General information for g5806.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5806 is located on chr_2: 12005197..12005654 (+ 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_2 | g5806 | g5806.t1 | isoform | g5806.t1 | 12005197 | 12005654 |
| chr_2 | g5806 | g5806.t1 | exon | g5806.t1.exon1 | 12005197 | 12005366 |
| chr_2 | g5806 | g5806.t1 | cds | g5806.t1.CDS1 | 12005197 | 12005366 |
| chr_2 | g5806 | g5806.t1 | exon | g5806.t1.exon2 | 12005423 | 12005654 |
| chr_2 | g5806 | g5806.t1 | cds | g5806.t1.CDS2 | 12005423 | 12005654 |
| chr_2 | g5806 | g5806.t1 | TSS | g5806.t1 | NA | NA |
| chr_2 | g5806 | g5806.t1 | TTS | g5806.t1 | NA | NA |
Sequences
>g5806.t1 Gene=g5806 Length=402
ATGCCGAGAGAAGATGACACTAAAGTTTGTGATCTTGATACATTAAAATGCTATTATGAC
GCTGCTATAAATTCGACAAAAGAAAGTGAAGGATGTAACTGTCTTCAACCATGCATAAAT
ATTGAGTATACTTTGGAAGTCGAACGAGAAACTTTTGAACATCGAAATAAAACTGGAATT
ACGATACTTTCACTAATATTTGAAAAACATTTAACTGAATTGCATACGAGTTATGTCGCT
TATACAATTCAAAATTTTGTAGCTGATTGTGGTGGATTATGTGGATTATTTTTTGGATTT
TCTTTGTTGTCAATTTATGAATTGATTTGTAATTTTATTGTGTTATGTTTAGATAAATTT
AGAAATCGATCAAACAGAAGAGTGATATGGATAATTGATTAA
>g5806.t1 Gene=g5806 Length=133
MPREDDTKVCDLDTLKCYYDAAINSTKESEGCNCLQPCINIEYTLEVERETFEHRNKTGI
TILSLIFEKHLTELHTSYVAYTIQNFVADCGGLCGLFFGFSLLSIYELICNFIVLCLDKF
RNRSNRRVIWIID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5806.t1 | Gene3D | G3DSA:1.10.287.820 | - | 5 | 38 | 8.0E-12 |
| 3 | g5806.t1 | Gene3D | G3DSA:2.60.470.10 | - | 39 | 79 | 8.0E-12 |
| 5 | g5806.t1 | Gene3D | G3DSA:1.10.287.770 | - | 80 | 109 | 8.0E-12 |
| 1 | g5806.t1 | Pfam | PF00858 | Amiloride-sensitive sodium channel | 1 | 110 | 2.7E-19 |
| 7 | g5806.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 95 | - |
| 8 | g5806.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 117 | - |
| 6 | g5806.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 118 | 133 | - |
| 2 | g5806.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 117 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5806/g5806.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5806.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005272 | sodium channel activity | MF |
| GO:0006814 | sodium ion transport | BP |
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