Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Excitatory amino acid transporter 4.

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.t14 isoform g12286.t14 22152329 22155164
chr_1 g12286 g12286.t14 exon g12286.t14.exon1 22152329 22152420
chr_1 g12286 g12286.t14 cds g12286.t14.CDS1 22152330 22152420
chr_1 g12286 g12286.t14 exon g12286.t14.exon2 22152579 22152765
chr_1 g12286 g12286.t14 cds g12286.t14.CDS2 22152579 22152765
chr_1 g12286 g12286.t14 exon g12286.t14.exon3 22154389 22154576
chr_1 g12286 g12286.t14 cds g12286.t14.CDS3 22154389 22154576
chr_1 g12286 g12286.t14 exon g12286.t14.exon4 22154633 22154794
chr_1 g12286 g12286.t14 cds g12286.t14.CDS4 22154633 22154794
chr_1 g12286 g12286.t14 exon g12286.t14.exon5 22154857 22155164
chr_1 g12286 g12286.t14 cds g12286.t14.CDS5 22154857 22155164
chr_1 g12286 g12286.t14 TSS g12286.t14 NA NA
chr_1 g12286 g12286.t14 TTS g12286.t14 NA NA

Sequences

>g12286.t14 Gene=g12286 Length=937
ATGAGCACGAATCATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGT
CGGAGTGTACTTGGCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGA
ACAATATTTGGACTTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATG
TACATTCAATATCCTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTG
CTTGTATCGTCAATCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATT
GCGTTGAGATCTATAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTATT
CTTCTTGTAACTGTTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATGCA
AAGGTTACTCGTGACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTATTT
CCACCAAATATCATACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAGAA
AATGCAACAGCTCGTGTTGGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCGAT
GTCCGTAATCACTTCACTATAAGCAAATATAATTTGACATATTTTAATAGCACAGAAGTG
GTACCTTTAACGGAATTTAAGATTAAAGGAGAATGGCGTGAAGGAATGAATGTCTTGGGT
TTAGTAATGTTCAGTGTTGTTCTTGGTGCAACAATTGGCAAAATGCGTGAACGTGGAAAG
CCCATTCAAGATTTCTTAGTATCACTGAGCGAGGCAATGATGATTATTACACGTTGGGTT
ATTTGGCTTTCACCAATCGGTGTCTTCTTCCTCATTACTGCTAAAATTCTTGAAATGGAT
TCACTAGCTGATGTCATTGGAAAATTGGGAAAATACT

>g12286.t14 Gene=g12286 Length=312
MSTNHNANHDQQPLAREKERRSVLGENLLTIVTIIGVVGGTIFGLILKKSDQKWTQRDIM
YIQYPGDLFLRMLKCLIVPLLVSSITSAIGALDLSLSKRIALRSIIYYFTTTICAVILGI
LLVTVFKPGKGYQTEVQNDAKVTRDVLTADTLLDLVRNLFPPNIIQATMFQYRTQLEPPE
NATARVGNGTEIKISDLSPDVRNHFTISKYNLTYFNSTEVVPLTEFKIKGEWREGMNVLG
LVMFSVVLGATIGKMRERGKPIQDFLVSLSEAMMIITRWVIWLSPIGVFFLITAKILEMD
SLADVIGKLGKY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12286.t14 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 21 175 1.5E-35
16 g12286.t14 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 220 312 7.3E-18
2 g12286.t14 PANTHER PTHR11958:SF63 AMINO ACID TRANSPORTER 16 312 6.5E-80
3 g12286.t14 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 16 312 6.5E-80
7 g12286.t14 PRINTS PR00173 Glutamate-aspartate symporter signature 27 47 5.1E-49
6 g12286.t14 PRINTS PR00173 Glutamate-aspartate symporter signature 72 92 5.1E-49
5 g12286.t14 PRINTS PR00173 Glutamate-aspartate symporter signature 101 126 5.1E-49
8 g12286.t14 PRINTS PR00173 Glutamate-aspartate symporter signature 233 255 5.1E-49
4 g12286.t14 PRINTS PR00173 Glutamate-aspartate symporter signature 280 299 5.1E-49
1 g12286.t14 Pfam PF00375 Sodium:dicarboxylate symporter family 29 312 2.6E-52
21 g12286.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
25 g12286.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
17 g12286.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 67 -
23 g12286.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 92 -
22 g12286.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 103 -
27 g12286.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
18 g12286.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 234 -
24 g12286.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 235 252 -
20 g12286.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 253 271 -
26 g12286.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 272 292 -
19 g12286.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 293 312 -
14 g12286.t14 SUPERFAMILY SSF118215 Proton glutamate symport protein 29 312 4.97E-45
12 g12286.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
10 g12286.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 90 -
11 g12286.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 126 -
9 g12286.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 252 -
13 g12286.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 272 294 -

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. There were no conditions that were differentially expressed