Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t5 TTS g4369.t5 1609654 1609654
chr_2 g4369 g4369.t5 isoform g4369.t5 1610504 1611854
chr_2 g4369 g4369.t5 exon g4369.t5.exon1 1610504 1610814
chr_2 g4369 g4369.t5 cds g4369.t5.CDS1 1610504 1610814
chr_2 g4369 g4369.t5 exon g4369.t5.exon2 1610871 1611345
chr_2 g4369 g4369.t5 cds g4369.t5.CDS2 1610871 1611345
chr_2 g4369 g4369.t5 exon g4369.t5.exon3 1611708 1611854
chr_2 g4369 g4369.t5 cds g4369.t5.CDS3 1611708 1611854
chr_2 g4369 g4369.t5 TSS g4369.t5 1612160 1612160

Sequences

>g4369.t5 Gene=g4369 Length=933
ATGACAGTCATCAAGTCCAAAAATAATAAGAATACGGGTGAAAAAGTTGGCGAAAAAATT
AATGGCTTTCATAAAAATGGATTTGTCAATCACAAATTAGTTTCAGTCGATGAAACATGT
ATTGATAAAAATGGAAGCATTGAATCAAACCAAGACATCAACAACCAGTACAAAAGAGAT
GAAAATTTCAAAGAAAGTTTCGAGCAACCAACTCTCATTACAGCCTGCCTCACCTACCTC
GGATTTTATTTGTTGATGATTATCGGGTACATCAATCAATTATTCTTCGTACCTAAAGTT
GCAACTGAGAAGAATCGAGATGACTATGTTCCCCTATTTGCTGCATTTGAAAGTTTCTAC
TTGCGATATGTATATCGTCGAGTAAAAGACTGTTGGAATAGACCAATTTGTAGTTGCCCA
GCTGACACTGTCACACTTAAAGATAGAGTAACGAAGGACTATGGATGGACATTTGAATTT
ACTGGAACAGAAACAAAATGTTTGAATCTTGGATCTTATAATTACTTGGGATTTGCACAA
AATAAAGGACCTTGTGCTGATGATGCCATTGAGTCAATTCATAAATATGGAATTGCTACT
TACAGCCCACGTCGAGAATTAGGCACAAATGCTTTGCATACAGAATTAGAAAAATTGACA
GCAGAATTTTTAGGAGTAGAAGATGCTATAGTTTTTGGTATGGGCTTCGCTACGAATGCA
CTCAATTTGCCGTCACTTTTATCACCCGGTTGCCTCGTCATATCAGACGAGAAAAATCAT
GCATCAATCATTCTTGGTTTAAGATTATCAGGCGCAACAATAAAAGTCTATAAGCACAAT
AATACACATCACTTAGAGAAAGTTATTCAACAAGCAATCGTCAATGGACAACCGAATGGT
AAACCATGGAAAAAGATACTGATTATTTTAGAA

>g4369.t5 Gene=g4369 Length=311
MTVIKSKNNKNTGEKVGEKINGFHKNGFVNHKLVSVDETCIDKNGSIESNQDINNQYKRD
ENFKESFEQPTLITACLTYLGFYLLMIIGYINQLFFVPKVATEKNRDDYVPLFAAFESFY
LRYVYRRVKDCWNRPICSCPADTVTLKDRVTKDYGWTFEFTGTETKCLNLGSYNYLGFAQ
NKGPCADDAIESIHKYGIATYSPRRELGTNALHTELEKLTAEFLGVEDAIVFGMGFATNA
LNLPSLLSPGCLVISDEKNHASIILGLRLSGATIKVYKHNNTHHLEKVIQQAIVNGQPNG
KPWKKILIILE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g4369.t5 Gene3D G3DSA:3.40.640.10 - 185 311 1.1E-32
2 g4369.t5 PANTHER PTHR13693:SF83 SERINE PALMITOYLTRANSFERASE, LONG CHAIN BASE SUBUNIT 2B 51 311 1.0E-91
3 g4369.t5 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE 51 311 1.0E-91
1 g4369.t5 Pfam PF00155 Aminotransferase class I and II 165 304 1.7E-20
7 g4369.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 71 -
10 g4369.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 97 -
9 g4369.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 108 -
11 g4369.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 125 -
8 g4369.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 126 311 -
5 g4369.t5 SUPERFAMILY SSF53383 PLP-dependent transferases 114 311 2.67E-34
4 g4369.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 91 -

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. There were no conditions that were differentially expressed