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.t11 TSS g3681.t11 27386206 27386206
chr_3 g3681 g3681.t11 isoform g3681.t11 27386221 27394068
chr_3 g3681 g3681.t11 exon g3681.t11.exon1 27386221 27386316
chr_3 g3681 g3681.t11 exon g3681.t11.exon2 27390194 27390227
chr_3 g3681 g3681.t11 exon g3681.t11.exon3 27390295 27390365
chr_3 g3681 g3681.t11 exon g3681.t11.exon4 27391844 27391988
chr_3 g3681 g3681.t11 exon g3681.t11.exon5 27392559 27393108
chr_3 g3681 g3681.t11 exon g3681.t11.exon6 27393228 27393325
chr_3 g3681 g3681.t11 cds g3681.t11.CDS1 27393259 27393325
chr_3 g3681 g3681.t11 exon g3681.t11.exon7 27393449 27394068
chr_3 g3681 g3681.t11 cds g3681.t11.CDS2 27393449 27394068
chr_3 g3681 g3681.t11 TTS g3681.t11 27394504 27394504

Sequences

>g3681.t11 Gene=g3681 Length=1614
CGCCAACTGAAGTAGAAAGAAATTTATTCTGTTAATTATTTTCTCTCTTTATACCGTTTC
ATATCCATTTTTGTGATAAAAAATATAAAATAAAAAATTAATTTAAAAAAGCAACGCTAA
AATGGTAAATGAATATACTGGTCCCCCACCTCAAGAACTCGAAACATTTATATCAAAAGA
CCAAAAGAATGGATCTTCAACGTACAAAATTGCACCCGCAACAAATGTCGAGAAAGGAAT
TTTATCGGATTATGATCCTTTCAAAGAAAGGAAAGTAGATCATCCTACGTCAGATATGGA
TACATTGACTCATTTATTGAAAGCATCACTTGGCACTGGAATATTGGCAATGCCATTGGC
ATTTAGCTATTCTGGTTTAGTGACAGGTATTTTTGCAACTATTCTGACGGCGCTTATATG
TACTCACTGCGCCTATATCCTTGTTAAATGCAGTCATTCATTATATTACCGCACTCGAAG
GTCAACAATGAACTTTTCTGAAGTAGCAGAAGCAGCTTGTTTAAATGGACCTGCGTGGGC
ACGTCCATGGGCACAATTTCTAAAGCATTTCATCAATTATGGTCTCTTCATTACATATTT
TGGAACATGTTCCGTATATACAGTGATTATTGCTGAAAATTTTCAACAAATTATTCAACA
TTACACTGAATGGAATGTCGATGTTCGTGTTTATATTGCAATTTTATTAATCCCATTGAT
TTTATTGTCATGGGTACCAAATCTCAAGTATCTTGCACCATTCTCTTCTGTGGCTAACAT
ATTCATGGGAATTGGATTATTGATAACATTTTACTATTGCGTAACAGATATGCCAAACAT
TAGTGAACGTGAAATGCATACATCATTATTGCAAATCCCGCCATTCTTTGGAATAACTAT
ATTTAAATTAAGGCAATAGGAGTTGTAATGCCGCTTGAAAATTCTATGAAAACACCTAAG
CACTTCATTGGAATCTGTGGTGTATTAAATCAAGGTATGAGCGGTGTAACTTTGGTTTAT
ATTCTACTCGGTTTCGTTGGTTATGTAAAATATGGAAATGAAGCAAAAGGATCAATAACA
TTGAATTTACCTATAGAGGATTTAGCAGCACAAACTGTGAAAATTTTAATTGCATTAGCT
GTTTATTGTACATTTGGTCTTCAATTTTATGTCTGCCTTGAAATTGGATGGGATTTTATT
AAAGATAAATTTAGAAAACGTCCTTTGCTAGTTAACTACATGATGAGAACAGTTCTTGTT
ACTGCCGCTGTCTTACTTGCTGTCGCTGTGCCTACAATTGGACCTTTTGTTGGCTTACTC
GGTGCCTTCTGTTTCTCAATTCTGGGATTACTCGTGCCTGTACTTATTGAAATGATTACA
TACTGGGATGAAGGATTTGGAAAATTGAACTGGATAATTTGGAAAAATGTAATTGTTTGC
ATTTTTGGAATTCTTGCTCTTGTTTTTGGTTCAAAGGATGCAATAGCTGATATTATGAAA
ATGTATAATGAAAACCCAAGTGCTGATAATGCAACAACAATATTAGCTATCACAAATATG
AATGAAATAGTAGAAGAACTCACCACACTATTACCAACTACTACAGGTGTTTGA

>g3681.t11 Gene=g3681 Length=228
MPLENSMKTPKHFIGICGVLNQGMSGVTLVYILLGFVGYVKYGNEAKGSITLNLPIEDLA
AQTVKILIALAVYCTFGLQFYVCLEIGWDFIKDKFRKRPLLVNYMMRTVLVTAAVLLAVA
VPTIGPFVGLLGAFCFSILGLLVPVLIEMITYWDEGFGKLNWIIWKNVIVCIFGILALVF
GSKDAIADIMKMYNENPSADNATTILAITNMNEIVEELTTLLPTTTGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t11 PANTHER PTHR22950 AMINO ACID TRANSPORTER 1 193 5.8E-99
3 g3681.t11 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 1 193 5.8E-99
1 g3681.t11 Pfam PF01490 Transmembrane amino acid transporter protein 2 183 1.9E-32
8 g3681.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g3681.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 39 -
11 g3681.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 40 58 -
18 g3681.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 84 -
10 g3681.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 85 103 -
14 g3681.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 124 -
13 g3681.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 125 129 -
17 g3681.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 150 -
9 g3681.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 151 161 -
16 g3681.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 181 -
12 g3681.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 182 228 -
6 g3681.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
5 g3681.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
7 g3681.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 143 -
4 g3681.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 163 182 -

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