General information for g13340.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13340 is located on chr_1: 29374714..29375269 (+ 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 | g13340 | g13340.t2 | isoform | g13340.t2 | 29374714 | 29375269 |
| chr_1 | g13340 | g13340.t2 | exon | g13340.t2.exon1 | 29374714 | 29375269 |
| chr_1 | g13340 | g13340.t2 | cds | g13340.t2.CDS1 | 29374715 | 29375269 |
| chr_1 | g13340 | g13340.t2 | TSS | g13340.t2 | NA | NA |
| chr_1 | g13340 | g13340.t2 | TTS | g13340.t2 | NA | NA |
Sequences
>g13340.t2 Gene=g13340 Length=556
TATAGCTGGTATTTTATTTGGAATTGATTTTGGTATCTATACTGGATTACTGATCTCAGT
TATTGCATGTTACATTAACGGACTTCAAAGTAAATCAAAATTGCTTGGGCAAATATTAAA
TACAGATATTTATGTTCCTTTAAAAGCTCACAAAAATGTCATTGATCTTCAAAAAATAAA
AATTTTCCACTATAGCGGAACAGTTAATTTCGCAACATGTGTAAAGTTCAAGAAAAATCT
ATTCAACACTATTGGTATTGATCAAAGTTTAATCAAACGTGCATCATTAGGTCAAGCACA
ATCAGAAGCCAGAGGATTTAACAATGGAATCAAATATTTGATTATAGATCTTGGATCAAT
TACAAATATCGACTTAAGTGGCTACAGAACTATCATTGAAATTAGAAGTGAAATTAAATT
GATTGATGTTCGAGTTTATCTTGCAAATGCTAATGATAATGTCTATGACACAATCATACA
TGCTGTTAAACTTGGCTATCCATCATTTGAATTATTTTCATCAGTTCACGATGCTGTTTT
ATTTGCACAGGGATAA
>g13340.t2 Gene=g13340 Length=184
IAGILFGIDFGIYTGLLISVIACYINGLQSKSKLLGQILNTDIYVPLKAHKNVIDLQKIK
IFHYSGTVNFATCVKFKKNLFNTIGIDQSLIKRASLGQAQSEARGFNNGIKYLIIDLGSI
TNIDLSGYRTIIEIRSEIKLIDVRVYLANANDNVYDTIIHAVKLGYPSFELFSSVHDAVL
FAQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13340.t2 | CDD | cd07042 | STAS_SulP_like_sulfate_transporter | 50 | 161 | 1.16968E-11 |
| 5 | g13340.t2 | Gene3D | G3DSA:3.30.750.24 | - | 31 | 184 | 2.6E-30 |
| 2 | g13340.t2 | PANTHER | PTHR11814 | SULFATE TRANSPORTER | 4 | 184 | 3.1E-36 |
| 3 | g13340.t2 | PANTHER | PTHR11814:SF189 | FI18412P1 | 4 | 184 | 3.1E-36 |
| 1 | g13340.t2 | Pfam | PF01740 | STAS domain | 51 | 178 | 1.9E-19 |
| 7 | g13340.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 8 | g13340.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 6 | g13340.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 184 | - |
| 11 | g13340.t2 | ProSiteProfiles | PS50801 | STAS domain profile. | 49 | 182 | 18.71 |
| 4 | g13340.t2 | SUPERFAMILY | SSF52091 | SpoIIaa-like | 55 | 178 | 1.0E-13 |
| 10 | g13340.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
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:0016020 | membrane | CC |
| GO:0055085 | transmembrane transport | BP |
| GO:0008272 | sulfate transport | BP |
| GO:0008271 | secondary active sulfate transmembrane transporter activity | 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