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.t1 TTS g4369.t1 1609426 1609426
chr_2 g4369 g4369.t1 isoform g4369.t1 1609732 1611854
chr_2 g4369 g4369.t1 exon g4369.t1.exon1 1609732 1609948
chr_2 g4369 g4369.t1 cds g4369.t1.CDS1 1609732 1609948
chr_2 g4369 g4369.t1 exon g4369.t1.exon2 1610010 1610814
chr_2 g4369 g4369.t1 cds g4369.t1.CDS2 1610010 1610814
chr_2 g4369 g4369.t1 exon g4369.t1.exon3 1610871 1611345
chr_2 g4369 g4369.t1 cds g4369.t1.CDS3 1610871 1611345
chr_2 g4369 g4369.t1 exon g4369.t1.exon4 1611708 1611854
chr_2 g4369 g4369.t1 cds g4369.t1.CDS4 1611708 1611854
chr_2 g4369 g4369.t1 TSS g4369.t1 1612160 1612160

Sequences

>g4369.t1 Gene=g4369 Length=1644
ATGACAGTCATCAAGTCCAAAAATAATAAGAATACGGGTGAAAAAGTTGGCGAAAAAATT
AATGGCTTTCATAAAAATGGATTTGTCAATCACAAATTAGTTTCAGTCGATGAAACATGT
ATTGATAAAAATGGAAGCATTGAATCAAACCAAGACATCAACAACCAGTACAAAAGAGAT
GAAAATTTCAAAGAAAGTTTCGAGCAACCAACTCTCATTACAGCCTGCCTCACCTACCTC
GGATTTTATTTGTTGATGATTATCGGGTACATCAATCAATTATTCTTCGTACCTAAAGTT
GCAACTGAGAAGAATCGAGATGACTATGTTCCCCTATTTGCTGCATTTGAAAGTTTCTAC
TTGCGATATGTATATCGTCGAGTAAAAGACTGTTGGAATAGACCAATTTGTAGTTGCCCA
GCTGACACTGTCACACTTAAAGATAGAGTAACGAAGGACTATGGATGGACATTTGAATTT
ACTGGAACAGAAACAAAATGTTTGAATCTTGGATCTTATAATTACTTGGGATTTGCACAA
AATAAAGGACCTTGTGCTGATGATGCCATTGAGTCAATTCATAAATATGGAATTGCTACT
TACAGCCCACGTCGAGAATTAGGCACAAATGCTTTGCATACAGAATTAGAAAAATTGACA
GCAGAATTTTTAGGAGTAGAAGATGCTATAGTTTTTGGTATGGGCTTCGCTACGAATGCA
CTCAATTTGCCGTCACTTTTATCACCCGGTTGCCTCGTCATATCAGACGAGAAAAATCAT
GCATCAATCATTCTTGGTTTAAGATTATCAGGCGCAACAATAAAAGTCTATAAGCACAAT
AATACACATCACTTAGAGAAAGTTATTCAACAAGCAATCGTCAATGGACAACCGAATGGT
AAACCATGGAAAAAGATACTGATTATTTTAGAAGGTGTGTTCAGTATGGAAGGATCTATT
GTTAAACTGCCAGAAATTATCGAAATTAAGAAAAAATATGGAGCCTTCATCTATTTAGAT
GAAGCACACAGTATTGGTGCAACTGGAAATCATGGACGTGGAGTTTGTGATTTCTATGGC
ATTAATCCAAAAGATGTGGATATTTTAATGGGAACTTTCACAAAAAGTTTTGGTTCGGCC
GGTGGGTACATTGGTGGTTCAAAGAGCCTTATTTCATTCTTACGTGCGAATAGTCATGCA
CACTGCTATGCAAGTTCAATGGCTCCTGCTGTAACTCAACAAATTCTTACATCGATGAAG
ATCATTATGGGTCTCGATGGTACAAATGAAGGGAAAAAGCGTATCGATCAATTGGCTAGA
AATACGAGATATTTTAGAAAACGTTTGGCACAGATTGGCGTTATCACCTATGGTCACGAA
GACTCACCCGTAGTGCCAATGTTAGTTTATTTGTTTTCTAAAATTGGTGCCGTTGTTCGA
ACATTGACAAAGAGACAAATAGCAGTGGTGGGTGCTGGTTTTCCAGCGACTCCAATTATG
GAAGGTCGCATTCGCTTTTGCTTATCAGCTGCCCATACCAAAGAACAACTTGATTATGCT
TTACAAGTTATTGACGAGATCGGTGATTCATTAGGACTAAAGTATTCAAGAAAACCGCGA
GATCTTAATCAAATCGAATATTAA

>g4369.t1 Gene=g4369 Length=547
MTVIKSKNNKNTGEKVGEKINGFHKNGFVNHKLVSVDETCIDKNGSIESNQDINNQYKRD
ENFKESFEQPTLITACLTYLGFYLLMIIGYINQLFFVPKVATEKNRDDYVPLFAAFESFY
LRYVYRRVKDCWNRPICSCPADTVTLKDRVTKDYGWTFEFTGTETKCLNLGSYNYLGFAQ
NKGPCADDAIESIHKYGIATYSPRRELGTNALHTELEKLTAEFLGVEDAIVFGMGFATNA
LNLPSLLSPGCLVISDEKNHASIILGLRLSGATIKVYKHNNTHHLEKVIQQAIVNGQPNG
KPWKKILIILEGVFSMEGSIVKLPEIIEIKKKYGAFIYLDEAHSIGATGNHGRGVCDFYG
INPKDVDILMGTFTKSFGSAGGYIGGSKSLISFLRANSHAHCYASSMAPAVTQQILTSMK
IIMGLDGTNEGKKRIDQLARNTRYFRKRLAQIGVITYGHEDSPVVPMLVYLFSKIGAVVR
TLTKRQIAVVGAGFPATPIMEGRIRFCLSAAHTKEQLDYALQVIDEIGDSLGLKYSRKPR
DLNQIEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4369.t1 CDD cd06454 KBL_like 166 528 2.26306E-154
5 g4369.t1 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 164 523 3.2E-114
6 g4369.t1 Gene3D G3DSA:3.40.640.10 - 181 431 3.2E-114
2 g4369.t1 PANTHER PTHR13693:SF83 SERINE PALMITOYLTRANSFERASE, LONG CHAIN BASE SUBUNIT 2B 52 541 2.9E-203
3 g4369.t1 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE 52 541 2.9E-203
1 g4369.t1 Pfam PF00155 Aminotransferase class I and II 165 524 6.7E-60
7 g4369.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 71 -
10 g4369.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 97 -
9 g4369.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 108 -
11 g4369.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 125 -
8 g4369.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 126 547 -
14 g4369.t1 ProSitePatterns PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site. 372 381 -
4 g4369.t1 SUPERFAMILY SSF53383 PLP-dependent transferases 114 532 2.37E-96
13 g4369.t1 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:0016740 transferase activity MF
GO:0003824 catalytic activity MF
GO:0030170 pyridoxal phosphate binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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