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.t40 isoform g3681.t40 27392553 27393373
chr_3 g3681 g3681.t40 exon g3681.t40.exon1 27392553 27392598
chr_3 g3681 g3681.t40 exon g3681.t40.exon2 27392693 27393108
chr_3 g3681 g3681.t40 cds g3681.t40.CDS1 27392700 27393108
chr_3 g3681 g3681.t40 exon g3681.t40.exon3 27393228 27393373
chr_3 g3681 g3681.t40 cds g3681.t40.CDS2 27393228 27393250
chr_3 g3681 g3681.t40 TSS g3681.t40 NA NA
chr_3 g3681 g3681.t40 TTS g3681.t40 NA NA

Sequences

>g3681.t40 Gene=g3681 Length=608
ATATAGGCAATGCCATTGGCATTTAGCTATTCTGGTTTAGTGACAGGTCAACAATGAACT
TTTCTGAAGTAGCAGAAGCAGCTTGTTTAAATGGACCTGCGTGGGCACGTCCATGGGCAC
AATTTCTAAAGCATTTCATCAATTATGGTCTCTTCATTACATATTTTGGAACATGTTCCG
TATATACAGTGATTATTGCTGAAAATTTTCAACAAATTATTCAACATTACACTGAATGGA
ATGTCGATGTTCGTGTTTATATTGCAATTTTATTAATCCCATTGATTTTATTGTCATGGG
TACCAAATCTCAAGTATCTTGCACCATTCTCTTCTGTGGCTAACATATTCATGGGAATTG
GATTATTGATAACATTTTACTATTGCGTAACAGATATGCCAAACATTAGTGAACGTGAAA
TGCATACATCATTATTGCAAATCCCGCCATTCTTTGGAATAACTATATTTAAATTAAGGC
AATAGGAGTTGTAATGCCGCTTGAAAATTCTATGAAAACACCTAAGCACTTCATTGGAAT
CTGTGGTGTATTAAATCAAGGTGATTGTTAATAAAATTATATATTAACAAAAACTATAGT
CTTCCTTC

>g3681.t40 Gene=g3681 Length=143
MNFSEVAEAACLNGPAWARPWAQFLKHFINYGLFITYFGTCSVYTVIIAENFQQIIQHYT
EWNVDVRVYIAILLIPLILLSWVPNLKYLAPFSSVANIFMGIGLLITFYYCVTDMPNISE
REMHTSLLQIPPFFGITIFKLRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t40 PANTHER PTHR22950 AMINO ACID TRANSPORTER 2 141 4.5E-53
3 g3681.t40 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 2 141 4.5E-53
1 g3681.t40 Pfam PF01490 Transmembrane amino acid transporter protein 23 139 1.5E-15
9 g3681.t40 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
11 g3681.t40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 52 -
8 g3681.t40 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 53 63 -
12 g3681.t40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 64 83 -
10 g3681.t40 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 88 -
13 g3681.t40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 112 -
7 g3681.t40 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 143 -
5 g3681.t40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
4 g3681.t40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 69 86 -
6 g3681.t40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -

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