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 g12614 g12614.t12 TSS g12614.t12 24791362 24791362
chr_1 g12614 g12614.t12 isoform g12614.t12 24792228 24793181
chr_1 g12614 g12614.t12 exon g12614.t12.exon1 24792228 24792569
chr_1 g12614 g12614.t12 cds g12614.t12.CDS1 24792278 24792569
chr_1 g12614 g12614.t12 exon g12614.t12.exon2 24792630 24792717
chr_1 g12614 g12614.t12 cds g12614.t12.CDS2 24792630 24792717
chr_1 g12614 g12614.t12 exon g12614.t12.exon3 24792781 24792915
chr_1 g12614 g12614.t12 cds g12614.t12.CDS3 24792781 24792915
chr_1 g12614 g12614.t12 exon g12614.t12.exon4 24792998 24793181
chr_1 g12614 g12614.t12 cds g12614.t12.CDS4 24792998 24793181
chr_1 g12614 g12614.t12 TTS g12614.t12 24793269 24793269

Sequences

>g12614.t12 Gene=g12614 Length=749
GGTTGACTCCAATTGGTGTCTTTTTCTTGATTCTTGCGAAATTCTTAGAAATGGATGATA
TTCTTGATGTTTTTGCTAAATTGGGACTTTATTTAGCCACAGTATCACTTGGAATTTTCG
TTCATGGTTTCATTTTCTTACCAGCAATATATTTTGCATTTACAAAGAAAAATCCATTAA
GATTTATTGCGCATATGGGACCAGCAATTTTGACAGCTCTTGGTACATCGTCTTCACTTG
CTACATTGCCAGTATCATTGAAATGTGTTGAAGAAAAGGCAAAAATTGATGTGAGAGTTT
CACGATTTATGCTGCCACTTGGAGCAACAATTAATATGAATGGCACTGCTCTTTATGAGG
CTGTTGCCGCAATTTTCATAGCACAACTGCGACAAATTGACTTATCAATTGGATCAATTA
TTGCCGTGTGTATCACTGCTACATGCGCTTCAATTGGGACAGCCGGTGTGCCTCAAGCTG
GCTTAGTAACGCTTGTAATGGTTCTTGATTCAATTGGAATTCCTGCTGAAGATATCAGTT
TAATTATTGCTATAGATTGGATTGTGAACCGAATTAGAGCATGTGTTAACATTCTTGGTG
ATGCTTATGGAGCAGCAATTATAGAAGCAATAAGCAAAAAAGAATTGGATAAACTTCCAA
TAGAAGCACCAAATGACGTTGAAACAGCAAAAGAAGAAACAACAAATCTTAATGGGAATG
CAACTGATGTAAGATTAAAGGAAGTTTAA

>g12614.t12 Gene=g12614 Length=232
MDDILDVFAKLGLYLATVSLGIFVHGFIFLPAIYFAFTKKNPLRFIAHMGPAILTALGTS
SSLATLPVSLKCVEEKAKIDVRVSRFMLPLGATINMNGTALYEAVAAIFIAQLRQIDLSI
GSIIAVCITATCASIGTAGVPQAGLVTLVMVLDSIGIPAEDISLIIAIDWIVNRIRACVN
ILGDAYGAAIIEAISKKELDKLPIEAPNDVETAKEETTNLNGNATDVRLKEV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12614.t12 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 1 210 5.9E-78
2 g12614.t12 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 1 215 7.3E-95
3 g12614.t12 PRINTS PR00173 Glutamate-aspartate symporter signature 19 38 3.1E-43
4 g12614.t12 PRINTS PR00173 Glutamate-aspartate symporter signature 86 112 3.1E-43
5 g12614.t12 PRINTS PR00173 Glutamate-aspartate symporter signature 121 140 3.1E-43
6 g12614.t12 PRINTS PR00173 Glutamate-aspartate symporter signature 148 168 3.1E-43
1 g12614.t12 Pfam PF00375 Sodium:dicarboxylate symporter family 5 193 9.9E-72
16 g12614.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
20 g12614.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 37 -
15 g12614.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 38 48 -
23 g12614.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 70 -
18 g12614.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 71 89 -
22 g12614.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 111 -
14 g12614.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 117 -
19 g12614.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 139 -
17 g12614.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 140 144 -
21 g12614.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 172 -
13 g12614.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 173 232 -
11 g12614.t12 SUPERFAMILY SSF118215 Proton glutamate symport protein 6 192 2.48E-60
8 g12614.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
9 g12614.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
7 g12614.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
10 g12614.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -

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. There were no conditions that were differentially expressed