Gene loci information

Transcript annotation

  • This transcript has been annotated as Excitatory amino acid transporter 1.

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.t7 TTS g12286.t7 22151194 22151194
chr_1 g12286 g12286.t7 isoform g12286.t7 22151207 22152595
chr_1 g12286 g12286.t7 exon g12286.t7.exon1 22151207 22151585
chr_1 g12286 g12286.t7 cds g12286.t7.CDS1 22151535 22151585
chr_1 g12286 g12286.t7 exon g12286.t7.exon2 22151646 22151748
chr_1 g12286 g12286.t7 cds g12286.t7.CDS2 22151646 22151748
chr_1 g12286 g12286.t7 exon g12286.t7.exon3 22151805 22151939
chr_1 g12286 g12286.t7 cds g12286.t7.CDS3 22151805 22151939
chr_1 g12286 g12286.t7 exon g12286.t7.exon4 22151995 22152420
chr_1 g12286 g12286.t7 cds g12286.t7.CDS4 22151995 22152371
chr_1 g12286 g12286.t7 exon g12286.t7.exon5 22152579 22152595
chr_1 g12286 g12286.t7 TSS g12286.t7 NA NA

Sequences

>g12286.t7 Gene=g12286 Length=1060
ACACGTTGGGTTATTTGGCTTTCACCAATCGGTGTCTTCTTCCTCATTACTGCTAAAATT
CTTGAAATGGATTCACTAGCTGATGTCATTGGAAAATTGGGAAAATACTTTATTACAGTC
ATGTTTGGTCTCTTTGTTCATGGTTTTGGAACAATTGCCGTCATTTTTTATATAACTGTA
AGAAAGCTGCCATATGGTTTTGTCTTTAAGATGTCACAAGTTTTAGCAACAGCCTTTGGT
ACTGGTTCAAGTTCTGCAACAATGCCAATCACAATCAATTGCTTAGATAATATGGGAATT
GATCCACGTGTTACAAGATTTGTGGTACCTGTAGGTGCAACAATCAACATGGATGGTACA
GCACTTTATGAGGCTGTTGCTGCTTTGTTTATTGCTCAATTACGTAATATACAATTAACA
TTTGGACATATCGTAGCTGTTAGTGTAACAGCCACTGCCGCGTCAATTGGTGCCGCAGGC
ATTCCGCAAGCTGGTTTAATCACAATGGTTATGGTTCTTGATACTGTGGGTTTGCCTGCT
GAAGATGTCACAATTATTATTGCAGTCGATTGGCTTCTTGATCGATTCCGAACAACAATT
AATGTTATGTGTGACGCACTTGGTACTATTCTTGTAGACCATTTATCAAAAGGAGAATTG
AGTGCAACTAATGCGAGATTGGAATCGGGTGAGCCACATGAGTTAGTTGAATTACATCAT
TCAAAGGAATAAAGTGAGGATAGTGAAAACGATGAATCCATTTAGAATTTTCAGAAAAGC
TTTTATTGATGAAAGCTTCCATTAAGTTTTTGTTTCATAAAAAATGATTTTTACTTACTA
AAAATGTGGCTCATATTGATTGTTTAAAATGAAGAGAGCTATCATTGATTTGTTCAAATT
AAAACAGTTGATATGAGTGTGGTCATGTTAATTTGAATGCATATTGAAGAAAAATTATTA
ATATGTAAAAATAGCAATTAGGAACAGAAGAAAAATTTTAATTTCGATTTCTGCTTTTTA
ATTTTTAATTTTTGTTTCCTTTAAAGTTCAAATAAAAAAA

>g12286.t7 Gene=g12286 Length=221
MDSLADVIGKLGKYFITVMFGLFVHGFGTIAVIFYITVRKLPYGFVFKMSQVLATAFGTG
SSSATMPITINCLDNMGIDPRVTRFVVPVGATINMDGTALYEAVAALFIAQLRNIQLTFG
HIVAVSVTATAASIGAAGIPQAGLITMVMVLDTVGLPAEDVTIIIAVDWLLDRFRTTINV
MCDALGTILVDHLSKGELSATNARLESGEPHELVELHHSKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12286.t7 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 1 208 1.3E-75
2 g12286.t7 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 1 209 3.4E-93
4 g12286.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 19 38 1.8E-42
6 g12286.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 85 111 1.8E-42
5 g12286.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 120 139 1.8E-42
3 g12286.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 147 167 1.8E-42
1 g12286.t7 Pfam PF00375 Sodium:dicarboxylate symporter family 5 192 2.5E-68
10 g12286.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 13 -
11 g12286.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 14 38 -
9 g12286.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 39 221 -
14 g12286.t7 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 88 111 -
7 g12286.t7 SUPERFAMILY SSF118215 Proton glutamate symport protein 6 193 2.35E-60
13 g12286.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
12 g12286.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -

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