General information for g18.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g18 is located on chr_3: 309758..310177 (+ 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_3 | g18 | g18.t1 | isoform | g18.t1 | 309758 | 310177 |
| chr_3 | g18 | g18.t1 | exon | g18.t1.exon1 | 309758 | 309887 |
| chr_3 | g18 | g18.t1 | cds | g18.t1.CDS1 | 309758 | 309887 |
| chr_3 | g18 | g18.t1 | exon | g18.t1.exon2 | 309999 | 310177 |
| chr_3 | g18 | g18.t1 | cds | g18.t1.CDS2 | 309999 | 310177 |
| chr_3 | g18 | g18.t1 | TSS | g18.t1 | NA | NA |
| chr_3 | g18 | g18.t1 | TTS | g18.t1 | NA | NA |
Sequences
>g18.t1 Gene=g18 Length=309
ATGCACTTTGGATGGTGCATGGAATGGCATCAAATCATACTTGCACTCAATGCTTCTTCT
TTCTTACAATTGGAATGGGTTGCATCATCATGTTTTCAAGCTATAATGAGTTTAATCATA
ACATCTAACGGTGGATTTATCATCTATGCAATTCTTGGAAATCTTTCAAAAAACAGTGGA
AAAGATGTAAAAGATGTTGTGTCTAGTACTTTTGGTTTGGCTTTTATCACATATCCAGAA
GCGATTGCAAAAATTAAAATTTCAATGGCTGACGCTTGGTATTTGTCTCAAATGAGTGAT
TCTATTTAA
>g18.t1 Gene=g18 Length=102
MHFGWCMEWHQIILALNASSFLQLEWVASSCFQAIMSLIITSNGGFIIYAILGNLSKNSG
KDVKDVVSSTFGLAFITYPEAIAKIKISMADAWYLSQMSDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g18.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 29 | 89 | 3.1E-9 |
| 5 | g18.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 6 | g18.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 52 | - |
| 4 | g18.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 53 | 102 | - |
| 3 | g18.t1 | SUPERFAMILY | SSF161070 | SNF-like | 27 | 88 | 2.22E-7 |
| 2 | g18.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 34 | 56 | - |
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:0016021 | integral component of membrane | CC |
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.
