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 g17483 g17483.t76 TSS g17483.t76 13659535 13659535
chr_4 g17483 g17483.t76 isoform g17483.t76 13660217 13661346
chr_4 g17483 g17483.t76 exon g17483.t76.exon1 13660217 13660591
chr_4 g17483 g17483.t76 cds g17483.t76.CDS1 13660445 13660591
chr_4 g17483 g17483.t76 exon g17483.t76.exon2 13660656 13660708
chr_4 g17483 g17483.t76 cds g17483.t76.CDS2 13660656 13660708
chr_4 g17483 g17483.t76 exon g17483.t76.exon3 13660794 13661195
chr_4 g17483 g17483.t76 cds g17483.t76.CDS3 13660794 13661195
chr_4 g17483 g17483.t76 exon g17483.t76.exon4 13661253 13661346
chr_4 g17483 g17483.t76 cds g17483.t76.CDS4 13661253 13661346
chr_4 g17483 g17483.t76 TTS g17483.t76 13661511 13661511

Sequences

>g17483.t76 Gene=g17483 Length=924
ATCGAATGTGCTTTTGTAAATTTGGTTGAAGACAACGATATAGTTGTTATTGGAAGTAGT
GGCTATTGGGGAATAAGAGCAGAAGATATTGCAAAACGATTAAATGCTGATGTAAAAGTC
ATCAATAAAGAATTAGGAGAGCAAATTGAATTAGAAGAAACACGAATATTTTTTGAGCAA
TATCATCCAAAAGTTTTCTTTTTGACTCATGGTGAATCAAGCACAGGAATGTTGCAACAA
AATTTGGAACAATTTGGAAATTTATGTCAGGAATTTAATTGTCTTTTTGTGGTTGATTGC
GTTATAACAGTTGGATGCACTCCAGTTTATGTTGATAAATGGAATATTGATGTTGCTTTT
ATGGGAACACAAAAGGTTCTTAATGCACCACCAGGAATTTCTCCGATTACATTCAGTGCA
CGAGCTTTGGATAAAATTGCAAAGAGAAAGACACCAGTAAAAAGCTATAATCTTGATGCA
GTAAACCTTGGTGAATATTGGAATTCTGGAAACCGTCCAAGAATTTATCATCATACAGTT
TGTTCAACATTACTCTACGGTTTGCGAGAGGCAATTGCAATTTTCATTGAGAATGGTGGT
TTAGAAGCTTCTTGGAAAAATCATGAAAATGTTGCCAAACATTTTTATACTCTGTTGGAA
AAGAATGGTTTGGAATTATTCATTACTGATCCTAAAAATCGTGTTCCATCAGTTACAGCT
ATAAAAGTACCTGAGAATATCGATGCAAATGAAATTATAAAACATTCAATGAATGAATAC
AATGTTGAAATTAGTGGTGGTATAGGACCAATGTTGGGGGTAGTTTTGAGAGTTGGACTA
ATGGGAATAAACTGTAATGAAAAAGTTGCAGAATGCGTTGCAAAAATTCTTATTGAAGCT
ATAAAAAAAATGAAAGAAGAATAA

>g17483.t76 Gene=g17483 Length=231
MLQQNLEQFGNLCQEFNCLFVVDCVITVGCTPVYVDKWNIDVAFMGTQKVLNAPPGISPI
TFSARALDKIAKRKTPVKSYNLDAVNLGEYWNSGNRPRIYHHTVCSTLLYGLREAIAIFI
ENGGLEASWKNHENVAKHFYTLLEKNGLELFITDPKNRVPSVTAIKVPENIDANEIIKHS
MNEYNVEISGGIGPMLGVVLRVGLMGINCNEKVAECVAKILIEAIKKMKEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17483.t76 Gene3D G3DSA:3.40.640.10 - 2 118 3.3E-28
6 g17483.t76 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 119 231 2.1E-27
2 g17483.t76 PANTHER PTHR21152 AMINOTRANSFERASE CLASS V 6 227 1.8E-68
3 g17483.t76 PANTHER PTHR21152:SF22 SERINE–PYRUVATE AMINOTRANSFERASE 6 227 1.8E-68
1 g17483.t76 Pfam PF00266 Aminotransferase class-V 4 213 3.1E-26
5 g17483.t76 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. 40 60 -
4 g17483.t76 SUPERFAMILY SSF53383 PLP-dependent transferases 4 228 5.88E-52

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.

Raw TPM values