General information for g590.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g590 is located on chr_3: 4355274..4357871 (+ 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 | g590 | g590.t3 | TSS | g590.t3 | 4352293 | 4352293 |
| chr_3 | g590 | g590.t3 | isoform | g590.t3 | 4352294 | 4353849 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon1 | 4352294 | 4352438 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon2 | 4352747 | 4352839 |
| chr_3 | g590 | g590.t3 | cds | g590.t3.CDS1 | 4352756 | 4352839 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon3 | 4352901 | 4352975 |
| chr_3 | g590 | g590.t3 | cds | g590.t3.CDS2 | 4352901 | 4352975 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon4 | 4353181 | 4353319 |
| chr_3 | g590 | g590.t3 | cds | g590.t3.CDS3 | 4353181 | 4353319 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon5 | 4353468 | 4353610 |
| chr_3 | g590 | g590.t3 | cds | g590.t3.CDS4 | 4353468 | 4353475 |
| chr_3 | g590 | g590.t3 | exon | g590.t3.exon6 | 4353663 | 4353849 |
| chr_3 | g590 | g590.t3 | TTS | g590.t3 | NA | NA |
Sequences
>g590.t3 Gene=g590 Length=782
AGTTAGATTTCAAATGTTGAACTGATGTGTTTAAAATTTTATAATTATAAAAAAGTTCAT
TTTATTTTAATATCATTGAAATTAAAGATTATTTTTAAAAAAATTTTCACAAGTTTTCTT
TTTTCAATTCAATCAGATCGACTTGTCAATTGCCATGTTTGCCGGTGTTGAGTTGTTGAA
TGAGCATTACGGTACGAATAGACAGAATGGCCAAAATTTTTTACTTCTTGAGATACAAAT
GTCCTTGATTTGCAACGAGGAAAATAAAATTAAAAATAATTGTGAAAAGAAAATTGAAAT
TATTGGCATCGAGAACTCAAAAAACGAAAAGAATTTCATAGCAAAAGATAAATGGGGTAA
AGATATTGAGTTTTTACTCTCATGCATAGCACTTTCAGTAGGATTAGGAAACTTGTTGAG
GTTCCCTTTTACGGCTCTTGAAAATGGAGGAGTATCATAGTTCTGTTGCTTGTCGGCAAA
CCGCTTTATTATATGGAGTTATTATTGGGACAATTTTCTTCACGTGGTTGCATCAAAGTA
TATGATATGGCGCCAGCAATGCGTGGAATTGGCATTGGACAAGTTATGTCAACATGTTTC
GTTACAACTTACTATGCATCACTAATGGGACTTACAATTCGGTATTTTTTGGCATCATTT
AGCAACCCACTGCCATGGAGTGAATGCAAAGAAGAATGGAATGTTTCTTGCATTGATAGC
AAAATAAAATCTGTCAATTTCTCAGATGAAATGCCAAAATCATCAGCTGAACTTTATTTT
AT
>g590.t3 Gene=g590 Length=101
MFAGVELLNEHYGTNRQNGQNFLLLEIQMSLICNEENKIKNNCEKKIEIIGIENSKNEKN
FIAKDKWGKDIEFLLSCIALSVGLGNLLRFPFTALENGGVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g590.t3 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 34 | 99 | 1.9E-16 |
| 3 | g590.t3 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 34 | 99 | 1.9E-16 |
| 1 | g590.t3 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 65 | 99 | 1.2E-8 |
| 6 | g590.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 72 | - |
| 8 | g590.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 92 | - |
| 7 | g590.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 93 | 101 | - |
| 5 | g590.t3 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 63 | 101 | 11.153 |
| 4 | g590.t3 | SUPERFAMILY | SSF161070 | SNF-like | 64 | 100 | 7.59E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g590/g590.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g590.t3.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed