Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g13851 g13851.t7 isoform g13851.t7 32839189 32840121
chr_1 g13851 g13851.t7 exon g13851.t7.exon1 32839189 32839573
chr_1 g13851 g13851.t7 cds g13851.t7.CDS1 32839209 32839573
chr_1 g13851 g13851.t7 exon g13851.t7.exon2 32839646 32839873
chr_1 g13851 g13851.t7 cds g13851.t7.CDS2 32839646 32839873
chr_1 g13851 g13851.t7 exon g13851.t7.exon3 32839935 32840121
chr_1 g13851 g13851.t7 cds g13851.t7.CDS3 32839935 32840121
chr_1 g13851 g13851.t7 TTS g13851.t7 32840304 32840304
chr_1 g13851 g13851.t7 TSS g13851.t7 NA NA

Sequences

>g13851.t7 Gene=g13851 Length=800
GTAATGAATTAAGTCATGTTATGATGAAAGTGACACGTTGGGTAATTTGGTTATCTCCAA
TTGGTGTATTCTTCTTAGTTCTCTCAAAGCTAATGGAAATGGAAAATATTTTGGATGTTT
TTGCTAAATTAGGACTTTACTTTGTAACAGTCGCTGGTGGCATCATTTTCCATGGTTTTG
TCATTTTACCAGCAATTTATTTCTTCCTTACTAAAAAAAATCCTGTTAAATTTGTTGGCA
ATATGGCACAAGCGATTGCTACTGCTTTCGGAACATCAAGTTCTTCAGCTACTCTTCCTG
TTACAATGGAGTGCCTTGAACATAACAATAAAGTTGATGGAAGAGTAACACGATTTGTTT
TGCCTATTGGTGCTACGATCAATATGGATGGTACTGCCTTATATGAAGCTGTTGCTGCCC
TTTTTATCGCACAATTAAGAAAAGTTCCTTTGAGCTTCACACAAATTGTTGCTGTAAGCA
TCACATCGACAGCAGCGTCAATTGGCGCGGCGGGAATTCCTCAAGCTGGCTTGGTGACAC
TTGTAATGGTGCTTGATACAGTCGGTTTGCCTGCTGAAGATGTTACATATATTATTGCTA
TTGATTGGATAATTGATAGAATAAGAACTGTAGTAAATGTTCTTGGTGACTCATTTGGTG
CAGCAATTGTTGAACATTATAGCAAGAAAGATCTTGAAAGATCAATGGAAACTCCTCCTC
GAGTAAATGGAAACATGATAGTGCCAATTGATGCCTATAAAGGAAATGATAACTCGACTT
TTGTCGATGAACGCATGTAA

>g13851.t7 Gene=g13851 Length=259
MMKVTRWVIWLSPIGVFFLVLSKLMEMENILDVFAKLGLYFVTVAGGIIFHGFVILPAIY
FFLTKKNPVKFVGNMAQAIATAFGTSSSSATLPVTMECLEHNNKVDGRVTRFVLPIGATI
NMDGTALYEAVAALFIAQLRKVPLSFTQIVAVSITSTAASIGAAGIPQAGLVTLVMVLDT
VGLPAEDVTYIIAIDWIIDRIRTVVNVLGDSFGAAIVEHYSKKDLERSMETPPRVNGNMI
VPIDAYKGNDNSTFVDERM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13851.t7 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 1 233 5.8E-92
2 g13851.t7 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 1 231 4.5E-116
5 g13851.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 8 27 3.5E-52
3 g13851.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 45 64 3.5E-52
7 g13851.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 112 138 3.5E-52
4 g13851.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 147 166 3.5E-52
6 g13851.t7 PRINTS PR00173 Glutamate-aspartate symporter signature 174 194 3.5E-52
1 g13851.t7 Pfam PF00375 Sodium:dicarboxylate symporter family 1 219 4.9E-85
10 g13851.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
13 g13851.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -
12 g13851.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 36 -
14 g13851.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 63 -
11 g13851.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 64 259 -
17 g13851.t7 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 115 138 -
8 g13851.t7 SUPERFAMILY SSF118215 Proton glutamate symport protein 1 220 7.32E-73
16 g13851.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -
15 g13851.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 62 -

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