Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine palmitoyltransferase 1.

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_1 g13963 g13963.t2 TSS g13963.t2 33641654 33641654
chr_1 g13963 g13963.t2 isoform g13963.t2 33641739 33642447
chr_1 g13963 g13963.t2 exon g13963.t2.exon1 33641739 33641798
chr_1 g13963 g13963.t2 cds g13963.t2.CDS1 33641739 33641798
chr_1 g13963 g13963.t2 exon g13963.t2.exon2 33641864 33642363
chr_1 g13963 g13963.t2 cds g13963.t2.CDS2 33641864 33642363
chr_1 g13963 g13963.t2 exon g13963.t2.exon3 33642443 33642447
chr_1 g13963 g13963.t2 cds g13963.t2.CDS3 33642443 33642446
chr_1 g13963 g13963.t2 TTS g13963.t2 NA NA

Sequences

>g13963.t2 Gene=g13963 Length=565
ATGTTGCAAACAGAATCAACACCGTACATTTTTAGTGAGCTTTATAATATTATATTTCAG
GCACCAGCATATGTCTTGTTTTTGGAATTTTCATTACTTCTACTCGTTGTTTGGATCATA
ATTCACAAACAATCAAATGGAGAGAAGTCATTGTCGAAAGAAGAGCGAGAGGAAATTATC
AGAAATTGGAAACCAGAGCCATTAGTGACAGAAATTGATCAAAATCACCCGGCATTAGTA
AATAATCATATTATTGATGGTACAGTAGGCAAATATATAACTGTTGATGGAATAAAATGC
TTGAATATGGCTACACATAACTATCTTGGTCTTGAAGAGTATCCAAAAATTAAGGAGAGT
GCAATCAATTGCATTCAAAAATATGGCGTTGGAAGTTGTGGACCGAGAGGATTTTACGGG
ACTGTTGATGTACATTTAGAGCTTGAAGAACGATTAGCAAAGTTTATGGATCAAGAAGAG
GCAGTTGTCTATTCGTATGCATTTTCAACAATTGCTAGTGCAATTCCAGCATATTCAAAA
CGTACCGACATCATTTTTGCTGACG

>g13963.t2 Gene=g13963 Length=188
MLQTESTPYIFSELYNIIFQAPAYVLFLEFSLLLLVVWIIIHKQSNGEKSLSKEEREEII
RNWKPEPLVTEIDQNHPALVNNHIIDGTVGKYITVDGIKCLNMATHNYLGLEEYPKIKES
AINCIQKYGVGSCGPRGFYGTVDVHLELEERLAKFMDQEEAVVYSYAFSTIASAIPAYSK
RTDIIFAD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g13963.t2 Gene3D G3DSA:3.40.640.10 - 114 188 3.4E-21
2 g13963.t2 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE 24 188 2.0E-51
3 g13963.t2 PANTHER PTHR13693:SF2 SERINE PALMITOYLTRANSFERASE 1 24 188 2.0E-51
1 g13963.t2 Pfam PF00155 Aminotransferase class I and II 99 187 1.6E-9
8 g13963.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 16 -
9 g13963.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 17 41 -
7 g13963.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 42 188 -
5 g13963.t2 SUPERFAMILY SSF53383 PLP-dependent transferases 55 188 1.93E-23
4 g13963.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -

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:0009058 biosynthetic process BP
GO:0003824 catalytic activity MF
GO:0030170 pyridoxal phosphate binding 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