Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Proton-coupled amino acid transporter-like protein pathetic.

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_3 g3681 g3681.t22 TSS g3681.t22 27386206 27386206
chr_3 g3681 g3681.t22 isoform g3681.t22 27386248 27392687
chr_3 g3681 g3681.t22 exon g3681.t22.exon1 27386248 27386387
chr_3 g3681 g3681.t22 exon g3681.t22.exon2 27390194 27390227
chr_3 g3681 g3681.t22 cds g3681.t22.CDS1 27390219 27390227
chr_3 g3681 g3681.t22 exon g3681.t22.exon3 27390295 27390365
chr_3 g3681 g3681.t22 cds g3681.t22.CDS2 27390295 27390365
chr_3 g3681 g3681.t22 exon g3681.t22.exon4 27391844 27391988
chr_3 g3681 g3681.t22 cds g3681.t22.CDS3 27391844 27391988
chr_3 g3681 g3681.t22 exon g3681.t22.exon5 27392559 27392687
chr_3 g3681 g3681.t22 cds g3681.t22.CDS4 27392559 27392687
chr_3 g3681 g3681.t22 TTS g3681.t22 NA NA

Sequences

>g3681.t22 Gene=g3681 Length=519
TCTGTTAATTATTTTCTCTCTTTATACCGTTTCATATCCATTTTTGTGATAAAAAATATA
AAATAAAAAGTGAGTGGAAAAATTATCAAATTATAAAATAATATTATTGTGTTATAAAAA
ATAAGGAAACTTTTAATATGATTAATTTAAAAAAGCAACGCTAAAATGGTAAATGAATAT
ACTGGTCCCCCACCTCAAGAACTCGAAACATTTATATCAAAAGACCAAAAGAATGGATCT
TCAACGTACAAAATTGCACCCGCAACAAATGTCGAGAAAGGAATTTTATCGGATTATGAT
CCTTTCAAAGAAAGGAAAGTAGATCATCCTACGTCAGATATGGATACATTGACTCATTTA
TTGAAAGCATCACTTGGCACTGGAATATTGGCAATGCCATTGGCATTTAGCTATTCTGGT
TTAGTGACAGGTATTTTTGCAACTATTCTGACGGCGCTTATATGTACTCACTGCGCCTAT
ATCCTTGTTAAATGCAGTCATTCATTATATTACCGCACT

>g3681.t22 Gene=g3681 Length=118
MVNEYTGPPPQELETFISKDQKNGSSTYKIAPATNVEKGILSDYDPFKERKVDHPTSDMD
TLTHLLKASLGTGILAMPLAFSYSGLVTGIFATILTALICTHCAYILVKCSHSLYYRT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t22 PANTHER PTHR22950 AMINO ACID TRANSPORTER 9 117 2.2E-41
3 g3681.t22 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 9 117 2.2E-41
1 g3681.t22 Pfam PF01490 Transmembrane amino acid transporter protein 55 113 3.2E-12
5 g3681.t22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 64 -
8 g3681.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 65 83 -
7 g3681.t22 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 88 -
9 g3681.t22 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 108 -
6 g3681.t22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 109 118 -
4 g3681.t22 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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.

Raw TPM values