General information for g17483.t54
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine–pyruvate aminotransferase, mitochondrial.
Parent gene
- The parent gene g17483 is located on chr_4: 13661346..13669405 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g17483 | g17483.t54 | TSS | g17483.t54 | 13659535 | 13659535 |
| chr_4 | g17483 | g17483.t54 | isoform | g17483.t54 | 13659588 | 13661512 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon1 | 13659588 | 13659651 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS1 | 13659588 | 13659651 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon2 | 13659877 | 13659991 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS2 | 13659877 | 13659991 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon3 | 13660046 | 13660095 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS3 | 13660046 | 13660095 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon4 | 13660224 | 13660591 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS4 | 13660224 | 13660591 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon5 | 13660656 | 13660708 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS5 | 13660656 | 13660708 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon6 | 13660794 | 13661195 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS6 | 13660794 | 13661195 |
| chr_4 | g17483 | g17483.t54 | exon | g17483.t54.exon7 | 13661253 | 13661512 |
| chr_4 | g17483 | g17483.t54 | cds | g17483.t54.CDS7 | 13661253 | 13661346 |
| chr_4 | g17483 | g17483.t54 | TTS | g17483.t54 | 13661511 | 13661511 |
Sequences
>g17483.t54 Gene=g17483 Length=1312
ATGGATGTGCCAATTCCGGAAATTTTACAGACACCAATGGAAGTTGATGAAATGATAATG
ACAGGTGCTGGACCTTCAAATTATCATCCAAGGATAAGACATGCAATGTCATTACCTGTT
CTTGGTCATCTTCATCCTAAAACATTTAAAATCATGGATGACATTAAAATTGGTGTCAAT
TATCTACTTCAGACAAATAATTCTTACACATTTTGTATCTCTGGACCAGGTGCTTTTGTA
AATTTGGTTGAAGACAACGATATAGTTGTTATTGGAAGTAGTGGCTATTGGGGAATAAGA
GCAGAAGATATTGCAAAACGATTAAATGCTGATGTAAAAGTCATCAATAAAGAATTAGGA
GAGCAAATTGAATTAGAAGAAACACGAATATTTTTTGAGCAATATCATCCAAAAGTTTTC
TTTTTGACTCATGGTGAATCAAGCACAGGAATGTTGCAACAAAATTTGGAACAATTTGGA
AATTTATGTCAGGAATTTAATTGTCTTTTTGTGGTTGATTGCGTTATAACAGTTGGATGC
ACTCCAGTTTATGTTGATAAATGGAATATTGATGTTGCTTTTATGGGAACACAAAAGGTT
CTTAATGCACCACCAGGAATTTCTCCGATTACATTCAGTGCACGAGCTTTGGATAAAATT
GCAAAGAGAAAGACACCAGTAAAAAGCTATAATCTTGATGCAGTAAACCTTGGTGAATAT
TGGAATTCTGGAAACCGTCCAAGAATTTATCATCATACAGTTTGTTCAACATTACTCTAC
GGTTTGCGAGAGGCAATTGCAATTTTCATTGAGAATGGTGGTTTAGAAGCTTCTTGGAAA
AATCATGAAAATGTTGCCAAACATTTTTATACTCTGTTGGAAAAGAATGGTTTGGAATTA
TTCATTACTGATCCTAAAAATCGTGTTCCATCAGTTACAGCTATAAAAGTACCTGAGAAT
ATCGATGCAAATGAAATTATAAAACATTCAATGAATGAATACAATGTTGAAATTAGTGGT
GGTATAGGACCAATGTTGGGGGTAGTTTTGAGAGTTGGACTAATGGGAATAAACTGTAAT
GAAAAAGTTGCAGAATGCGTTGCAAAAATTCTTATTGAAGCTATAAAAAAAATGAAAGAA
GAATAAAAATATTTATTGCTTGCTTGATTTTATTTGTACGATAAGTTCTTTATAACAGAA
TTAATTTAAAAGTCAGAATTAATTTATAAAATGATTAACATTAATAATGGTAAATTGACA
CACATGTTTTAAAAATTAATCAACAGTTAATAAACACATTTTTACAAATTGA
>g17483.t54 Gene=g17483 Length=381
MDVPIPEILQTPMEVDEMIMTGAGPSNYHPRIRHAMSLPVLGHLHPKTFKIMDDIKIGVN
YLLQTNNSYTFCISGPGAFVNLVEDNDIVVIGSSGYWGIRAEDIAKRLNADVKVINKELG
EQIELEETRIFFEQYHPKVFFLTHGESSTGMLQQNLEQFGNLCQEFNCLFVVDCVITVGC
TPVYVDKWNIDVAFMGTQKVLNAPPGISPITFSARALDKIAKRKTPVKSYNLDAVNLGEY
WNSGNRPRIYHHTVCSTLLYGLREAIAIFIENGGLEASWKNHENVAKHFYTLLEKNGLEL
FITDPKNRVPSVTAIKVPENIDANEIIKHSMNEYNVEISGGIGPMLGVVLRVGLMGINCN
EKVAECVAKILIEAIKKMKEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17483.t54 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 17 | 371 | 4.1E-127 |
| 7 | g17483.t54 | Gene3D | G3DSA:3.40.640.10 | - | 29 | 272 | 4.1E-127 |
| 2 | g17483.t54 | PANTHER | PTHR21152 | AMINOTRANSFERASE CLASS V | 2 | 377 | 1.6E-111 |
| 3 | g17483.t54 | PANTHER | PTHR21152:SF22 | SERINE–PYRUVATE AMINOTRANSFERASE | 2 | 377 | 1.6E-111 |
| 8 | g17483.t54 | PIRSF | PIRSF000524 | SPT | 10 | 381 | 8.0E-90 |
| 1 | g17483.t54 | Pfam | PF00266 | Aminotransferase class-V | 42 | 363 | 3.3E-38 |
| 5 | g17483.t54 | ProSitePatterns | PS00595 | Aminotransferases class-V pyridoxal-phosphate attachment site. | 190 | 210 | - |
| 4 | g17483.t54 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 5 | 378 | 2.02E-78 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00830 (alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
