACTCCGATCTTGGAAGCCCTTGTCCTCCGACAAGAGCGCGACAACATTTCTTTCCTCAAAGTGTTAACGAGTCAGATTCTGAGCTAAGAGATCTTAGCCCCACGACCGAAACAAATCCATTTGAGCGATCGAGTGGAGGGTTTTCAAACTACAGCCAAAGATCATTTGCAAATTACCGGCTTTGGAGTAACCAAGCTGAATCAGCCTCACCAAATGTCACTTTGGTGCCAAACCCGAGGGGTAAACTATCGCAGCTTTTCAAGTCTGGCAGTCGCACAAAATCAGAGGAAATTCTTAAAGATCATTTACAAAATTTCGGCAAGTTTTTGCCTTCGGAAGGAGGGAAAGAACAGGAGAAAACACCTCAAAATGACATCGAAGATAGCTGGAGTAGCGAAGAAGAAATCAAGGAGACGAAAAAGACAGCAGTGAAATCGAGCGCAAAGGAATCCAGCGCCAGTGCGAGCGAAGAGAACACATTATTCCCTTGTAAATGGATTGGATGTGATGGAGTTTATTCGGAAAGAGATGATTTGGTTCGGCATATCGAAAAGGTCCACATCGACCAGAGAAAAGCGGACGATTTGTATATTTGCTATTGGAAAGATTGTAGCAGGCAGAGACGAGCATTTAACGCGAGATACAAGCTTGTTATACACATGAGAGTTCACTCTGGGGAGAAGCCAAATCGGTGTACGTTCCCAGGATGTAACAAGGCATTTTCGAGGCTGGAGAACCTAAAAATCCATATGAGATCCCATACTGGTGAGAAGCCATATCTTTGCCAGCATCTTGGCTGTCCAAAAGCTTTCAGCAATTCCTCAGATAGAGCAAAGCATCAAAGGACACATCAGGATACTAAACCATATGCTTGTCAAGTTCCAGGCTGTCCAAAAAGATACACAGATCCAAGTTCCCTAAGAAAGCACTTTAAACAGCATGCAAATGGAAAGATGCCTCAAGCAAATGCAAGTGGAAAGCCCAAACAGAAACCCAGAGGAAACAGGTCATCAAAGAGAGACCTCCTGAGTGCAGGAGTGACAAGACCCCTCTCTGAGTTCACTTACATTGATGAGTATCAGGCAAGAAAGCGGCAGAAGACATTAGACACTCTCCGacaaacaacagagaaaaaactTGCCCTTGAACGTAGCTTTAGTCCTTTTGAAACTCAGAGGGCATGGTATGGAGAGGCACTCTATGGTCCATTCAGCCCACCCCCTTTGCAACCAGTGGCAAGGGCCAGCACACCGACACTTGAAGAGGAACAAGGCTCCTTTCGATACACCCAAATGTTGAGTACGATGGAAATACCAACCTTTGAAGACACTTTAAAACCTCTCACAAGTGGATATTCAACATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8NEA6	Zinc finger protein GLIS3 OS=Homo sapiens OX=9606 GN=GLIS3 PE=1 SV=5
Q6XP49	Zinc finger protein GLIS3 OS=Mus musculus OX=10090 GN=Glis3 PE=1 SV=2
Q8NBF1	Zinc finger protein GLIS1 OS=Homo sapiens OX=9606 GN=GLIS1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004801 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00096 all species →	zf-C2H2	Zinc finger, C2H2 type	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR043359 all species →	Family	C2H2-type zinc-finger protein GLI-like	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45718 all species →	TRANSCRIPTIONAL ACTIVATOR CUBITUS INTERRUPTUS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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
K09232	GLIS1_3; zinc finger protein GLIS1/3	-	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 g5439.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

40TPM > 0

3Conditions

59.1Max TPM

14.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	16	15.16	59.09
whole organisms · low pH treatment	15	13	11.83	39.10
whole organisms · extra low pH treatment pH treatment	12	11	16.58	57.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	59.09
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	54.92
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	43.04
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	38.87
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	26.77
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	22.46
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	14.84
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	13.67
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	12.85
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	11.64
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	10.16
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	4.40
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	3.67
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	1.10
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.63
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.34
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	39.10
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	38.35
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	35.80
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	19.68
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	15.69
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	11.45
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	7.16
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	3.52
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	3.37
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	1.17
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.77
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.74
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.72
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	57.63
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	57.10
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	36.25
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	22.77
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	15.25
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	3.55
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	3.44
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.94
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.81
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.77
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.50
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00

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.