Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t39 TSS g3681.t39 27391001 27391001
chr_3 g3681 g3681.t39 isoform g3681.t39 27391858 27393647
chr_3 g3681 g3681.t39 exon g3681.t39.exon1 27391858 27391988
chr_3 g3681 g3681.t39 cds g3681.t39.CDS1 27391938 27391988
chr_3 g3681 g3681.t39 exon g3681.t39.exon2 27392559 27393108
chr_3 g3681 g3681.t39 cds g3681.t39.CDS2 27392559 27393108
chr_3 g3681 g3681.t39 exon g3681.t39.exon3 27393228 27393325
chr_3 g3681 g3681.t39 cds g3681.t39.CDS3 27393228 27393250
chr_3 g3681 g3681.t39 exon g3681.t39.exon4 27393449 27393647
chr_3 g3681 g3681.t39 TTS g3681.t39 27394504 27394504

Sequences

>g3681.t39 Gene=g3681 Length=978
CCGCAACAAATGTCGAGAAAGGAATTTTATCGGATTATGATCCTTTCAAAGAAAGGAAAG
TAGATCATCCTACGTCAGATATGGATACATTGACTCATTTATTGAAAGCATCACTTGGCA
CTGGAATATTGGCAATGCCATTGGCATTTAGCTATTCTGGTTTAGTGACAGGTATTTTTG
CAACTATTCTGACGGCGCTTATATGTACTCACTGCGCCTATATCCTTGTTAAATGCAGTC
ATTCATTATATTACCGCACTCGAAGGTCAACAATGAACTTTTCTGAAGTAGCAGAAGCAG
CTTGTTTAAATGGACCTGCGTGGGCACGTCCATGGGCACAATTTCTAAAGCATTTCATCA
ATTATGGTCTCTTCATTACATATTTTGGAACATGTTCCGTATATACAGTGATTATTGCTG
AAAATTTTCAACAAATTATTCAACATTACACTGAATGGAATGTCGATGTTCGTGTTTATA
TTGCAATTTTATTAATCCCATTGATTTTATTGTCATGGGTACCAAATCTCAAGTATCTTG
CACCATTCTCTTCTGTGGCTAACATATTCATGGGAATTGGATTATTGATAACATTTTACT
ATTGCGTAACAGATATGCCAAACATTAGTGAACGTGAAATGCATACATCATTATTGCAAA
TCCCGCCATTCTTTGGAATAACTATATTTAAATTAAGGCAATAGGAGTTGTAATGCCGCT
TGAAAATTCTATGAAAACACCTAAGCACTTCATTGGAATCTGTGGTGTATTAAATCAAGG
TATGAGCGGTGTAACTTTGGTTTATATTCTACTCGGTTTCGTTGGTTATGTAAAATATGG
AAATGAAGCAAAAGGATCAATAACATTGAATTTACCTATAGAGGATTTAGCAGCACAAAC
TGTGAAAATTTTAATTGCATTAGCTGTTTATTGTACATTTGGTCTTCAATTTTATGTCTG
CCTTGAAATTGGATGGGA

>g3681.t39 Gene=g3681 Length=207
MDTLTHLLKASLGTGILAMPLAFSYSGLVTGIFATILTALICTHCAYILVKCSHSLYYRT
RRSTMNFSEVAEAACLNGPAWARPWAQFLKHFINYGLFITYFGTCSVYTVIIAENFQQII
QHYTEWNVDVRVYIAILLIPLILLSWVPNLKYLAPFSSVANIFMGIGLLITFYYCVTDMP
NISEREMHTSLLQIPPFFGITIFKLRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t39 PANTHER PTHR22950 AMINO ACID TRANSPORTER 2 205 1.7E-88
3 g3681.t39 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 2 205 1.7E-88
1 g3681.t39 Pfam PF01490 Transmembrane amino acid transporter protein 3 203 1.9E-30
8 g3681.t39 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
16 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 25 -
14 g3681.t39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 30 -
20 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 50 -
10 g3681.t39 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 69 -
15 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 70 86 -
12 g3681.t39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 91 -
17 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 116 -
11 g3681.t39 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 117 127 -
19 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
13 g3681.t39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 148 152 -
18 g3681.t39 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 153 176 -
9 g3681.t39 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 177 207 -
5 g3681.t39 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 50 -
7 g3681.t39 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 113 -
6 g3681.t39 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
4 g3681.t39 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 174 -

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. There were no conditions that were differentially expressed