General information for g13963.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine palmitoyltransferase 1.
Parent gene
- The parent gene g13963 is located on chr_1: 33643355..33648109 (+ strand)
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.t3 | TSS | g13963.t3 | 33641654 | 33641654 |
| chr_1 | g13963 | g13963.t3 | isoform | g13963.t3 | 33641739 | 33643355 |
| chr_1 | g13963 | g13963.t3 | exon | g13963.t3.exon1 | 33641739 | 33642363 |
| chr_1 | g13963 | g13963.t3 | cds | g13963.t3.CDS1 | 33641828 | 33642363 |
| chr_1 | g13963 | g13963.t3 | exon | g13963.t3.exon2 | 33642443 | 33643133 |
| chr_1 | g13963 | g13963.t3 | cds | g13963.t3.CDS2 | 33642443 | 33643133 |
| chr_1 | g13963 | g13963.t3 | exon | g13963.t3.exon3 | 33643194 | 33643355 |
| chr_1 | g13963 | g13963.t3 | cds | g13963.t3.CDS3 | 33643194 | 33643355 |
| chr_1 | g13963 | g13963.t3 | TTS | g13963.t3 | 33643516 | 33643516 |
Sequences
>g13963.t3 Gene=g13963 Length=1478
ATGTTGCAAACAGAATCAACACCGTACATTTTTAGTGAGCTTTATAATATTATATTTCAG
GTAATGATATTGTATTTTATAAGAAATTTATGATAACAATATTGATTCATAATTTTCTCA
TAAAGGCACCAGCATATGTCTTGTTTTTGGAATTTTCATTACTTCTACTCGTTGTTTGGA
TCATAATTCACAAACAATCAAATGGAGAGAAGTCATTGTCGAAAGAAGAGCGAGAGGAAA
TTATCAGAAATTGGAAACCAGAGCCATTAGTGACAGAAATTGATCAAAATCACCCGGCAT
TAGTAAATAATCATATTATTGATGGTACAGTAGGCAAATATATAACTGTTGATGGAATAA
AATGCTTGAATATGGCTACACATAACTATCTTGGTCTTGAAGAGTATCCAAAAATTAAGG
AGAGTGCAATCAATTGCATTCAAAAATATGGCGTTGGAAGTTGTGGACCGAGAGGATTTT
ACGGGACTGTTGATGTACATTTAGAGCTTGAAGAACGATTAGCAAAGTTTATGGATCAAG
AAGAGGCAGTTGTCTATTCGTATGCATTTTCAACAATTGCTAGTGCAATTCCAGCATATT
CAAAACGTACCGACATCATTTTTGCTGACGAATGTGTAAATTTCGCAATACAAAAAGGTA
TCGATGCATCGCGTAGTCGTGTTGTATACTTCAAACACAATGACATGCGAGATCTCGAGA
AAAAGCTTATAGAGCAACATAAGCTGGATTTAAAAAATCCTAAAAAAGCAGCAAAAACTC
GTCGCTTTTTGGTCGCAGAAGGAATTTATGTAAACACAGGTGAAATGTGCCCATTAAGAG
AACTCGTTGAATTGCGAAGTAAATATAAATTACGACTTTTCCTCGATGAGACAGTATCAT
TTGGTACAATAGGACAGCATGGAAGAGGTATAACTGAATTGCTATGTGTAGACAAATCAG
AAGTTGATCTTATCTCTGCATCACTTGAGAATGCAGTTGAATCTATCGGAGGATTTTGCG
TCGGTTCTCATTTTATAGTCGAACATCAGCGATTATCTGGACTTGGTTATTGTTTCTCTG
CATCACAACCACCATTTTTGACGCAAGCAGCAATTTCTGCATTGGACATTTTTGAAAATG
AACCAAAAATTTTTAACCAATTGAACGATACTGCAGAAAAAGTTGATGAACAATTTAGAT
ACTTCTCAAAACTTGAATTAAGAGGTCATCCAATTTCACCAGTCAAACATTTATATTTAA
AAGACATTGACGATAGCGATAAATGCGAAAAAATTCTTCGTAAAATTGCTGATGAATGCA
TTAAAAAAGGACTTGCAGTTGCATATTCTGAATATCTTCCTGTAGAAAAATTTCCACCAA
GAAGAAGCTTGCGAATCACAATCAATAGACTTTTAACTGAAGACGATATAACAAATGCAT
TTAAAATATTAGAAGAAGTCTCAAAGAGTGTAGTTTGA
>g13963.t3 Gene=g13963 Length=462
MITILIHNFLIKAPAYVLFLEFSLLLLVVWIIIHKQSNGEKSLSKEEREEIIRNWKPEPL
VTEIDQNHPALVNNHIIDGTVGKYITVDGIKCLNMATHNYLGLEEYPKIKESAINCIQKY
GVGSCGPRGFYGTVDVHLELEERLAKFMDQEEAVVYSYAFSTIASAIPAYSKRTDIIFAD
ECVNFAIQKGIDASRSRVVYFKHNDMRDLEKKLIEQHKLDLKNPKKAAKTRRFLVAEGIY
VNTGEMCPLRELVELRSKYKLRLFLDETVSFGTIGQHGRGITELLCVDKSEVDLISASLE
NAVESIGGFCVGSHFIVEHQRLSGLGYCFSASQPPFLTQAAISALDIFENEPKIFNQLND
TAEKVDEQFRYFSKLELRGHPISPVKHLYLKDIDDSDKCEKILRKIADECIKKGLAVAYS
EYLPVEKFPPRRSLRITINRLLTEDDITNAFKILEEVSKSVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13963.t3 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 85 | 452 | 8.6E-80 |
| 7 | g13963.t3 | Gene3D | G3DSA:3.40.640.10 | - | 106 | 351 | 8.6E-80 |
| 2 | g13963.t3 | PANTHER | PTHR13693 | CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE | 18 | 461 | 3.0E-154 |
| 3 | g13963.t3 | PANTHER | PTHR13693:SF2 | SERINE PALMITOYLTRANSFERASE 1 | 18 | 461 | 3.0E-154 |
| 1 | g13963.t3 | Pfam | PF00155 | Aminotransferase class I and II | 91 | 451 | 1.5E-30 |
| 9 | g13963.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 14 | - |
| 10 | g13963.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 33 | - |
| 8 | g13963.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 34 | 462 | - |
| 5 | g13963.t3 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 48 | 459 | 1.57E-71 |
| 4 | g13963.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 33 | - |
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 transcript has been annotated with K00654 (serine palmitoyltransferase)
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.
