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.t6 TSS g13851.t6 32837143 32837143
chr_1 g13851 g13851.t6 isoform g13851.t6 32838118 32839568
chr_1 g13851 g13851.t6 exon g13851.t6.exon1 32838118 32838560
chr_1 g13851 g13851.t6 cds g13851.t6.CDS1 32838118 32838560
chr_1 g13851 g13851.t6 exon g13851.t6.exon2 32838935 32839568
chr_1 g13851 g13851.t6 cds g13851.t6.CDS2 32838935 32839568
chr_1 g13851 g13851.t6 TTS g13851.t6 32840304 32840304

Sequences

>g13851.t6 Gene=g13851 Length=1077
ATGAATAATAAGTTTTTGAAAGAGCATTTGCTCACAATTTTAACTGTGAGTTCTGTTGTG
CTTGGAGTAATTGTTGGTATCATAGTGAGAGCTTCAGTATTAGATGGAGATGATGACAAA
TTTAAAGCTCGTACAATTATGTACGTCAATTTCCTTGGAGATTTATTTCTGAGAATGCTA
AAATCCTTAATTCTACCACTCATCATTTCATCACTAATAGCAGCAGTTGGAAGTCTCGAT
ATCTCACTTTCAAAAACAATTGGACTTCGTGCAATTGCATATTATTTATTAACAACAGTA
TTTGCTGTCATTTTGGGCATTATTTTAGTAATGACAATTCGTCCAGGAGTAGATAGATCA
GAAAATTCAAATGAAAACACTACGACGCCAGCAGCAGTTCAACGAGCAATTACAACACCT
GATACTATGTTAGATTTAGTTCGAAACATCTTTCCACCAAATTTAGTACAAGCATGTATG
CAACAGTATCAGACAGTTCTTACTCCAAACAAAATACAAAATATGAGTGATCCAACAAAT
AGTTCAAATTATGTTCTTGGAACTGACTTGGATGAATTTATTATATCTGGAAAGTATGTG
GATTCTATGAATGTTATGGGCATTGTCGTAGCTTCGATTGTGTTTGGGATTGCAATTGCT
TCAACACGTGAACACTCGAGAAATCTTTTGTCAGTTTGTAATGAATTAAGTCATGTTATG
ATGAAAGTGACACGTTGGGTAATTTGGTTATCTCCAATTGGTGTATTCTTCTTAGTTCTC
TCAAAGCTAATGGAAATGGAAAATATTTTGGATGTTTTTGCTAAATTAGGACTTTACTTT
GTAACAGTCGCTGGTGGCATCATTTTCCATGGTTTTGTCATTTTACCAGCAATTTATTTC
TTCCTTACTAAAAAAAATCCTGTTAAATTTGTTGGCAATATGGCACAAGCGATTGCTACT
GCTTTCGGAACATCAAGTTCTTCAGCTACTCTTCCTGTTACAATGGAGTGCCTTGAACAT
AACAATAAAGTTGATGGAAGAGTAACACGATTTGTTTTGCCTATTGGTGCTACGATC

>g13851.t6 Gene=g13851 Length=359
MNNKFLKEHLLTILTVSSVVLGVIVGIIVRASVLDGDDDKFKARTIMYVNFLGDLFLRML
KSLILPLIISSLIAAVGSLDISLSKTIGLRAIAYYLLTTVFAVILGIILVMTIRPGVDRS
ENSNENTTTPAAVQRAITTPDTMLDLVRNIFPPNLVQACMQQYQTVLTPNKIQNMSDPTN
SSNYVLGTDLDEFIISGKYVDSMNVMGIVVASIVFGIAIASTREHSRNLLSVCNELSHVM
MKVTRWVIWLSPIGVFFLVLSKLMEMENILDVFAKLGLYFVTVAGGIIFHGFVILPAIYF
FLTKKNPVKFVGNMAQAIATAFGTSSSSATLPVTMECLEHNNKVDGRVTRFVLPIGATI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g13851.t6 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 2 168 2.5E-31
17 g13851.t6 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 190 359 3.2E-51
2 g13851.t6 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 3 359 1.9E-115
6 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 13 33 1.1E-56
4 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 59 79 1.1E-56
9 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 88 113 1.1E-56
5 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 200 222 1.1E-56
3 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 247 266 1.1E-56
8 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 284 303 1.1E-56
7 g13851.t6 PRINTS PR00173 Glutamate-aspartate symporter signature 351 359 1.1E-56
1 g13851.t6 Pfam PF00375 Sodium:dicarboxylate symporter family 11 359 6.1E-85
19 g13851.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
27 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
23 g13851.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 62 -
30 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 81 -
20 g13851.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 82 92 -
31 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 113 -
25 g13851.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 202 -
29 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 203 222 -
21 g13851.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 223 242 -
26 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 264 -
24 g13851.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 265 275 -
28 g13851.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 276 302 -
22 g13851.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 303 359 -
16 g13851.t6 SUPERFAMILY SSF118215 Proton glutamate symport protein 11 359 1.15E-71
14 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
10 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 62 84 -
15 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 113 -
12 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 203 222 -
11 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 243 260 -
13 g13851.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 280 302 -

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