Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Excitatory amino acid transporter 3.

Parent gene

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.t16 isoform g12286.t16 22154431 22158231
chr_1 g12286 g12286.t16 exon g12286.t16.exon1 22154431 22154576
chr_1 g12286 g12286.t16 cds g12286.t16.CDS1 22154432 22154576
chr_1 g12286 g12286.t16 exon g12286.t16.exon2 22154633 22154794
chr_1 g12286 g12286.t16 cds g12286.t16.CDS2 22154633 22154794
chr_1 g12286 g12286.t16 exon g12286.t16.exon3 22154857 22155330
chr_1 g12286 g12286.t16 cds g12286.t16.CDS3 22154857 22155164
chr_1 g12286 g12286.t16 exon g12286.t16.exon4 22158111 22158231
chr_1 g12286 g12286.t16 TSS g12286.t16 22158228 22158228
chr_1 g12286 g12286.t16 TTS g12286.t16 NA NA

Sequences

>g12286.t16 Gene=g12286 Length=903
GACGGGAGTCTAATTTAATTGCTCAGTGGTAGCAGATAACAGCGCTGAGTAAATATATAT
CACAGCATTGTAGTGATAAATAAATCTAGAAAATTCTGTCTGAAGTGCACTTGAATTCAT
GGGAAGAGAGGAGGATAAATATACCGAGATTGTTATTTGACGAGGAAGGAACAATAATCA
ACAATCATTATCATCATCATCTATAATTAATATAGAATAAAACAATTAAAGACAATACTT
TTTATACACAATAATCACGATAGGAGATAAATTTAAAAGTCTAAAAGATGAGCACGAATC
ATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGTCGGAGTGTACTTG
GCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGAACAATATTTGGAC
TTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATGTACATTCAATATC
CTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTGCTTGTATCGTCAA
TCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATTGCGTTGAGATCTA
TAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTATTCTTCTTGTAACTG
TTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATGCAAAGGTTACTCGTG
ACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTATTTCCACCAAATATCA
TACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAGAAAATGCAACAGCTC
GTGTTGGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCGATGTCCGTAATCACT
TCA

>g12286.t16 Gene=g12286 Length=205
MSTNHNANHDQQPLAREKERRSVLGENLLTIVTIIGVVGGTIFGLILKKSDQKWTQRDIM
YIQYPGDLFLRMLKCLIVPLLVSSITSAIGALDLSLSKRIALRSIIYYFTTTICAVILGI
LLVTVFKPGKGYQTEVQNDAKVTRDVLTADTLLDLVRNLFPPNIIQATMFQYRTQLEPPE
NATARVGNGTEIKISDLSPDVRNHF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12286.t16 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 21 175 4.9E-36
2 g12286.t16 PANTHER PTHR11958:SF63 AMINO ACID TRANSPORTER 15 171 1.1E-48
3 g12286.t16 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 15 171 1.1E-48
6 g12286.t16 PRINTS PR00173 Glutamate-aspartate symporter signature 27 47 1.6E-26
5 g12286.t16 PRINTS PR00173 Glutamate-aspartate symporter signature 72 92 1.6E-26
4 g12286.t16 PRINTS PR00173 Glutamate-aspartate symporter signature 101 126 1.6E-26
1 g12286.t16 Pfam PF00375 Sodium:dicarboxylate symporter family 29 169 3.2E-31
14 g12286.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
17 g12286.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
13 g12286.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 67 -
16 g12286.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 92 -
15 g12286.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 103 -
18 g12286.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
12 g12286.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 205 -
10 g12286.t16 SUPERFAMILY SSF118215 Proton glutamate symport protein 29 169 7.45E-27
9 g12286.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
7 g12286.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 90 -
8 g12286.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 126 -

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.

Raw TPM values