Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t2 TSS g12614.t2 24791362 24791362
chr_1 g12614 g12614.t2 isoform g12614.t2 24791403 24792569
chr_1 g12614 g12614.t2 exon g12614.t2.exon1 24791403 24791833
chr_1 g12614 g12614.t2 cds g12614.t2.CDS1 24791403 24791833
chr_1 g12614 g12614.t2 exon g12614.t2.exon2 24791962 24792569
chr_1 g12614 g12614.t2 cds g12614.t2.CDS2 24791962 24792568
chr_1 g12614 g12614.t2 TTS g12614.t2 24793269 24793269

Sequences

>g12614.t2 Gene=g12614 Length=1039
ATGAATCGCGCAAGATTTTACAAAGCAATAAAACCACATTTGCTTACAATTTTGACTGTT
CTCGCTGTGATTTTCAGTATTGTTCTTGGAATAATTTTAAGAGTAAATCATGATAAATAT
TCAGCAAGGACTGTGATGTATGTCAATTTTTTGGGCGATCTCTTTCTTCGTATGATCAGA
GCTCTCATTTTGCCTTTGATTATTTCATCCCTTATTAGCGCGATTGCGCCACTTGATTTT
TTATTAAGCAAGAAAATAGGTCTAAGAGCAATAGTTTATATTCTTGTAACAACTATCATT
GCTGTCATTCTTGGAATTGTTCTTGTGGTAACTATAAAACCGGGTGGAGCTGGTCTAGAA
GATAATGAAGAAGGAATTGTTTCTAATAGAAAATCATCAACGATTGTTGACACTTTGCTT
GATTTAATAAGAAACATTTTTCCACCGAATATTGTTCAAGCGACACTACAAACTTATCAA
ACGACCTTAACACCACCAGAAGACAATCCTGATGCGGACATTAATGATTGGATAATTAGC
TCTCATTATGTAGATGGAACAAATATGCTTGGTGTGGTGGCAGTGTCAATCATTTTTGGC
ATAACAATGAGTTTGGTACGAGAAAAAGTCAAAGGTTTAATCGATGTCACACTTGAATTT
ACATTAATTATGATGAAAATTATTCAATTTGTAATTTGGTTGACTCCAATTGGTGTCTTT
TTCTTGATTCTTGCGAAATTCTTAGAAATGGATGATATTCTTGATGTTTTTGCTAAATTG
GGACTTTATTTAGCCACAGTATCACTTGGAATTTTCGTTCATGGTTTCATTTTCTTACCA
GCAATATATTTTGCATTTACAAAGAAAAATCCATTAAGATTTATTGCGCATATGGGACCA
GCAATTTTGACAGCTCTTGGTACATCGTCTTCACTTGCTACATTGCCAGTATCATTGAAA
TGTGTTGAAGAAAAGGCAAAAATTGATGTGAGAGTTTCACGATTTATGCTGCCACTTGGA
GCAACAATTAATATGAATG

>g12614.t2 Gene=g12614 Length=346
MNRARFYKAIKPHLLTILTVLAVIFSIVLGIILRVNHDKYSARTVMYVNFLGDLFLRMIR
ALILPLIISSLISAIAPLDFLLSKKIGLRAIVYILVTTIIAVILGIVLVVTIKPGGAGLE
DNEEGIVSNRKSSTIVDTLLDLIRNIFPPNIVQATLQTYQTTLTPPEDNPDADINDWIIS
SHYVDGTNMLGVVAVSIIFGITMSLVREKVKGLIDVTLEFTLIMMKIIQFVIWLTPIGVF
FLILAKFLEMDDILDVFAKLGLYLATVSLGIFVHGFIFLPAIYFAFTKKNPLRFIAHMGP
AILTALGTSSSLATLPVSLKCVEEKAKIDVRVSRFMLPLGATINMN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12614.t2 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 5 166 1.5E-29
17 g12614.t2 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 168 346 4.3E-51
2 g12614.t2 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 3 346 5.1E-107
6 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 13 33 2.1E-62
5 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 58 78 2.1E-62
4 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 87 112 2.1E-62
3 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 184 206 2.1E-62
9 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 231 250 2.1E-62
8 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 268 287 2.1E-62
7 g12614.t2 PRINTS PR00173 Glutamate-aspartate symporter signature 335 346 2.1E-62
1 g12614.t2 Pfam PF00375 Sodium:dicarboxylate symporter family 15 346 5.2E-81
20 g12614.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
31 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
24 g12614.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
30 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 78 -
22 g12614.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 89 -
29 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
25 g12614.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 113 188 -
27 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 189 206 -
21 g12614.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 226 -
26 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 248 -
23 g12614.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 249 259 -
28 g12614.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 260 286 -
19 g12614.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 287 346 -
16 g12614.t2 SUPERFAMILY SSF118215 Proton glutamate symport protein 15 346 4.18E-67
13 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
15 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
12 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
10 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 206 -
11 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -
14 g12614.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 264 286 -

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