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.t2 TTS g12286.t2 22151194 22151194
chr_1 g12286 g12286.t2 isoform g12286.t2 22151535 22155164
chr_1 g12286 g12286.t2 exon g12286.t2.exon1 22151535 22151585
chr_1 g12286 g12286.t2 cds g12286.t2.CDS1 22151535 22151585
chr_1 g12286 g12286.t2 exon g12286.t2.exon2 22151646 22151748
chr_1 g12286 g12286.t2 cds g12286.t2.CDS2 22151646 22151748
chr_1 g12286 g12286.t2 exon g12286.t2.exon3 22151805 22151939
chr_1 g12286 g12286.t2 cds g12286.t2.CDS3 22151805 22151939
chr_1 g12286 g12286.t2 exon g12286.t2.exon4 22151995 22152420
chr_1 g12286 g12286.t2 cds g12286.t2.CDS4 22151995 22152420
chr_1 g12286 g12286.t2 exon g12286.t2.exon5 22152579 22152765
chr_1 g12286 g12286.t2 cds g12286.t2.CDS5 22152579 22152765
chr_1 g12286 g12286.t2 exon g12286.t2.exon6 22154389 22154576
chr_1 g12286 g12286.t2 cds g12286.t2.CDS6 22154389 22154576
chr_1 g12286 g12286.t2 exon g12286.t2.exon7 22154633 22154794
chr_1 g12286 g12286.t2 cds g12286.t2.CDS7 22154633 22154794
chr_1 g12286 g12286.t2 exon g12286.t2.exon8 22154857 22155164
chr_1 g12286 g12286.t2 cds g12286.t2.CDS8 22154857 22155164
chr_1 g12286 g12286.t2 TSS g12286.t2 NA NA

Sequences

>g12286.t2 Gene=g12286 Length=1560
ATGAGCACGAATCATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGT
CGGAGTGTACTTGGCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGA
ACAATATTTGGACTTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATG
TACATTCAATATCCTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTG
CTTGTATCGTCAATCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATT
GCGTTGAGATCTATAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTATT
CTTCTTGTAACTGTTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATGCA
AAGGTTACTCGTGACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTATTT
CCACCAAATATCATACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAGAA
AATGCAACAGCTCGTGTTGGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCGAT
GTCCGTAATCACTTCACTATAAGCAAATATAATTTGACATATTTTAATAGCACAGAAGTG
GTACCTTTAACGGAATTTAAGATTAAAGGAGAATGGCGTGAAGGAATGAATGTCTTGGGT
TTAGTAATGTTCAGTGTTGTTCTTGGTGCAACAATTGGCAAAATGCGTGAACGTGGAAAG
CCCATTCAAGATTTCTTAGTATCACTGAGCGAGGCAATGATGATTATTACACGTTGGGTT
ATTTGGCTTTCACCAATCGGTGTCTTCTTCCTCATTACTGCTAAAATTCTTGAAATGGAT
TCACTAGCTGATGTCATTGGAAAATTGGGAAAATACTTTATTACAGTCATGTTTGGTCTC
TTTGTTCATGGTTTTGGAACAATTGCCGTCATTTTTTATATAACTGTAAGAAAGCTGCCA
TATGGTTTTGTCTTTAAGATGTCACAAGTTTTAGCAACAGCCTTTGGTACTGGTTCAAGT
TCTGCAACAATGCCAATCACAATCAATTGCTTAGATAATATGGGAATTGATCCACGTGTT
ACAAGATTTGTGGTACCTGTAGGTGCAACAATCAACATGGATGGTACAGCACTTTATGAG
GCTGTTGCTGCTTTGTTTATTGCTCAATTACGTAATATACAATTAACATTTGGACATATC
GTAGCTGTTAGTGTAACAGCCACTGCCGCGTCAATTGGTGCCGCAGGCATTCCGCAAGCT
GGTTTAATCACAATGGTTATGGTTCTTGATACTGTGGGTTTGCCTGCTGAAGATGTCACA
ATTATTATTGCAGTCGATTGGCTTCTTGATCGATTCCGAACAACAATTAATGTTATGTGT
GACGCACTTGGTACTATTCTTGTAGACCATTTATCAAAAGGAGAATTGAGTGCAACTAAT
GCGAGATTGGAATCGGGTGAGCCACATGAGTTAGTTGAATTACATCATTCAAAGGAATAA

>g12286.t2 Gene=g12286 Length=519
MSTNHNANHDQQPLAREKERRSVLGENLLTIVTIIGVVGGTIFGLILKKSDQKWTQRDIM
YIQYPGDLFLRMLKCLIVPLLVSSITSAIGALDLSLSKRIALRSIIYYFTTTICAVILGI
LLVTVFKPGKGYQTEVQNDAKVTRDVLTADTLLDLVRNLFPPNIIQATMFQYRTQLEPPE
NATARVGNGTEIKISDLSPDVRNHFTISKYNLTYFNSTEVVPLTEFKIKGEWREGMNVLG
LVMFSVVLGATIGKMRERGKPIQDFLVSLSEAMMIITRWVIWLSPIGVFFLITAKILEMD
SLADVIGKLGKYFITVMFGLFVHGFGTIAVIFYITVRKLPYGFVFKMSQVLATAFGTGSS
SATMPITINCLDNMGIDPRVTRFVVPVGATINMDGTALYEAVAALFIAQLRNIQLTFGHI
VAVSVTATAASIGAAGIPQAGLITMVMVLDTVGLPAEDVTIIIAVDWLLDRFRTTINVMC
DALGTILVDHLSKGELSATNARLESGEPHELVELHHSKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12286.t2 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 21 175 4.5E-35
15 g12286.t2 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 221 506 8.7E-97
2 g12286.t2 PANTHER PTHR11958:SF63 AMINO ACID TRANSPORTER 16 505 4.0E-177
3 g12286.t2 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 16 505 4.0E-177
11 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 27 47 3.9E-95
12 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 72 92 3.9E-95
9 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 101 126 3.9E-95
6 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 233 255 3.9E-95
8 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 280 299 3.9E-95
5 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 317 336 3.9E-95
7 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 383 409 3.9E-95
10 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 418 437 3.9E-95
4 g12286.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 445 465 3.9E-95
1 g12286.t2 Pfam PF00375 Sodium:dicarboxylate symporter family 29 490 1.1E-123
20 g12286.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
26 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
17 g12286.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 67 -
23 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 92 -
22 g12286.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 103 -
28 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
18 g12286.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 234 -
24 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 235 252 -
19 g12286.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 253 271 -
27 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 272 292 -
16 g12286.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 293 311 -
25 g12286.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
21 g12286.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 335 519 -
38 g12286.t2 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 386 409 -
13 g12286.t2 SUPERFAMILY SSF118215 Proton glutamate symport protein 29 491 1.96E-107
35 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
32 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 90 -
36 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 126 -
34 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 236 253 -
31 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 273 292 -
33 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
29 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 349 371 -
30 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 383 405 -
37 g12286.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 415 437 -

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