Gene loci information

Transcript annotation

  • This transcript has been annotated as Excitatory amino acid transporter 1.

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 g12286 g12286.t9 TTS g12286.t9 22151194 22151194
chr_1 g12286 g12286.t9 isoform g12286.t9 22151207 22154488
chr_1 g12286 g12286.t9 exon g12286.t9.exon1 22151207 22151585
chr_1 g12286 g12286.t9 cds g12286.t9.CDS1 22151535 22151585
chr_1 g12286 g12286.t9 exon g12286.t9.exon2 22151646 22151748
chr_1 g12286 g12286.t9 cds g12286.t9.CDS2 22151646 22151748
chr_1 g12286 g12286.t9 exon g12286.t9.exon3 22151805 22151939
chr_1 g12286 g12286.t9 cds g12286.t9.CDS3 22151805 22151939
chr_1 g12286 g12286.t9 exon g12286.t9.exon4 22151995 22152420
chr_1 g12286 g12286.t9 cds g12286.t9.CDS4 22151995 22152420
chr_1 g12286 g12286.t9 exon g12286.t9.exon5 22152579 22152765
chr_1 g12286 g12286.t9 cds g12286.t9.CDS5 22152579 22152718
chr_1 g12286 g12286.t9 exon g12286.t9.exon6 22154389 22154488
chr_1 g12286 g12286.t9 TSS g12286.t9 NA NA

Sequences

>g12286.t9 Gene=g12286 Length=1330
GGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCGATGTCCGTAATCACTTCACT
ATAAGCAAATATAATTTGACATATTTTAATAGCACAGAAGTGGTACCTTTAACGGAATTT
AAGATTAAAGGAGAATGGCGTGAAGGAATGAATGTCTTGGGTTTAGTAATGTTCAGTGTT
GTTCTTGGTGCAACAATTGGCAAAATGCGTGAACGTGGAAAGCCCATTCAAGATTTCTTA
GTATCACTGAGCGAGGCAATGATGATTATTACACGTTGGGTTATTTGGCTTTCACCAATC
GGTGTCTTCTTCCTCATTACTGCTAAAATTCTTGAAATGGATTCACTAGCTGATGTCATT
GGAAAATTGGGAAAATACTTTATTACAGTCATGTTTGGTCTCTTTGTTCATGGTTTTGGA
ACAATTGCCGTCATTTTTTATATAACTGTAAGAAAGCTGCCATATGGTTTTGTCTTTAAG
ATGTCACAAGTTTTAGCAACAGCCTTTGGTACTGGTTCAAGTTCTGCAACAATGCCAATC
ACAATCAATTGCTTAGATAATATGGGAATTGATCCACGTGTTACAAGATTTGTGGTACCT
GTAGGTGCAACAATCAACATGGATGGTACAGCACTTTATGAGGCTGTTGCTGCTTTGTTT
ATTGCTCAATTACGTAATATACAATTAACATTTGGACATATCGTAGCTGTTAGTGTAACA
GCCACTGCCGCGTCAATTGGTGCCGCAGGCATTCCGCAAGCTGGTTTAATCACAATGGTT
ATGGTTCTTGATACTGTGGGTTTGCCTGCTGAAGATGTCACAATTATTATTGCAGTCGAT
TGGCTTCTTGATCGATTCCGAACAACAATTAATGTTATGTGTGACGCACTTGGTACTATT
CTTGTAGACCATTTATCAAAAGGAGAATTGAGTGCAACTAATGCGAGATTGGAATCGGGT
GAGCCACATGAGTTAGTTGAATTACATCATTCAAAGGAATAAAGTGAGGATAGTGAAAAC
GATGAATCCATTTAGAATTTTCAGAAAAGCTTTTATTGATGAAAGCTTCCATTAAGTTTT
TGTTTCATAAAAAATGATTTTTACTTACTAAAAATGTGGCTCATATTGATTGTTTAAAAT
GAAGAGAGCTATCATTGATTTGTTCAAATTAAAACAGTTGATATGAGTGTGGTCATGTTA
ATTTGAATGCATATTGAAGAAAAATTATTAATATGTAAAAATAGCAATTAGGAACAGAAG
AAAAATTTTAATTTCGATTTCTGCTTTTTAATTTTTAATTTTTGTTTCCTTTAAAGTTCA
AATAAAAAAA

>g12286.t9 Gene=g12286 Length=284
MNVLGLVMFSVVLGATIGKMRERGKPIQDFLVSLSEAMMIITRWVIWLSPIGVFFLITAK
ILEMDSLADVIGKLGKYFITVMFGLFVHGFGTIAVIFYITVRKLPYGFVFKMSQVLATAF
GTGSSSATMPITINCLDNMGIDPRVTRFVVPVGATINMDGTALYEAVAALFIAQLRNIQL
TFGHIVAVSVTATAASIGAAGIPQAGLITMVMVLDTVGLPAEDVTIIIAVDWLLDRFRTT
INVMCDALGTILVDHLSKGELSATNARLESGEPHELVELHHSKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12286.t9 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 1 271 3.6E-96
2 g12286.t9 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 1 272 5.6E-122
1 g12286.t9 Pfam PF00375 Sodium:dicarboxylate symporter family 2 255 5.8E-88
14 g12286.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 14 -
15 g12286.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
16 g12286.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 10 -
19 g12286.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 14 -
13 g12286.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 15 37 -
18 g12286.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 57 -
11 g12286.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 58 76 -
17 g12286.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 77 99 -
12 g12286.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 100 284 -
9 g12286.t9 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 151 174 -
8 g12286.t9 SUPERFAMILY SSF118215 Proton glutamate symport protein 2 256 1.15E-78
6 g12286.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 57 -
4 g12286.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 99 -
3 g12286.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 114 136 -
7 g12286.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 148 170 -
5 g12286.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -

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

Pathway

This gene does not belong to any 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