Gene loci information

Transcript annotation

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

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.t105 TSS g17482.t105 13657411 13657411
chr_4 g17482 g17482.t105 isoform g17482.t105 13658035 13659248
chr_4 g17482 g17482.t105 exon g17482.t105.exon1 13658035 13658078
chr_4 g17482 g17482.t105 exon g17482.t105.exon2 13658217 13658509
chr_4 g17482 g17482.t105 cds g17482.t105.CDS1 13658363 13658509
chr_4 g17482 g17482.t105 exon g17482.t105.exon3 13658572 13658624
chr_4 g17482 g17482.t105 cds g17482.t105.CDS2 13658572 13658624
chr_4 g17482 g17482.t105 exon g17482.t105.exon4 13658682 13659083
chr_4 g17482 g17482.t105 cds g17482.t105.CDS3 13658682 13659083
chr_4 g17482 g17482.t105 exon g17482.t105.exon5 13659155 13659248
chr_4 g17482 g17482.t105 cds g17482.t105.CDS4 13659155 13659248
chr_4 g17482 g17482.t105 TTS g17482.t105 13659279 13659279

Sequences

>g17482.t105 Gene=g17482 Length=886
ACGAATAATTCTTACACATTTTGTATATCTGGATCAGGTCAAGCAAAACATTGCAAAACG
ATTAAATGCTGATGTAAAAGTCATCAATAAAGAACCAGGAGAGCAAATTGAAGTAGAAGA
AACCCGAATATTTTTTGAGCAATATCACCCAAAAGTTTTCTTTTTGACTCATGGTGAATC
AAGCACAGGAATGTTGCAACAAAATTTGGAACAATTTGGAAATTTGTGTCAGGAATTCGA
TTGTCTCTTTGTGGTTGATTGTGTTATAACAGTTGGATGCACTCCAGTTTATGTTGATAA
ATGGAAAATTGATGTTGCTTTTATGGGAACACAAAAGGTTCTTAATGCTCCACCAGGAAT
TTCTCCGATTACATTCAGTGCACGAGCTTTTGAAAAAATCGTTAAAAGAAAGTCACCAGT
AAAAAGCTACAATTATGATGCAGTAAATCTCAGTAAATATTGGAAATCGGGCGATGAACC
AAGAGTTTATCATCATACAGTTTGCTCAACATTACTCTACGGTTTGCGAGAGGCAATTGC
AATTTTCATTGAGAATGGTGGTTTAGAAGCTTCTTGGAAAAATCATCAAAATGTTGCCAA
ACATTTTTATACTCTGTTGGAAAAGAATGGTTTGGAATTATTCATTACTGATCCTAAAAA
TCGTGTTCCATCAGTTACAGCTGTAAAAGTTCCTGAGAATATCGATGCAAATGAAATTAT
AAAACATTCAATGAATGAATATAATGTTGAAATCAGTGGTGGAATGGGACAAACTAAAGG
AAAAATTTTAAGAGTTGGACTTATGGGAATAAATTGTAAAGAAATCGTTGCAGAATGCGT
TGCAAAAATTCTTATTGAAGCAACGAGAAAGTTGAATGAAGAATAA

>g17482.t105 Gene=g17482 Length=231
MLQQNLEQFGNLCQEFDCLFVVDCVITVGCTPVYVDKWKIDVAFMGTQKVLNAPPGISPI
TFSARAFEKIVKRKSPVKSYNYDAVNLSKYWKSGDEPRVYHHTVCSTLLYGLREAIAIFI
ENGGLEASWKNHQNVAKHFYTLLEKNGLELFITDPKNRVPSVTAVKVPENIDANEIIKHS
MNEYNVEISGGMGQTKGKILRVGLMGINCKEIVAECVAKILIEATRKLNEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17482.t105 Gene3D G3DSA:3.40.640.10 - 2 118 2.1E-27
6 g17482.t105 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 119 231 3.6E-29
2 g17482.t105 PANTHER PTHR21152 AMINOTRANSFERASE CLASS V 6 224 7.4E-64
3 g17482.t105 PANTHER PTHR21152:SF22 SERINE–PYRUVATE AMINOTRANSFERASE 6 224 7.4E-64
1 g17482.t105 Pfam PF00266 Aminotransferase class-V 4 213 4.2E-27
5 g17482.t105 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. 40 60 -
4 g17482.t105 SUPERFAMILY SSF53383 PLP-dependent transferases 4 218 3.59E-51

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