Gene detail

Detailed information of g11459.t1 in Montipora capitata

Genomic Location: Sc0000344:228751...248748
NR annotation: XP_029191085.2, transcription factor 25-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g11459.t1

atgtcttcacgcgttttgagaaagctgcagggtggtaacgaactggacatttcccgtgatgacgaggaagacgaagacgaatttcatttcttgccagttacgtcaaagaagacgaaagagaaagccttggccaatcctttcgatttgttaaatgtagaggatcagccatcaaatgaagattctcaagatagtcaagaagatgaaattccaagagaaaatgcgagggagaatttaacagaagagaagccatgttcaactgagcctttatctaaaaggacaaagaaaaagaaaaaaaagaaaggaaagagagacattaaaaatgaagcaataatcaagcaaaaagaaaagactgatgagcccaagaacaaggataatgaaaatcatgggaaaatacgtggtcctattcatgttgctacttctggacagacaacttccagacctttggatactaaagctttgcttggtatagaacatagaaacttgaatgcagaaaatgaaatgagaaagcgatttggatctcatgttgtgagggcagaaaacaacagacagcggaaatcacatcaaagagtgtatcaaccagcaactaggctggttacaccaaaacaatcttggcctcgaattggagcaacagggataagaatggaaatggatgaaatgaaccgtggacacagcttctttgcatttcaccattctccgtcataccaggaagtccagtttcaatttcttgatgcagtggaatcacttaatcccaacaacatttctgatattttaaatacacatccttaccatgtggactccctgcttcaactgagtgaaatatgcaaaatgggagaggattatcaaatggctgcagagctaattgaaagagcgctttactgctttgaaagaagtttccacacaatctttaatcttacaacgggctactcaagacttcgatacagaagagcagagaacagatccttctatgttgcattgtttcgtcaaatcatttttgtgggacaaaaaggttgctacagaacagctttggaattgtgcaaacttttactcaaccttgatccagatgaagatccccttgctgtgctcctaatgattgatttctatgccctgagatcagagcagtttgatttccttgtacgattgtttgaagaatgggggcctcacagaaacttgtctcagctccccaactttgcattttctgtggcccttgctcactttcattccagtaaaaaagatggagaaacaaagaaagctgatgagatgctccaggaagctttgattatgtttccaatggttttgttgcctcttatggacaagtgtaatgttgcgttagactcctctctgatcaagcatccattcttttctcctgcatcagcaatgagttacccattggccttaaagcaacttgaagctctgtacattggcagaacataccatgcttggaaagaaacagaggtgattgactggttagctatgaacgtgaaaatcgttttggaaagagtagacgccaaggatcctttggtagagcagtgtacacacaagcgtcaagtacggtacataggaacaccacggaatgtttaccgacacattataatgtcagatatcaaggatgctactgcttctctgcctgtggatttggctaatgtgcctcttttgtcttacgatcctcttccgcctctggattcggtgtcaggatacaagcggccatcgaggagcactcgtcttgaccaagaacacggtgcgctatcgatgttcttccgttcattattaccgtcctttaacactcaggctcctattggtcaacgtgaacggttgcaagcgaggctggaacctcccatagaaggagcagaaggtgcacccaggcctctgcatgacacagacctcgcgcgaggagttgagaatttgttgactgccatgagagagctgttgaacactctaagccagagggatccaccggagggcgaacaacaaggtgaaacgggagacgatgatcgtgatccagacgaatgggaggacggcgacgaaaataactga

