Gene detail

Detailed information of g16723.t1 in Acropora digitifera

Genomic Location: chr8Alt:440435...448075
NR annotation: XP_015752236.1, PREDICTED: LOW QUALITY PROTEIN: tRNA wybutosine-synthesizing protein 4-like [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g16723.t1

ATGGCGGCTGATAATATCGTTTTTGATGAAAGGAAAGCATATGAAGAGAAGACAGACGTTCAGGTTCAAGGGACAAACGACCATGCTACGCTCAGCAAACTTTCCACTGTTAGAATGGGTTACTTTGAAGACAGGTTTCTGCCATATTTTGTATCCAAGAGGTCCAGAAGAGCACCTGTTATTCATAGGTCATATTACATAAGGACAAAGGCAATTCATTTTGTGGTAAAAGGATTTCTGCAAAGTCTGAAGTTTAGAGGATCAAAAAAGCAGATAGTTTCCCTTGGAGCAGGATATGACACACTTTTCTTTTCCCTTGCTAATCAAGGACTCTTGAAAGAAACCAAATATTTTGAGGTTGATTTTCCAGAGGTTGTTCAAAAGAAGACAAATTTAATTTTAAAAAACCAAGAATTGGCTCAAGTGCTTGGAACGGTCATTTCCCAGAATGAGCATTGGCTCGGAGGAGGAATTAACAGTGAAAAGTATTCTTTGTTGGGCTGCAACTTGAAGAACTGTTCAGCACTGGAGAGGTGTCTTTTGAAATGCGGTTTGAACACCTCATCTGTCACACTTTTGTTATCTGAAGTGGTACTTACATACCTTAATCCACCTGAAAGTGCCACAGACATTATTGGATGGGCAGCACTTTTCTTCACATCTGCAATGTTTGTCATGTTTGAGCAGGTTCACCCAAGTGACCCGTTTGGAATCAAGATGATGAATCATTTTCAGCATACAGTGGGCGCCCCCCTGTATGGCACGGAAGCTTTCCCCACCCAGCAAAGTCAAATTCAACGTTTTATGAAAGAGGGTTGGCCTCTTGTTAACTGTCCAACGTTAGACTTTATTTACTACGAGACACTCTCGATTGAAGAAAAAGCTCGCGTTGAAGGAATTGAACCTTTCGATGAATTTGAGGAGTGGCACCTGATGTGTTCACATTATGTCATCTTAACAGCCTTCAAAGGATCCTGTCAAAATATTCAAGAGGAATTGTTTTGTTCGCAAAATGAAAACAAGCAGTTAACCGATCAGCCGTGTCTTGTTGATAATAAGCAGTGTATTATTCAACCCTTGAGTGTTTTACCTTCATCGGATGGAGTAAGAAGGTTTGGACACACAGCCACTTCTTTGTCGGCTGACATAGTTCTTCTTGTTGGAGGGTTTGGTCCTCAAAATAAAAAACACACGCGACTTGATGGAGCACAGCTGTTACACTTTGTACAAGATAAGTGGCATTGTGTGGACATCACAACAACTTCGGACATTGCACTTGGCAGCCGGATGTTTCACACTGCAACCAGACTAAGTAATGAAGATGTCTTTATTTACGGTGGCCGAACGTCGCCATCCAAGCCTTGCGAAGAAGCTATTTCACTATCTTTAACGACAAGCATTGTATCGCAGTCAACTTCTTCACACACAAAAGACGACAGTTCCAGTCGCTCAGAGACTGATTGTGAAGGAAGCAAATGTTTAGCAAACGCTGTTATTTCTGAGAAGAGTTATACGCATTCTGTTGTACGTTGTCATGGAGACATTCCTGAGCCGAGATGGCGGCACACCGCGTCGTATGTTGTCCTTCCTGATGGTAGTGAGAATATATTAGTGTTTGGAGGTCGCAGTTCCACCCAAGTCGCAATGGGGGATTGTTACTTGCTTCATATCAAGTCACAAACGTGGCGAAAGGTGTTCTTCGTTGGAGATACCGCTGTACCGCGCCATTCCCATACTGCGTGCGTCTGGAAGGACAAAGTAATACTAGCGGGGGGTCTGGATGCAAATCTTCGTGCTCTCAACATCATCCAGATATTAGACATTCAGGTTAGTCCAATGATGTTGCAAACGTTGAACATTGATCCACAGTTGATGCCAAGATACTCTCATACAGCACATGTGGTAGATGACAAACTTATACTTGTCGGCGGAGTCACGACCAATTCATCGCATACTCCTGGAATAGTGATTCTTAATCTTGAGTCATTGACGTGGAACTCGTTTACTCTACCGGCCATGTCAGCTCCCAATACACCTTTGATGCTTCACAATCACGACAGTGTCTACTGGGAAGATGTGCAAGGTATTATGGTCCTTGGTGGTGGAGGGAATTGTTTTTCATTCGGAACTCATTTTAATGAGGGACCAATCATGATCAAACTTCTGCAGAACTGA

