Gene detail

Detailed information of g13765.t1 in Montipora capitata

Genomic Location: Sc0000483:64998...88824
NR annotation: XP_029184586.2, tRNA (uracil-5-)-methyltransferase homolog A-like isoform X1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g13765.t1

atggcggacggacaaaacgtggaagacaatacaaaccaaacatctaatttgagtggggaccagaccgtttttcttggtttaaaatcggtaaaaactgagacagaagatccttcgccaattcctggctttccgccgtttttccagtttgcaaaactgcaaacagaagcgagttcgtggggtgcaaatgctggcgcaagctcatcgacatcgtcttacgaatttgcagagaaaacgcaagttgtcaaaacagagccttgcagccctcagcaaagcagttcagaggaaatcaataccacaaattcaagctctgtgaagggagttgacccttctagttcgggagagaatccttggcctgggcttgggaatgttacgaaaattaaaacagaagatgaagagatggcggaagacaatgagacggacaaaggcgaagagaaagtcgaagaagcggctgcaaatgatgatccggacgaggaagaggctgaatccgatccttatttctacaccaaacgtgatgagtttacttcagaaatttacaaaatcgagctgcaaaatctaccaaagaaatgtggttacaagcaattcaagaaaatgattgccaacagactaaatgtgagacctgttaaggtgaaattgccaccaggtgcaagccatgcttatgtcacattcaggaatgaagaggaaagacgtttggctatcagatcattatcaggccataagtggaaaggaaaagttctttctgctaagactgctcagcctcttccagacccactggctcttcaacgagctgaaggaatggcaagaaaaagaatgatccaggatgctgctcgtgccaatgttgacgctaagagaataaaacttgatggtgatgtagtagatgagcttgctatttctgttaggttgaatcatgtggtcacaccattgtgggatcagccatacagcaaacaaatggagaccaagaagaacaacatgattgaagtattggggaaactgaccaggaagttgaaagccatcatggtgctaaagaacaactgggtggaggaagaaagtgctaaaagaaatggaatttgctgtgaactcctagattgtgtagaatcgcctgttcttgatggctatcgaaataagtgtgagttcacgatagctgaaggtcctgacggagctaaaactgttggattccgtcttggttcatacaaagagggttacagtggagttgtcgagccatctgaatgtatccacatttcagacaaggctaaaaccatctcaaaggctttccagacttatgtaaggcagtctccgctcccagtctatgacctctgctttcacactggttattggcagacactgactgttcggagctccatgtatggtgacaccatggctgtcctgcagtttagtccacaaaaaatgaccaaggatgaaatcgaagcagaaaaaaatcgcatttgtgagtatttcaagactggcgaaggcaaagatgtacagctgacatctctttatctgcaaattaaccatacgagggcggttggtggcaatgccgaagctccttttgttcacattatgggcgaagagcatatttatgaggagctctgtggcttgaaattcagaatctccccggactcgttcttccaagtgaacacaaaggcaacagagaagctgtttaatttgctcaaagactggtgtggcgaccatctggacgaaacagtagtgctagacatttgttgcggcactggtgcgcttggtctgtgtctggctcagagcgtcaagcgtgtgatcggtgttgaaataattgaaaatgctgttgaggatgcgaaagccaacgctcaactgaatggagtgacgaacgctcagtttgtttgtggtaaagcagaagatatcattgttgatgtcttcaaaaacatgccacggaaaaccaaaatcatcggcatcatggatccaccgcgagctggactgcaccaatctgtccttcatgccatccggaagagccgccgaatggacaaactcatctatgtgtcttgcaacccaagcgccgccttcgtcaactttctcgacttgtgcagacctacttccaagaggatcaagacagcgcccttccgcttggtcaaagctgtacccgtggatctgtttccacacaccaaacattgtgaactactcctcctctttgagagagatatgacttcagtggacgccgccaagttttacaagtggtattactaa

Transcript

g13765.t1

atggcggacggaCAAAACGTGGAAGACAATACAAACCAAACATCTAATTTGAGTGGGGACCAGACcgtttttcttggtttaaaatcGGTAAAAACTGAGACAGAAGATCCTTCGCCAATTCCTGGCTTTCCGCCGTTTTTCCAGTTTGCAAAACTGCAAACAGAAGCGAGTTCGTGGGGTGCAAATGCTGGCGCAAGCTCATCGACATCGTCTTACGAATTTGCAGAGAAAACGCAAGTTGTCAAAACAGAGCCTTGCAGCCCTCAGCAAAGCAGTTCAGAGGAAATCAATACCACAAATTCAAGCTCTGTGAAGGGAGTTGACCCTTCTAGTTCGGGAGAGAATCCTTGGCCTGGGCTTGGGAATGTTACGAAAATTAAAACAGAAGATGAAGAGATGGCGGAAGACAATGAGACGGACAAAGGCGAAGAGAAAGTCGAAGAAGCGGCTGCAAATGATGATCCGGACGAGGAAGAGGCTGAATCCGATCCTTATTTCTACACCAAACGTGATGAGTTTACTTCAGAAATTTACAAAATCGAGCTGCAAAATCTACCAAAGAAATGTGGTTACAAGCAATTCAAGAAAATGATTGCCAACAGACTAAATGTGAGACCTGTTAAGGTGAAATTGCCACCAGGTGCAAGCCATGCTTATGTCACATTCAGGAATGAAGAGGAAAGACGTTTGGCTATCAGATCATTATCAGGCCATAAGTGGAAAGGAAAAGTTCTTTCTGCTAAGACTGCTCAGCCTCTTCCAGACCCACTGGCTCTTCAACGAGCTGAAGGAATGGCAAGAAAAAGAATGATCCAGGATGCTGCTCGTGCCAATGTTGACGCTAAGAGAATAAAACTTGATGGTGATGTAGTAGATGAGCTTGCTATTTCTGTTAGGTTGAATCATGTGGTCACACCATTGTGGGATCAGCCATACAGCAAACAAATGGAGACCAAGAAGAACAACATGATTGAAGTATTGGGGAAACTGACCAGGAAGTTGAAAGCCATCATggtgctaaagAACAACTGGGTGGAGGAAGAAAGTGCTAAAAGAAATGGAATTTGCTGTGAACTCCTAGATTGTGTAGAATCGCCTGTTCTTGATGGCTATCGAAATAAGTGTGAGTTCACGATAGCTGAAGGTCCTGACGGAGCTAAAACTGTTGGATTCCGTCTTGGTTCATACAAAGagGGTTACAGTGGAGTTGTCGAGCCATCTGAATGTATCCACATTTCAGACAAGGCTAAAACCATCTCAAAGGCTTTCCAGACTTATGTAAGGCAGTCTCCGCTCCCAGTCTATGACCTCTGCTTTCACACTGGTTATTGGCAGACACTGACTGTTCGGAGCTCCATGTATGGTGACACCATGGCTGTCCTGCAGTTTAGTCCACAAAAAATGACCAAGGatgaaatcgaagcagaaaaaaatcgcatttGTGAGTATTTCAAGACTGGCGAAGGCAAAGATGTACAGCTGACATCTCTTTATCTGCAAATTAACCATACGAGGGCGGTTGGTGGCAATGCCGAAGCTCCTTTTGTTCACATTATGGGCGAAGAGCATATTTATGAGGAGCTCTGTGGCTTGAAATTCAGAATCTCCCCGGACTCGTTCTTCCAAGTGAACACAAAGGCAACAGAGAAGCTGTTTAATTTGCTCAAAGACTGGTGTGGCGACCATCTGGACGAAACAGTAGTGCTAGACATTTGTTGCGGCACTGGTGCGCTTGGTCTGTGTCTGGCTCAGAGCGTCAAGCGTGTGATCGGTGttgaaataattgaaaatgcTGTTGAGGATGCGAAAGCCAACGCTCAACTGAATGGAGTGACGAACGCTCAGTTTGTTTGTGGTAAAGCAGAAGATATCATTGTTGATGTCTTCAAAAACATGCCACGGAAAACCAAAATCATCGGCATCATGGATCCACCGCGAGCTGGACTGCACCAATCTGTCCTTCATGCCATCCGGAAGAGCCGCCGAATGGACAAACTCATCTATGTGTCTTGCAACCCAAGCGCCGCCTTCGTCAACTTTCTCGACTTGTGCAGACCTACTTCCAAGAGGATCAAGACAGCGCCCTTCCGCTTGGTCAAAGCTGTACCCGTGGATCTGTTTCCACACACCAAACATTGTGAACTACTCCTCCTCTTTGAGAGAGATATGACTTCAGTGGACGCCGCCAAGTTTTACAAGTGGTATTACTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8IZ69	tRNA (uracil-5-)-methyltransferase homolog A OS=Homo sapiens OX=9606 GN=TRMT2A PE=1 SV=2
Q8BNV1	tRNA (uracil-5-)-methyltransferase homolog A OS=Mus musculus OX=10090 GN=Trmt2a PE=1 SV=2
Q96GJ1	tRNA (uracil-5-)-methyltransferase homolog B OS=Homo sapiens OX=9606 GN=TRMT2B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003170 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05958 all species →	tRNA_U5-meth_tr	tRNA (Uracil-5-)-methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR034262 all species →	Domain	TRMT2A, RNA recognition motif	Interproscan
IPR010280 all species →	Family	(Uracil-5)-methyltransferase family	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR045850 all species →	Family	tRNA (uracil(54)-C(5))-methyltransferase, metazoa type	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR030390 all species →	Active_site	RNA methyltransferase TrmA, active site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45904 all species →	TRNA (URACIL-5-)-METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0008173 all species →	Molecular Function	RNA methyltransferase activity	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA 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
K15332	TRMT2A; tRNA (uracil-5-)-methyltransferase	EC:2.1.1.-	Transfer RNA biogenesis	ko03016	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g13765.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

68.3Max TPM

25.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	28.88	68.30
whole organisms · low pH treatment	15	15	21.74	60.99
whole organisms · extra low pH treatment pH treatment	12	12	24.86	64.30

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	68.30
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	60.31
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	53.26
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	51.98
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	47.87
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	47.40
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	44.71
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	35.44
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	35.27
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	21.43
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	20.96
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	19.55
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	16.20
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	16.01
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	15.12
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	13.64
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	9.34
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	7.76
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	7.51
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	7.21
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	7.16
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	60.99
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	52.40
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	41.20
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	26.27
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	24.33
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.83
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.45
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.28
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	18.66
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	7.99
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	7.75
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	6.37
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.95
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.04
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	4.65
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	64.30
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	56.45
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	33.53
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	29.57
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	25.81
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	20.22
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	17.45
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	12.32
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	11.68
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	10.67
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	8.48
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	7.85

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.