Transcript

g11459.t1

ATGTCTTCACGCGTTTTGAGAAAGCTGCAGGGTGGTAACGAACTGGACATTTCCCGTGATGACGAGGAAGACGAAGACGAATTTCATTTCTTGCCAGTTACGTCAAAGAAGACGAAAGAGAAAGCCTTGGCCAATCCTTTCGATTTGTTAAATGTAGAGGATCAGCCATCAAATGAAGATTCTCAAGATAGTCAAGAAGATGAAATTCCAAGAGAAAATGCGAGGGAGAATTTAACAGAAGAGAAGCCATGTTCAACTGAGCCTTTATCtaaaaggacaaagaaaaagaaaaaaaagaaaggaaagagagACATTAAAAATGAAGCAATAATCAAGcaaaaagaaaagactGATGAGCCCAAGAACAAGGATAATGAAAATCATGGGAAAATACGTGGTCCTATTCATGTTGCTACTTCTGGACAGACAACTTCCAGACCTTTGGATACTAAAGCTTTGCTTGGTATAGAACATAGAAACTTGAATGCAGAAAATGAAATGAGAAAGCGATTTGGATCTCATGTTGTGAGGGCAGAAAACAACAGACAGCGGAAATCACATCAAAGAGTGTATCAACCAGCAACTAGGCTGGTTACACCAAAACAATCTTGGCCTCGAATTGGAGCAACAGgGATAAGAATGGAAATGGATGAAATGAACCGTGGACACAGCTTCTTTGCATTTCACCATTCTCCGTCATACCAGGAAGTCCAGTTTCAATTTCTTGATGCAGTGGAATCACTTAATCCCAACAACATTTCTGATATTTTAAATACACATCCTTACCATGTGGACTCCCTGCTTCAACTGAGTGAAATATGCAAAATGGGAGAGGATTATCAAATGGCTGCAGAGCTAATTGAAAGAGCGCTTTACTGCTTTGAAAGAAGTTTCCACACAATCTTTAATCTTACAACGGGCTACTCAAGACTTCGATACAGAAGAGCAGAGAACAGATCCTTCTATGTTGCATTGTTTCGTCAAATCATTTTTGTGGGACAAAAAGGTTGCTACAGAACAGCTTTGGAATTGTGCAAACTTTTACTCAACCTTGATCCAGATGAAGATCCCCTTGCTGTGCTCCTAATGATTGATTTCTATGCCCTGAGATCAGAGCAGTTTGATTTCCTTGTACGATTGTTTGAAGAATGGGGGCCTCACAGAAACTTGTCTCAGCTCCCCAACTTTGCATTTTCTGTGGCCCTTGCTCACTTTCATTCCAGTAAAAAAGATGGAGAAACAAAGAAAGCTGATGAGATGctCCAGGAAGCTTTGATTATGTTTCCAATGGTTTTGTTGCCTCTTATGGACAAGTGTAATGTTGCGTTAGACTCCTCTCTGATCAAGCATCCATTCTTTTCTCCTGCATCAGCAATGAGTTACCCATTGGCCTTAAAGCAACTTGAAGCTCTGTACATTGGCAGAACATACCATGCTTGGAAAGAAACAGAGGTGATTGACTGGTTAGCTATGAACGTGAAAATCGTTTTGGAAAGAGTAGACGCCAAGGATCCTTTGGTAGAGCAGTGTACACACAAGCGTCAAGTACGGTACATAGGAACACCACGGAATGTTTACCGACACATTATAATGTCAGATATCAAGGATGCTACTGCTTCTCTGCCTGTGGATTTGGCTAATGTGCCTCTTTTGTCTTACGATCCTCTTCCGCCTCTGGATTCGGTGTCAGGATACAAGCGGCCATCGAGGAGCACTCGTCTTGACCAAGAACACGGTGCGCTATCGATGTTCTTCCGTTCATTATTACCGTCCTTTAACACTCAGGCTCCTATTGGTCAACGTGAACGGTTGCAAGCGAGGCTGGAACCTCCCATAGAAGGAGCAGAAGGTGCACCCAGGCCTCTGCATGACACAGACCTCGCGCGAGGAGTTGAGAATTTGTTGACTGCCATGAGAGAGCTGTTGAACACTCTAAGCCAGAGGGATCCACCGGAGGGCGAACAACAAGGTGAAACGGGAGACGATGATCGTGATCCAGACGAATGGGAGGACGGCGACGAAAATAACTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8R3L2	Ribosome quality control complex subunit TCF25 OS=Mus musculus OX=10090 GN=Tcf25 PE=1 SV=2
Q9BQ70	Ribosome quality control complex subunit TCF25 OS=Homo sapiens OX=9606 GN=TCF25 PE=1 SV=1
A0A8I6ASZ5	Ribosome quality control complex subunit TCF25 OS=Rattus norvegicus OX=10116 GN=Tcf25 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004349 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04910 all species →	Tcf25	Transcriptional repressor TCF25	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR006994 all species →	Family	TCF25/Rqc1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22684 all species →	NULP1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:1990112 all species →	Cellular Component	RQC complex	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
K24970	TCF25, RQC1; transcription factor 25	-	Ribosome biogenesis	ko03009	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g11459.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

74.0Max TPM

30.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	35.35	73.95
whole organisms · low pH treatment	15	15	26.24	55.13
whole organisms · extra low pH treatment pH treatment	12	12	26.60	61.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	73.95
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	69.62
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	63.37
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	59.50
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	56.32
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	56.16
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	55.99
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	47.21
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	45.68
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	44.95
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	39.79
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	32.63
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	28.71
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	13.61
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	11.84
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	11.64
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	10.63
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	8.02
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	5.22
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	3.92
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	3.61
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	55.13
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	54.68
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	51.44
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	44.88
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	33.03
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	30.17
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	29.22
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	26.40
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	24.84
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	11.22
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	9.96
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	8.73
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	6.43
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.79
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.64
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	61.58
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	58.48
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	57.97
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	40.54
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	28.64
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	25.66
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	20.00
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	6.29
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.06
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.02
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	5.75
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	2.18

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.