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.t5 TSS g13851.t5 32837143 32837143
chr_1 g13851 g13851.t5 isoform g13851.t5 32837278 32840121
chr_1 g13851 g13851.t5 exon g13851.t5.exon1 32837278 32837317
chr_1 g13851 g13851.t5 exon g13851.t5.exon2 32838064 32838560
chr_1 g13851 g13851.t5 cds g13851.t5.CDS1 32838106 32838560
chr_1 g13851 g13851.t5 exon g13851.t5.exon3 32838935 32839573
chr_1 g13851 g13851.t5 cds g13851.t5.CDS2 32838935 32839573
chr_1 g13851 g13851.t5 exon g13851.t5.exon4 32839646 32839873
chr_1 g13851 g13851.t5 cds g13851.t5.CDS3 32839646 32839873
chr_1 g13851 g13851.t5 exon g13851.t5.exon5 32839935 32840121
chr_1 g13851 g13851.t5 cds g13851.t5.CDS4 32839935 32840121
chr_1 g13851 g13851.t5 TTS g13851.t5 32840304 32840304

Sequences

>g13851.t5 Gene=g13851 Length=1591
ACTAAAAAAGTAAGAGGTGCACACACACCGGATATTCAAGAGTTTAATTTAATACGTAAA
ATAAGATTCGTTCAAAACAAAAATGAAATTAAAAATGAATAATAAGTTTTTGAAAGAGCA
TTTGCTCACAATTTTAACTGTGAGTTCTGTTGTGCTTGGAGTAATTGTTGGTATCATAGT
GAGAGCTTCAGTATTAGATGGAGATGATGACAAATTTAAAGCTCGTACAATTATGTACGT
CAATTTCCTTGGAGATTTATTTCTGAGAATGCTAAAATCCTTAATTCTACCACTCATCAT
TTCATCACTAATAGCAGCAGTTGGAAGTCTCGATATCTCACTTTCAAAAACAATTGGACT
TCGTGCAATTGCATATTATTTATTAACAACAGTATTTGCTGTCATTTTGGGCATTATTTT
AGTAATGACAATTCGTCCAGGAGTAGATAGATCAGAAAATTCAAATGAAAACACTACGAC
GCCAGCAGCAGTTCAACGAGCAATTACAACACCTGATACTATGTTAGATTTAGTTCGAAA
CATCTTTCCACCAAATTTAGTACAAGCATGTATGCAACAGTATCAGACAGTTCTTACTCC
AAACAAAATACAAAATATGAGTGATCCAACAAATAGTTCAAATTATGTTCTTGGAACTGA
CTTGGATGAATTTATTATATCTGGAAAGTATGTGGATTCTATGAATGTTATGGGCATTGT
CGTAGCTTCGATTGTGTTTGGGATTGCAATTGCTTCAACACGTGAACACTCGAGAAATCT
TTTGTCAGTTTGTAATGAATTAAGTCATGTTATGATGAAAGTGACACGTTGGGTAATTTG
GTTATCTCCAATTGGTGTATTCTTCTTAGTTCTCTCAAAGCTAATGGAAATGGAAAATAT
TTTGGATGTTTTTGCTAAATTAGGACTTTACTTTGTAACAGTCGCTGGTGGCATCATTTT
CCATGGTTTTGTCATTTTACCAGCAATTTATTTCTTCCTTACTAAAAAAAATCCTGTTAA
ATTTGTTGGCAATATGGCACAAGCGATTGCTACTGCTTTCGGAACATCAAGTTCTTCAGC
TACTCTTCCTGTTACAATGGAGTGCCTTGAACATAACAATAAAGTTGATGGAAGAGTAAC
ACGATTTGTTTTGCCTATTGGTGCTACGATCAATATGGATGGTACTGCCTTATATGAAGC
TGTTGCTGCCCTTTTTATCGCACAATTAAGAAAAGTTCCTTTGAGCTTCACACAAATTGT
TGCTGTAAGCATCACATCGACAGCAGCGTCAATTGGCGCGGCGGGAATTCCTCAAGCTGG
CTTGGTGACACTTGTAATGGTGCTTGATACAGTCGGTTTGCCTGCTGAAGATGTTACATA
TATTATTGCTATTGATTGGATAATTGATAGAATAAGAACTGTAGTAAATGTTCTTGGTGA
CTCATTTGGTGCAGCAATTGTTGAACATTATAGCAAGAAAGATCTTGAAAGATCAATGGA
AACTCCTCCTCGAGTAAATGGAAACATGATAGTGCCAATTGATGCCTATAAAGGAAATGA
TAACTCGACTTTTGTCGATGAACGCATGTAA

>g13851.t5 Gene=g13851 Length=502
MKLKMNNKFLKEHLLTILTVSSVVLGVIVGIIVRASVLDGDDDKFKARTIMYVNFLGDLF
LRMLKSLILPLIISSLIAAVGSLDISLSKTIGLRAIAYYLLTTVFAVILGIILVMTIRPG
VDRSENSNENTTTPAAVQRAITTPDTMLDLVRNIFPPNLVQACMQQYQTVLTPNKIQNMS
DPTNSSNYVLGTDLDEFIISGKYVDSMNVMGIVVASIVFGIAIASTREHSRNLLSVCNEL
SHVMMKVTRWVIWLSPIGVFFLVLSKLMEMENILDVFAKLGLYFVTVAGGIIFHGFVILP
AIYFFLTKKNPVKFVGNMAQAIATAFGTSSSSATLPVTMECLEHNNKVDGRVTRFVLPIG
ATINMDGTALYEAVAALFIAQLRKVPLSFTQIVAVSITSTAASIGAAGIPQAGLVTLVMV
LDTVGLPAEDVTYIIAIDWIIDRIRTVVNVLGDSFGAAIVEHYSKKDLERSMETPPRVNG
NMIVPIDAYKGNDNSTFVDERM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13851.t5 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 3 172 5.3E-31
14 g13851.t5 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 197 475 5.7E-101
2 g13851.t5 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 4 474 1.7E-180
3 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 17 37 6.7E-90
8 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 63 83 6.7E-90
6 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 92 117 6.7E-90
7 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 204 226 6.7E-90
10 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 251 270 6.7E-90
5 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 288 307 6.7E-90
4 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 355 381 6.7E-90
11 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 390 409 6.7E-90
9 g13851.t5 PRINTS PR00173 Glutamate-aspartate symporter signature 417 437 6.7E-90
1 g13851.t5 Pfam PF00375 Sodium:dicarboxylate symporter family 15 462 2.6E-129
15 g13851.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
23 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
21 g13851.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 66 -
27 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 85 -
17 g13851.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 86 96 -
25 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 117 -
20 g13851.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 118 206 -
24 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 207 226 -
18 g13851.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 227 246 -
26 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 247 268 -
19 g13851.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 269 279 -
22 g13851.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 306 -
16 g13851.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 307 502 -
34 g13851.t5 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 358 381 -
12 g13851.t5 SUPERFAMILY SSF118215 Proton glutamate symport protein 15 463 3.27E-109
31 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
30 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
28 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -
29 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 207 226 -
33 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 247 264 -
32 g13851.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 284 306 -

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

Pathway

  • This transcript belongs to the following pathways

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