Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine palmitoyltransferase 2.

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_2 g4369 g4369.t7 isoform g4369.t7 1610870 1611854
chr_2 g4369 g4369.t7 exon g4369.t7.exon1 1610870 1611345
chr_2 g4369 g4369.t7 cds g4369.t7.CDS1 1610872 1611345
chr_2 g4369 g4369.t7 exon g4369.t7.exon2 1611708 1611854
chr_2 g4369 g4369.t7 cds g4369.t7.CDS2 1611708 1611854
chr_2 g4369 g4369.t7 TSS g4369.t7 1612160 1612160
chr_2 g4369 g4369.t7 TTS g4369.t7 NA NA

Sequences

>g4369.t7 Gene=g4369 Length=623
ATGACAGTCATCAAGTCCAAAAATAATAAGAATACGGGTGAAAAAGTTGGCGAAAAAATT
AATGGCTTTCATAAAAATGGATTTGTCAATCACAAATTAGTTTCAGTCGATGAAACATGT
ATTGATAAAAATGGAAGCATTGAATCAAACCAAGACATCAACAACCAGTACAAAAGAGAT
GAAAATTTCAAAGAAAGTTTCGAGCAACCAACTCTCATTACAGCCTGCCTCACCTACCTC
GGATTTTATTTGTTGATGATTATCGGGTACATCAATCAATTATTCTTCGTACCTAAAGTT
GCAACTGAGAAGAATCGAGATGACTATGTTCCCCTATTTGCTGCATTTGAAAGTTTCTAC
TTGCGATATGTATATCGTCGAGTAAAAGACTGTTGGAATAGACCAATTTGTAGTTGCCCA
GCTGACACTGTCACACTTAAAGATAGAGTAACGAAGGACTATGGATGGACATTTGAATTT
ACTGGAACAGAAACAAAATGTTTGAATCTTGGATCTTATAATTACTTGGGATTTGCACAA
AATAAAGGACCTTGTGCTGATGATGCCATTGAGTCAATTCATAAATATGGAATTGCTACT
TACAGCCCACGTCGAGAATTAGG

>g4369.t7 Gene=g4369 Length=207
MTVIKSKNNKNTGEKVGEKINGFHKNGFVNHKLVSVDETCIDKNGSIESNQDINNQYKRD
ENFKESFEQPTLITACLTYLGFYLLMIIGYINQLFFVPKVATEKNRDDYVPLFAAFESFY
LRYVYRRVKDCWNRPICSCPADTVTLKDRVTKDYGWTFEFTGTETKCLNLGSYNYLGFAQ
NKGPCADDAIESIHKYGIATYSPRREL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g4369.t7 PANTHER PTHR13693:SF83 SERINE PALMITOYLTRANSFERASE, LONG CHAIN BASE SUBUNIT 2B 49 206 2.0E-42
2 g4369.t7 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE 49 206 2.0E-42
5 g4369.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 71 -
8 g4369.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 97 -
7 g4369.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 108 -
9 g4369.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 125 -
6 g4369.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 126 207 -
3 g4369.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 94 -
4 g4369.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 126 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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