General information for g13853.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13853 is located on chr_1: 32843995..32847370 (+ 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 | g13853 | g13853.t1 | TSS | g13853.t1 | 32843168 | 32843168 |
| chr_1 | g13853 | g13853.t1 | isoform | g13853.t1 | 32843293 | 32844157 |
| chr_1 | g13853 | g13853.t1 | exon | g13853.t1.exon1 | 32843293 | 32843321 |
| chr_1 | g13853 | g13853.t1 | cds | g13853.t1.CDS1 | 32843293 | 32843321 |
| chr_1 | g13853 | g13853.t1 | exon | g13853.t1.exon2 | 32843508 | 32843995 |
| chr_1 | g13853 | g13853.t1 | cds | g13853.t1.CDS2 | 32843508 | 32843995 |
| chr_1 | g13853 | g13853.t1 | exon | g13853.t1.exon3 | 32844054 | 32844157 |
| chr_1 | g13853 | g13853.t1 | cds | g13853.t1.CDS3 | 32844054 | 32844157 |
| chr_1 | g13853 | g13853.t1 | TTS | g13853.t1 | 32844245 | 32844245 |
Sequences
>g13853.t1 Gene=g13853 Length=621
ATGGAAATACTGAATTCTGGTTTTCATCGAGAATTAAAATACAGTCTAAAATTTGCACCC
GTTATAAGTTGTGAAGTGCTGCTCGTACAAGAAATTCCAAGTTCTGTGTATGTGGATGTG
GATCAGTTATTCAACCTCAACAAATTAAATAAAATCAAAACCTTTGTTCCTTATTACATC
GATGTAGAATTACCGACATCAAAATCGAGTCCATTTAAAGTATACATGTTTGAGAATGTT
AGAAAATCAGTAAACATCACATTACCACTTCATTTTCGATATCATGAACCGAGTGACAAA
AAGTTCAATCGAGTAGAAATTGAGTCACCAAAAATATATTTATCGAATTGTCCTGTCAGC
AGAGGTCAAGGAGTTCTTCTTCCATGCAGAAATTCATCCGAGATAACAGACTTTTTAGAA
CTCGCATCTGCATCATTTTGTGAATGGACTGAAACGCAATATAGCACACCCATAACATTA
AGTTTTTTGATTCCAGTCGGAAATATAAAATCTTATGCATTCGTTCTACCTATAACAATT
TTCATAAGTTGGATTGCGTGTCTGTTTCTCACGTATGTCATTATTAAGAAATCAAGAGAG
ATTAGTAAGAAAGTGCTATGA
>g13853.t1 Gene=g13853 Length=206
MEILNSGFHRELKYSLKFAPVISCEVLLVQEIPSSVYVDVDQLFNLNKLNKIKTFVPYYI
DVELPTSKSSPFKVYMFENVRKSVNITLPLHFRYHEPSDKKFNRVEIESPKIYLSNCPVS
RGQGVLLPCRNSSEITDFLELASASFCEWTETQYSTPITLSFLIPVGNIKSYAFVLPITI
FISWIACLFLTYVIIKKSREISKKVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13853.t1 | PANTHER | PTHR28650 | PHOSPHATIDYLINOSITOL-GLYCAN BIOSYNTHESIS CLASS X PROTEIN | 3 | 205 | 1.1E-31 |
| 1 | g13853.t1 | Pfam | PF08320 | PIG-X / PBN1 | 6 | 194 | 5.5E-32 |
| 6 | g13853.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 171 | - |
| 7 | g13853.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 172 | 195 | - |
| 5 | g13853.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 196 | 206 | - |
| 4 | g13853.t1 | SMART | SM00780 | pig_x_1 | 4 | 197 | 8.0E-5 |
| 3 | g13853.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 172 | 194 | - |
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:0006506 | GPI anchor biosynthetic process | BP |
| GO:0005789 | endoplasmic reticulum membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K07541 (GPI mannosyltransferase 1 subunit X)
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.
