General information for g12286.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Excitatory amino acid transporter 3.
Parent gene
- The parent gene g12286 is located on chr_1: 22154864..22158231 (- 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 | g12286 | g12286.t1 | TTS | g12286.t1 | 22151194 | 22151194 |
| chr_1 | g12286 | g12286.t1 | isoform | g12286.t1 | 22151535 | 22155164 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon1 | 22151535 | 22151585 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS1 | 22151535 | 22151585 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon2 | 22151646 | 22151748 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS2 | 22151646 | 22151748 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon3 | 22151805 | 22151939 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS3 | 22151805 | 22151939 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon4 | 22151995 | 22152420 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS4 | 22151995 | 22152420 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon5 | 22152579 | 22152765 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS5 | 22152579 | 22152765 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon6 | 22154488 | 22154576 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS6 | 22154488 | 22154576 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon7 | 22154633 | 22154794 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS7 | 22154633 | 22154794 |
| chr_1 | g12286 | g12286.t1 | exon | g12286.t1.exon8 | 22154857 | 22155164 |
| chr_1 | g12286 | g12286.t1 | cds | g12286.t1.CDS8 | 22154857 | 22155164 |
| chr_1 | g12286 | g12286.t1 | TSS | g12286.t1 | NA | NA |
Sequences
>g12286.t1 Gene=g12286 Length=1461
ATGAGCACGAATCATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGT
CGGAGTGTACTTGGCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGA
ACAATATTTGGACTTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATG
TACATTCAATATCCTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTG
CTTGTATCGTCAATCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATT
GCGTTGAGATCTATAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTATT
CTTCTTGTAACTGTTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATGCA
AAGGTTACTCGTGACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTATTT
CCACCAAATATCATACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAGAA
AATGCAACAGCTCGTGTTGTGGTACCTTTAACGGAATTTAAGATTAAAGGAGAATGGCGT
GAAGGAATGAATGTCTTGGGTTTAGTAATGTTCAGTGTTGTTCTTGGTGCAACAATTGGC
AAAATGCGTGAACGTGGAAAGCCCATTCAAGATTTCTTAGTATCACTGAGCGAGGCAATG
ATGATTATTACACGTTGGGTTATTTGGCTTTCACCAATCGGTGTCTTCTTCCTCATTACT
GCTAAAATTCTTGAAATGGATTCACTAGCTGATGTCATTGGAAAATTGGGAAAATACTTT
ATTACAGTCATGTTTGGTCTCTTTGTTCATGGTTTTGGAACAATTGCCGTCATTTTTTAT
ATAACTGTAAGAAAGCTGCCATATGGTTTTGTCTTTAAGATGTCACAAGTTTTAGCAACA
GCCTTTGGTACTGGTTCAAGTTCTGCAACAATGCCAATCACAATCAATTGCTTAGATAAT
ATGGGAATTGATCCACGTGTTACAAGATTTGTGGTACCTGTAGGTGCAACAATCAACATG
GATGGTACAGCACTTTATGAGGCTGTTGCTGCTTTGTTTATTGCTCAATTACGTAATATA
CAATTAACATTTGGACATATCGTAGCTGTTAGTGTAACAGCCACTGCCGCGTCAATTGGT
GCCGCAGGCATTCCGCAAGCTGGTTTAATCACAATGGTTATGGTTCTTGATACTGTGGGT
TTGCCTGCTGAAGATGTCACAATTATTATTGCAGTCGATTGGCTTCTTGATCGATTCCGA
ACAACAATTAATGTTATGTGTGACGCACTTGGTACTATTCTTGTAGACCATTTATCAAAA
GGAGAATTGAGTGCAACTAATGCGAGATTGGAATCGGGTGAGCCACATGAGTTAGTTGAA
TTACATCATTCAAAGGAATAA
>g12286.t1 Gene=g12286 Length=486
MSTNHNANHDQQPLAREKERRSVLGENLLTIVTIIGVVGGTIFGLILKKSDQKWTQRDIM
YIQYPGDLFLRMLKCLIVPLLVSSITSAIGALDLSLSKRIALRSIIYYFTTTICAVILGI
LLVTVFKPGKGYQTEVQNDAKVTRDVLTADTLLDLVRNLFPPNIIQATMFQYRTQLEPPE
NATARVVVPLTEFKIKGEWREGMNVLGLVMFSVVLGATIGKMRERGKPIQDFLVSLSEAM
MIITRWVIWLSPIGVFFLITAKILEMDSLADVIGKLGKYFITVMFGLFVHGFGTIAVIFY
ITVRKLPYGFVFKMSQVLATAFGTGSSSATMPITINCLDNMGIDPRVTRFVVPVGATINM
DGTALYEAVAALFIAQLRNIQLTFGHIVAVSVTATAASIGAAGIPQAGLITMVMVLDTVG
LPAEDVTIIIAVDWLLDRFRTTINVMCDALGTILVDHLSKGELSATNARLESGEPHELVE
LHHSKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12286.t1 | PANTHER | PTHR11958:SF63 | AMINO ACID TRANSPORTER | 16 | 472 | 8.7E-177 |
| 3 | g12286.t1 | PANTHER | PTHR11958 | SODIUM/DICARBOXYLATE SYMPORTER-RELATED | 16 | 472 | 8.7E-177 |
| 9 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 27 | 47 | 2.5E-95 |
| 10 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 72 | 92 | 2.5E-95 |
| 6 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 101 | 126 | 2.5E-95 |
| 7 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 200 | 222 | 2.5E-95 |
| 4 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 247 | 266 | 2.5E-95 |
| 12 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 284 | 303 | 2.5E-95 |
| 11 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 350 | 376 | 2.5E-95 |
| 8 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 385 | 404 | 2.5E-95 |
| 5 | g12286.t1 | PRINTS | PR00173 | Glutamate-aspartate symporter signature | 412 | 432 | 2.5E-95 |
| 1 | g12286.t1 | Pfam | PF00375 | Sodium:dicarboxylate symporter family | 29 | 457 | 3.3E-123 |
| 25 | g12286.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 27 | - |
| 32 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 48 | - |
| 30 | g12286.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 49 | 67 | - |
| 31 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 94 | - |
| 27 | g12286.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 95 | 105 | - |
| 33 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 126 | - |
| 29 | g12286.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 127 | 201 | - |
| 36 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 220 | - |
| 24 | g12286.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 221 | 231 | - |
| 35 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 259 | - |
| 28 | g12286.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 260 | 278 | - |
| 34 | g12286.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 279 | 303 | - |
| 26 | g12286.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 304 | 486 | - |
| 23 | g12286.t1 | ProSitePatterns | PS00714 | Sodium:dicarboxylate symporter family signature 2. | 353 | 376 | - |
| 22 | g12286.t1 | SUPERFAMILY | SSF118215 | Proton glutamate symport protein | 29 | 458 | 1.7E-107 |
| 20 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 47 | - |
| 18 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 90 | - |
| 21 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 105 | 126 | - |
| 13 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 220 | - |
| 19 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 240 | 259 | - |
| 16 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 279 | 301 | - |
| 17 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 316 | 338 | - |
| 15 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 350 | 372 | - |
| 14 | g12286.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 382 | 404 | - |
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 |
| GO:0015293 | symporter 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.
