Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine–pyruvate aminotransferase, mitochondrial.

Parent gene

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 g17482 g17482.t8 TSS g17482.t8 13657411 13657411
chr_4 g17482 g17482.t8 isoform g17482.t8 13657464 13658687
chr_4 g17482 g17482.t8 exon g17482.t8.exon1 13657464 13657527
chr_4 g17482 g17482.t8 cds g17482.t8.CDS1 13657464 13657527
chr_4 g17482 g17482.t8 exon g17482.t8.exon2 13657853 13657967
chr_4 g17482 g17482.t8 cds g17482.t8.CDS2 13657853 13657967
chr_4 g17482 g17482.t8 exon g17482.t8.exon3 13658022 13658071
chr_4 g17482 g17482.t8 cds g17482.t8.CDS3 13658022 13658071
chr_4 g17482 g17482.t8 exon g17482.t8.exon4 13658133 13658509
chr_4 g17482 g17482.t8 cds g17482.t8.CDS4 13658133 13658509
chr_4 g17482 g17482.t8 exon g17482.t8.exon5 13658572 13658624
chr_4 g17482 g17482.t8 cds g17482.t8.CDS5 13658572 13658624
chr_4 g17482 g17482.t8 exon g17482.t8.exon6 13658682 13658687
chr_4 g17482 g17482.t8 cds g17482.t8.CDS6 13658682 13658685
chr_4 g17482 g17482.t8 TTS g17482.t8 13659279 13659279

Sequences

>g17482.t8 Gene=g17482 Length=665
ATGGATGTGCCAATTCCAGAAATTTTAAAGAAACCAATGGAAGTTGATGAAAAAATAATG
ACAGGTGCTGGACCTTCAAATTATCATCCAAGAATAAGACATGCAATGTCATTACCTGTT
CTTGGTCATCTTCATCCTGAAACATTCAAAATCATGGATGACATTAAAATTGGTGTCAAT
TATCTACTTCAGACGAATAATTCTTACACATTTTGTATATCTGGATCAGCTATCGAATGT
GCTCTTATGAATGTGATTGAAGACAATGACGTTATTGTTATCGGATGTTGTGGCCAATGG
GGTACGCGTGCAGAAAACATTGCAAAACGATTAAATGCTGATGTAAAAGTCATCAATAAA
GAACCAGGAGAGCAAATTGAAGTAGAAGAAACCCGAATATTTTTTGAGCAATATCACCCA
AAAGTTTTCTTTTTGACTCATGGTGAATCAAGCACAGGAATGTTGCAACAAAATTTGGAA
CAATTTGGAAATTTGTGTCAGGAATTCGATTGTCTCTTTGTGGTTGATTGTGTTATAACA
GTTGGATGCACTCCAGTTTATGTTGATAAATGGAAAATTGATGTTGCTTTTATGGGAACA
CAAAAGGTTCTTAATGCTCCACCAGGAATTTCTCCGATTACATTCAGTGCACGAGCTTTT
GAAAA

>g17482.t8 Gene=g17482 Length=221
MDVPIPEILKKPMEVDEKIMTGAGPSNYHPRIRHAMSLPVLGHLHPETFKIMDDIKIGVN
YLLQTNNSYTFCISGSAIECALMNVIEDNDVIVIGCCGQWGTRAENIAKRLNADVKVINK
EPGEQIEVEETRIFFEQYHPKVFFLTHGESSTGMLQQNLEQFGNLCQEFDCLFVVDCVIT
VGCTPVYVDKWKIDVAFMGTQKVLNAPPGISPITFSARAFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g17482.t8 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 15 28 2.1E-78
7 g17482.t8 Gene3D G3DSA:3.40.640.10 - 29 221 2.1E-78
2 g17482.t8 PANTHER PTHR21152 AMINOTRANSFERASE CLASS V 2 219 3.5E-66
3 g17482.t8 PANTHER PTHR21152:SF22 SERINE–PYRUVATE AMINOTRANSFERASE 2 219 3.5E-66
1 g17482.t8 Pfam PF00266 Aminotransferase class-V 41 218 3.9E-26
5 g17482.t8 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. 193 213 -
4 g17482.t8 SUPERFAMILY SSF53383 PLP-dependent transferases 19 220 2.45E-47

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed