Gene loci information

Transcript annotation

  • This transcript has been annotated as Excitatory amino acid transporter 4.

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.t4 isoform g12286.t4 22150489 22155164
chr_1 g12286 g12286.t4 exon g12286.t4.exon1 22150489 22151585
chr_1 g12286 g12286.t4 cds g12286.t4.CDS1 22151535 22151585
chr_1 g12286 g12286.t4 exon g12286.t4.exon2 22151646 22151748
chr_1 g12286 g12286.t4 cds g12286.t4.CDS2 22151646 22151748
chr_1 g12286 g12286.t4 exon g12286.t4.exon3 22151805 22151939
chr_1 g12286 g12286.t4 cds g12286.t4.CDS3 22151805 22151939
chr_1 g12286 g12286.t4 exon g12286.t4.exon4 22151995 22152420
chr_1 g12286 g12286.t4 cds g12286.t4.CDS4 22151995 22152420
chr_1 g12286 g12286.t4 exon g12286.t4.exon5 22152579 22152765
chr_1 g12286 g12286.t4 cds g12286.t4.CDS5 22152579 22152765
chr_1 g12286 g12286.t4 exon g12286.t4.exon6 22154389 22154576
chr_1 g12286 g12286.t4 cds g12286.t4.CDS6 22154389 22154542
chr_1 g12286 g12286.t4 exon g12286.t4.exon7 22154633 22155164
chr_1 g12286 g12286.t4 TSS g12286.t4 NA NA
chr_1 g12286 g12286.t4 TTS g12286.t4 NA NA

Sequences

>g12286.t4 Gene=g12286 Length=2668
ATGAGCACGAATCATAACGCAAATCATGATCAGCAGCCGCTAGCGAGAGAAAAAGAACGT
CGGAGTGTACTTGGCGAGAACCTTTTGACTATTGTGACGATAATTGGTGTTGTTGGAGGA
ACAATATTTGGACTTATTTTAAAAAAATCCGACCAAAAATGGACACAGCGTGACATTATG
TACATTCAATATCCTGGTGATTTATTCTTAAGGATGCTTAAATGTCTTATTGTGCCATTG
CTTGTATCGTCAATCACGAGTGCAATAGGTGCTCTAGATTTAAGTTTATCTAAACGAATT
GCGTTGAGGTAAATTAACCTGGTTTTTTTTTAAAAAGTCATTTTAAATTATAAATTTATT
TAATTTATAGATCTATAATTTATTATTTTACTACTACAATATGTGCGGTAATTCTCGGTA
TTCTTCTTGTAACTGTTTTCAAACCTGGTAAAGGATATCAAACAGAAGTACAAAATGATG
CAAAGGTTACTCGTGACGTACTCACAGCTGACACACTTCTTGATTTAGTGAGAAACTTAT
TTCCACCAAATATCATACAGGCAACAATGTTTCAGTATAGAACGCAATTGGAACCACCAG
AAAATGCAACAGCTCGTGTTGGTAATGGCACAGAAATAAAAATTTCAGACCTCTCCCCCG
ATGTCCGTAATCACTTCACTATAAGCAAATATAATTTGACATATTTTAATAGCACAGAAG
TGGTACCTTTAACGGAATTTAAGATTAAAGGAGAATGGCGTGAAGGAATGAATGTCTTGG
GTTTAGTAATGTTCAGTGTTGTTCTTGGTGCAACAATTGGCAAAATGCGTGAACGTGGAA
AGCCCATTCAAGATTTCTTAGTATCACTGAGCGAGGCAATGATGATTATTACACGTTGGG
TTATTTGGCTTTCACCAATCGGTGTCTTCTTCCTCATTACTGCTAAAATTCTTGAAATGG
ATTCACTAGCTGATGTCATTGGAAAATTGGGAAAATACTTTATTACAGTCATGTTTGGTC
TCTTTGTTCATGGTTTTGGAACAATTGCCGTCATTTTTTATATAACTGTAAGAAAGCTGC
CATATGGTTTTGTCTTTAAGATGTCACAAGTTTTAGCAACAGCCTTTGGTACTGGTTCAA
GTTCTGCAACAATGCCAATCACAATCAATTGCTTAGATAATATGGGAATTGATCCACGTG
TTACAAGATTTGTGGTACCTGTAGGTGCAACAATCAACATGGATGGTACAGCACTTTATG
AGGCTGTTGCTGCTTTGTTTATTGCTCAATTACGTAATATACAATTAACATTTGGACATA
TCGTAGCTGTTAGTGTAACAGCCACTGCCGCGTCAATTGGTGCCGCAGGCATTCCGCAAG
CTGGTTTAATCACAATGGTTATGGTTCTTGATACTGTGGGTTTGCCTGCTGAAGATGTCA
CAATTATTATTGCAGTCGATTGGCTTCTTGATCGATTCCGAACAACAATTAATGTTATGT
GTGACGCACTTGGTACTATTCTTGTAGACCATTTATCAAAAGGAGAATTGAGTGCAACTA
ATGCGAGATTGGAATCGGGTGAGCCACATGAGTTAGTTGAATTACATCATTCAAAGGAAT
AAAGTGAGGATAGTGAAAACGATGAATCCATTTAGAATTTTCAGAAAAGCTTTTATTGAT
GAAAGCTTCCATTAAGTTTTTGTTTCATAAAAAATGATTTTTACTTACTAAAAATGTGGC
TCATATTGATTGTTTAAAATGAAGAGAGCTATCATTGATTTGTTCAAATTAAAACAGTTG
ATATGAGTGTGGTCATGTTAATTTGAATGCATATTGAAGAAAAATTATTAATATGTAAAA
ATAGCAATTAGGAACAGAAGAAAAATTTTAATTTCGATTTCTGCTTTTTAATTTTTAATT
TTTGTTTCCTTTAAAGTTCAAATAAAAAAAAATGAAAATTCAGAAAAATTTATTTTTTAT
ATTTTTTTTCGCATGAATTATATAAAGAGATGAGAAAAGAAATTAAGTATGTATGTAATG
ATAGGATATAAGAAAAGAAGAAGAAAAATAAAGACGAAATTATATTAGTGACAATAATTT
ATTATGTAATCCCATTAAACAATCATGTTCCCCTCCCTTTACATACATGAAAATATTGAT
AAAGAAAAACCTCTATTTGATCAATCTCATACCTTTTTTGTTGTTGTTAATCTATAGCTA
TATTTCTATTTTGTTGACTTATTCTTATTCTACCTTTTTATTCGAATCATGTCATATTGA
GAAAAAAAGATAATAATGATAAAATTTTAAGAAAAAATTAAACGTGGATGTGTTAATGGA
TAATAATTTTGAATCAATCTATAGCATGAAAAAAGAAGAAGAAAAATATTAAAATGAAAA
AATTGTTAGAAAAATAAACCATTTGGATACCAATATTATAATTATAATAATAATGGCGAA
ACGATATTTTTTGTGTAATAAATAAAAATTAAATGTGTTCAAAAATGCATCATCACTGAA
AAATTCATTTAAAATTCTCTCTTTTTCTAGTCAATAGCAGCAACTGATTAAAATTTTTTA
TGTACATAACTTTTATTAATAATTCATTTACACACTTCAGTTTCTGATTGTTATTCATCA
AAATTATTATTTTTTTGTCACAAGCATT

>g12286.t4 Gene=g12286 Length=351
MFQYRTQLEPPENATARVGNGTEIKISDLSPDVRNHFTISKYNLTYFNSTEVVPLTEFKI
KGEWREGMNVLGLVMFSVVLGATIGKMRERGKPIQDFLVSLSEAMMIITRWVIWLSPIGV
FFLITAKILEMDSLADVIGKLGKYFITVMFGLFVHGFGTIAVIFYITVRKLPYGFVFKMS
QVLATAFGTGSSSATMPITINCLDNMGIDPRVTRFVVPVGATINMDGTALYEAVAALFIA
QLRNIQLTFGHIVAVSVTATAASIGAAGIPQAGLITMVMVLDTVGLPAEDVTIIIAVDWL
LDRFRTTINVMCDALGTILVDHLSKGELSATNARLESGEPHELVELHHSKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12286.t4 Gene3D G3DSA:1.10.3860.10 Proton glutamate symport protein 52 338 4.0E-97
2 g12286.t4 PANTHER PTHR11958 SODIUM/DICARBOXYLATE SYMPORTER-RELATED 49 339 1.9E-126
3 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 65 87 8.8E-65
4 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 112 131 8.8E-65
7 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 149 168 8.8E-65
8 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 215 241 8.8E-65
6 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 250 269 8.8E-65
5 g12286.t4 PRINTS PR00173 Glutamate-aspartate symporter signature 277 297 8.8E-65
1 g12286.t4 Pfam PF00375 Sodium:dicarboxylate symporter family 69 322 3.3E-90
13 g12286.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 66 -
17 g12286.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 85 -
12 g12286.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 86 96 -
16 g12286.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 124 -
14 g12286.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 125 143 -
15 g12286.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 144 168 -
11 g12286.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 169 351 -
24 g12286.t4 ProSitePatterns PS00714 Sodium:dicarboxylate symporter family signature 2. 218 241 -
9 g12286.t4 SUPERFAMILY SSF118215 Proton glutamate symport protein 66 323 8.5E-81
20 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 85 -
21 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 124 -
23 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 144 166 -
18 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 181 203 -
22 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 237 -
19 g12286.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 247 269 -

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