General information for g9869.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Sodium- and chloride-dependent GABA transporter 2.
Parent gene
- The parent gene g9869 is located on chr_1: 5774709..5776427 (+ 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 | g9869 | g9869.t3 | TSS | g9869.t3 | 5770746 | 5770746 |
| chr_1 | g9869 | g9869.t3 | isoform | g9869.t3 | 5771012 | 5775120 |
| chr_1 | g9869 | g9869.t3 | exon | g9869.t3.exon1 | 5771012 | 5771768 |
| chr_1 | g9869 | g9869.t3 | cds | g9869.t3.CDS1 | 5771707 | 5771768 |
| chr_1 | g9869 | g9869.t3 | exon | g9869.t3.exon2 | 5771825 | 5771970 |
| chr_1 | g9869 | g9869.t3 | cds | g9869.t3.CDS2 | 5771825 | 5771970 |
| chr_1 | g9869 | g9869.t3 | exon | g9869.t3.exon3 | 5774693 | 5774836 |
| chr_1 | g9869 | g9869.t3 | cds | g9869.t3.CDS3 | 5774693 | 5774836 |
| chr_1 | g9869 | g9869.t3 | exon | g9869.t3.exon4 | 5774898 | 5775120 |
| chr_1 | g9869 | g9869.t3 | cds | g9869.t3.CDS4 | 5774898 | 5775118 |
| chr_1 | g9869 | g9869.t3 | TTS | g9869.t3 | NA | NA |
Sequences
>g9869.t3 Gene=g9869 Length=1270
ATGGATGTGAAATCTTTTGATGTGCCAAATATTAGTGGCATAGAAAAATCCTCGAATAAT
GGAAGCAATGTTGAAATTTCAACGTCATCTACTGTCAATTTAATTGAAGATCGAACAAAT
TGGAGTCGACCAATTGAATTTATTTTATCGTGCTTGAGGTAAAAATATGAAATATTTATG
ACCGCTGTGATTAATTTATTAGTTGTTTTGAAGTGGAATGTGAGTTAAATGCGATTTAAT
ATTTTAAAACGATTCAATTGTCATTCAATTGCTCTTGAGTGGAATTTTTGGGTGAAAGAT
AAGAACTTAGTTGTGTTAAATTTTTGTGTAATTACTTTTTAAGTTGTCAATAAAAATGAT
AAGAAAGATTTTGCTAAAAATATCTCACTCAAGTGATTGTCTAAATTTTGAACTTTCTCT
TAATCGCAACAGCTGAGTTTTCTATTAAAACAATATAAACAATAAATTCATTATTGACTT
AATGAAACAACTTGCTAATTTGCTGTGCAATAATGTGTTTATAATATATAAAAGAGGAAA
TGTAAATTTCTAGACAAAACCGTTACACAACCTAAATGAATAACTTGGACATTTTTTTTT
ATTTTATTTTTTGATTAAAAATTTTTATTACTCTTCTTTTAGTTATGCAATAGGTAACAA
AATAAATTTAAATTTTTCTAATTATTTGAATTCTAATGTTTCAATTGTCTTTCGAAGGAT
TGGGGAACATTTGGAGATTTCCTCATCTTGCTTATAGGAATGGCGGTGGAGCTTTTTTAC
TGCCATATTTTCTTGCAGCAGTTTTTATTGGTTTGCCAATATTTTTTGCTGAACTGATTA
CAGGACAATATAGTGGACTTGGGCCGATTAAAGCTTATAGTTATCTTGCTCCGCTCTTTA
AAGGCTTGGGCTACTGCACATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGA
TTATTGCGTGGGTCTTATTTTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCA
CATGTGACAATGATTGGAATTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTC
GTCAAGAAAATGTTGGTAGTGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGA
TTAACGAAATTTGTTCAATTCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATA
CAACAACAAATGAACTTGTTCCCATTAATGATGTCATCACAAGAAGCCTCTCATCTGAAG
AGTTTTTCTA
>g9869.t3 Gene=g9869 Length=191
MFQLSFEGLGNIWRFPHLAYRNGGGAFLLPYFLAAVFIGLPIFFAELITGQYSGLGPIKA
YSYLAPLFKGLGYCTFMVISFVSIYYQLIIAWVLFYLYSSFFPSLRWGTCDNDWNSENCF
STIEDLYCRQENVGSASDQIFYRGGCREINEICSIHDLVGVNASNCMNTTTNELVPINDV
ITRSLSSEEFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g9869.t3 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 8 | 133 | 2.7E-49 |
| 3 | g9869.t3 | PANTHER | PTHR11616:SF241 | TRANSPORTER | 8 | 133 | 2.7E-49 |
| 4 | g9869.t3 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 26 | 45 | 2.1E-16 |
| 5 | g9869.t3 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 70 | 96 | 2.1E-16 |
| 1 | g9869.t3 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 8 | 134 | 3.8E-48 |
| 12 | g9869.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 27 | - |
| 13 | g9869.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 49 | - |
| 10 | g9869.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 50 | 69 | - |
| 14 | g9869.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 98 | - |
| 11 | g9869.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 99 | 191 | - |
| 9 | g9869.t3 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 8 | 102 | 25.089 |
| 8 | g9869.t3 | SUPERFAMILY | SSF161070 | SNF-like | 8 | 140 | 5.89E-45 |
| 6 | g9869.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 23 | 45 | - |
| 7 | g9869.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 98 | - |
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. There were no conditions that were differentially expressed