Transcript

chr8Alt.g16723.t1

TTTAGAGAGATACGTGTTCGGTACAATATATGTCCCCATACACCACGTACCTACCTTCTAGTTCCAGACCTCTCCAGGCGAGAAAGAAAGATGGCGGCTGATAATATCGTTTTTGATGAAAGGAAAGCATATGAAGAGAAGACAGACGTTCAGGTTCAAGGGACAAACGACCATGCTACGCTCAGCAAACTTTCCACTGTTAGAATGGGTTACTTTGAAGACAGGTTTCTGCCATATTTTGTATCCAAGAGGTCCAGAAGAGCACCTGTTATTCATAGGTCATATTACATAAGGACAAAGGCAATTCATTTTGTGGTAAAAGGATTTCTGCAAAGTCTGAAGTTTAGAGGATCAAAAAAGCAGATAGTTTCCCTTGGAGCAGGATATGACACACTTTTCTTTTCCCTTGCTAATCAAGGACTCTTGAAAGAAACCAAATATTTTGAGGTTGATTTTCCAGAGGTTGTTCAAAAGAAGACAAATTTAATTTTAAAAAACCAAGAATTGGCTCAAGTGCTTGGAACGGTCATTTCCCAGAATGAGCATTGGCTCGGAGGAGGAATTAACAGTGAAAAGTATTCTTTGTTGGGCTGCAACTTGAAGAACTGTTCAGCACTGGAGAGGTGTCTTTTGAAATGCGGTTTGAACACCTCATCTGTCACACTTTTGTTATCTGAAGTGGTACTTACATACCTTAATCCACCTGAAAGTGCCACAGACATTATTGGATGGGCAGCACTTTTCTTCACATCTGCAATGTTTGTCATGTTTGAGCAGGTTCACCCAAGTGACCCGTTTGGAATCAAGATGATGAATCATTTTCAGCATACAGTGGGCGCCCCCCTGTATGGCACGGAAGCTTTCCCCACCCAGCAAAGTCAAATTCAACGTTTTATGAAAGAGGGTTGGCCTCTTGTTAACTGTCCAACGTTAGACTTTATTTACTACGAGACACTCTCGATTGAAGAAAAAGCTCGCGTTGAAGGAATTGAACCTTTCGATGAATTTGAGGAGTGGCACCTGATGTGTTCACATTATGTCATCTTAACAGCCTTCAAAGGATCCTGTCAAAATATTCAAGAGGAATTGTTTTGTTCGCAAAATGAAAACAAGCAGTTAACCGATCAGCCGTGTCTTGTTGATAATAAGCAGTGTATTATTCAACCCTTGAGTGTTTTACCTTCATCGGATGGAGTAAGAAGGTTTGGACACACAGCCACTTCTTTGTCGGCTGACATAGTTCTTCTTGTTGGAGGGTTTGGTCCTCAAAATAAAAAACACACGCGACTTGATGGAGCACAGCTGTTACACTTTGTACAAGATAAGTGGCATTGTGTGGACATCACAACAACTTCGGACATTGCACTTGGCAGCCGGATGTTTCACACTGCAACCAGACTAAGTAATGAAGATGTCTTTATTTACGGTGGCCGAACGTCGCCATCCAAGCCTTGCGAAGAAGCTATTTCACTATCTTTAACGACAAGCATTGTATCGCAGTCAACTTCTTCACACACAAAAGACGACAGTTCCAGTCGCTCAGAGACTGATTGTGAAGGAAGCAAATGTTTAGCAAACGCTGTTATTTCTGAGAAGAGTTATACGCATTCTGTTGTACGTTGTCATGGAGACATTCCTGAGCCGAGATGGCGGCACACCGCGTCGTATGTTGTCCTTCCTGATGGTAGTGAGAATATATTAGTGTTTGGAGGTCGCAGTTCCACCCAAGTCGCAATGGGGGATTGTTACTTGCTTCATATCAAGTCACAAACGTGGCGAAAGGTGTTCTTCGTTGGAGATACCGCTGTACCGCGCCATTCCCATACTGCGTGCGTCTGGAAGGACAAAGTAATACTAGCGGGGGGTCTGGATGCAAATCTTCGTGCTCTCAACATCATCCAGATATTAGACATTCAGGTTAGTCCAATGATGTTGCAAACGTTGAACATTGATCCACAGTTGATGCCAAGATACTCTCATACAGCACATGTGGTAGATGACAAACTTATACTTGTCGGCGGAGTCACGACCAATTCATCGCATACTCCTGGAATAGTGATTCTTAATCTTGAGTCATTGACGTGGAACTCGTTTACTCTACCGGCCATGTCAGCTCCCAATACACCTTTGATGCTTCACAATCACGACAGTGTCTACTGGGAAGATGTGCAAGGTATTATGGTCCTTGGTGGTGGAGGGAATTGTTTTTCATTCGGAACTCATTTTAATGAGGGACCAATCATGATCAAACTTCTGCAGAACTGACTTATTTCTATTCGTACGTCAATGTAACCAGCCTTGTGTGATGTTGGCTGTTATGAAAGAAATCCTTGTAAACAAGAGATTTGATATTATTGTAAATAAACAACGCCGGAATCT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O60294	tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3
Q5XIA3	tRNA wybutosine-synthesizing protein 4 OS=Rattus norvegicus OX=10116 GN=Lcmt2 PE=2 SV=1
Q8BYR1	tRNA wybutosine-synthesizing protein 4 OS=Mus musculus OX=10090 GN=Lcmt2 PE=2 SV=4

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04072 all species →	LCM	Leucine carboxyl methyltransferase	Family	Interproscan
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR007213 all species →	Family	Methyltransferase Ppm1/Ppm2/Tcmp	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46529 all species →	TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008175 all species →	Molecular Function	tRNA methyltransferase activity	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0031591 all species →	Biological Process	wybutosine biosynthetic process	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0032259 all species →	Biological Process	methylation	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
K15451	PPM2, LCMT2, TYW4; tRNA wybutosine-synthesizing protein 4	EC:2.1.1.290 EC:2.3.1.231	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 g16723.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples

39TPM > 0

1Conditions

38.7Max TPM

25.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	25.18	38.71

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	38.71
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	38.46
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	34.89
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	34.15
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	34.09
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	33.05
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	32.96
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	32.64
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	32.34
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	28.58
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	28.33
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	28.29
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	27.75
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	27.67
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	27.42
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	26.56
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	26.42
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	26.16
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	24.91
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	24.58
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	24.20
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	23.65
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	23.65
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	23.58
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	22.85
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	22.70
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	21.72
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	21.28
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	20.96
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	19.89
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	19.22
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	18.54
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	18.54
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	18.47
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	15.89
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	15.51
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	15.51
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	14.55
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	13.41

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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.