Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t13 TTS g12286.t13 22151194 22151194
chr_1 g12286 g12286.t13 isoform g12286.t13 22152002 22158231
chr_1 g12286 g12286.t13 exon g12286.t13.exon1 22152002 22152420
chr_1 g12286 g12286.t13 cds g12286.t13.CDS1 22152003 22152420
chr_1 g12286 g12286.t13 exon g12286.t13.exon2 22152579 22152765
chr_1 g12286 g12286.t13 cds g12286.t13.CDS2 22152579 22152765
chr_1 g12286 g12286.t13 exon g12286.t13.exon3 22154389 22154576
chr_1 g12286 g12286.t13 cds g12286.t13.CDS3 22154389 22154576
chr_1 g12286 g12286.t13 exon g12286.t13.exon4 22154633 22154794
chr_1 g12286 g12286.t13 cds g12286.t13.CDS4 22154633 22154794
chr_1 g12286 g12286.t13 exon g12286.t13.exon5 22154857 22155330
chr_1 g12286 g12286.t13 cds g12286.t13.CDS5 22154857 22155164
chr_1 g12286 g12286.t13 exon g12286.t13.exon6 22158111 22158231
chr_1 g12286 g12286.t13 TSS g12286.t13 22158228 22158228

Sequences

>g12286.t13 Gene=g12286 Length=1551
GACGGGAGTCTAATTTAATTGCTCAGTGGTAGCAGATAACAGCGCTGAGTAAATATATAT
CACAGCATTGTAGTGATAAATAAATCTAGAAAATTCTGTCTGAAGTGCACTTGAATTCAT
GGGAAGAGAGGAGGATAAATATACCGAGATTGTTATTTGACGAGGAAGGAACAATAATCA
ACAATCATTATCATCATCATCTATAATTAATATAGAATAAAACAATTAAAGACAATACTT
TTTATACACAATAATCACGATAGGAGATAAATTTAAAAGTCTAAAAGATGAGCACGAATC
ATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGTCGGAGTGTACTTG
GCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGAACAATATTTGGAC
TTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATGTACATTCAATATC
CTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTGCTTGTATCGTCAA
TCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATTGCGTTGAGATCTA
TAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTATTCTTCTTGTAACTG
TTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATGCAAAGGTTACTCGTG
ACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTATTTCCACCAAATATCA
TACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAGAAAATGCAACAGCTC
GTGTTGGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCGATGTCCGTAATCACT
TCACTATAAGCAAATATAATTTGACATATTTTAATAGCACAGAAGTGGTACCTTTAACGG
AATTTAAGATTAAAGGAGAATGGCGTGAAGGAATGAATGTCTTGGGTTTAGTAATGTTCA
GTGTTGTTCTTGGTGCAACAATTGGCAAAATGCGTGAACGTGGAAAGCCCATTCAAGATT
TCTTAGTATCACTGAGCGAGGCAATGATGATTATTACACGTTGGGTTATTTGGCTTTCAC
CAATCGGTGTCTTCTTCCTCATTACTGCTAAAATTCTTGAAATGGATTCACTAGCTGATG
TCATTGGAAAATTGGGAAAATACTTTATTACAGTCATGTTTGGTCTCTTTGTTCATGGTT
TTGGAACAATTGCCGTCATTTTTTATATAACTGTAAGAAAGCTGCCATATGGTTTTGTCT
TTAAGATGTCACAAGTTTTAGCAACAGCCTTTGGTACTGGTTCAAGTTCTGCAACAATGC
CAATCACAATCAATTGCTTAGATAATATGGGAATTGATCCACGTGTTACAAGATTTGTGG
TACCTGTAGGTGCAACAATCAACATGGATGGTACAGCACTTTATGAGGCTGTTGCTGCTT
TGTTTATTGCTCAATTACGTAATATACAATTAACATTTGGACATATCGTAG

>g12286.t13 Gene=g12286 Length=421
MSTNHNANHDQQPLAREKERRSVLGENLLTIVTIIGVVGGTIFGLILKKSDQKWTQRDIM
YIQYPGDLFLRMLKCLIVPLLVSSITSAIGALDLSLSKRIALRSIIYYFTTTICAVILGI
LLVTVFKPGKGYQTEVQNDAKVTRDVLTADTLLDLVRNLFPPNIIQATMFQYRTQLEPPE
NATARVGNGTEIKISDLSPDVRNHFTISKYNLTYFNSTEVVPLTEFKIKGEWREGMNVLG
LVMFSVVLGATIGKMRERGKPIQDFLVSLSEAMMIITRWVIWLSPIGVFFLITAKILEMD
SLADVIGKLGKYFITVMFGLFVHGFGTIAVIFYITVRKLPYGFVFKMSQVLATAFGTGSS
SATMPITINCLDNMGIDPRVTRFVVPVGATINMDGTALYEAVAALFIAQLRNIQLTFGHI
V

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12286.t13 Coils Coil Coil 421 421 -
13 g12286.t13 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 21 175 3.0E-35
12 g12286.t13 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 221 421 4.4E-65
2 g12286.t13 PANTHER PTHR11958:SF63 AMINO ACID TRANSPORTER 16 421 1.2E-131
3 g12286.t13 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 16 421 1.2E-131
7 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 27 47 7.3E-70
6 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 72 92 7.3E-70
5 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 101 126 7.3E-70
9 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 233 255 7.3E-70
4 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 280 299 7.3E-70
8 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 317 336 7.3E-70
10 g12286.t13 PRINTS PR00173 Glutamate-aspartate symporter signature 383 409 7.3E-70
1 g12286.t13 Pfam PF00375 Sodium:dicarboxylate symporter family 29 420 1.8E-93
19 g12286.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
25 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
16 g12286.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 67 -
22 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 92 -
21 g12286.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 103 -
27 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
17 g12286.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 234 -
23 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 235 252 -
18 g12286.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 253 271 -
26 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 272 292 -
15 g12286.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 293 311 -
24 g12286.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
20 g12286.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 335 421 -
35 g12286.t13 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 386 409 -
11 g12286.t13 SUPERFAMILY SSF118215 Proton glutamate symport protein 29 420 9.29E-82
33 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
30 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 90 -
32 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 126 -
31 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 236 253 -
34 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 273 292 -
29 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
28 g12286.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 349 371 -

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