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.t5 TSS g3681.t5 27385902 27385902
chr_3 g3681 g3681.t5 isoform g3681.t5 27386065 27394647
chr_3 g3681 g3681.t5 exon g3681.t5.exon1 27386065 27386221
chr_3 g3681 g3681.t5 exon g3681.t5.exon2 27390295 27390365
chr_3 g3681 g3681.t5 exon g3681.t5.exon3 27391844 27391988
chr_3 g3681 g3681.t5 exon g3681.t5.exon4 27392559 27393108
chr_3 g3681 g3681.t5 exon g3681.t5.exon5 27393228 27393325
chr_3 g3681 g3681.t5 cds g3681.t5.CDS1 27393259 27393325
chr_3 g3681 g3681.t5 exon g3681.t5.exon6 27393449 27394647
chr_3 g3681 g3681.t5 cds g3681.t5.CDS2 27393449 27394068
chr_3 g3681 g3681.t5 TTS g3681.t5 NA NA

Sequences

>g3681.t5 Gene=g3681 Length=2220
AGTAAAGAACATGCGCACACATAATATAAGTACATTCAAGAAATGAGACAAAAAACAGAG
AGCACAAAAAAGAAGAAGTAAAAAATGACTTGCCGAGTTAACTAACGAACAGAAACCCCA
TTTCTCCATAGATTCTCAGTTCAGTTTAGTTTGAATCGAATATACTGGTCCCCCACCTCA
AGAACTCGAAACATTTATATCAAAAGACCAAAAGAATGGATCTTCAACGTACAAAATTGC
ACCCGCAACAAATGTCGAGAAAGGAATTTTATCGGATTATGATCCTTTCAAAGAAAGGAA
AGTAGATCATCCTACGTCAGATATGGATACATTGACTCATTTATTGAAAGCATCACTTGG
CACTGGAATATTGGCAATGCCATTGGCATTTAGCTATTCTGGTTTAGTGACAGGTATTTT
TGCAACTATTCTGACGGCGCTTATATGTACTCACTGCGCCTATATCCTTGTTAAATGCAG
TCATTCATTATATTACCGCACTCGAAGGTCAACAATGAACTTTTCTGAAGTAGCAGAAGC
AGCTTGTTTAAATGGACCTGCGTGGGCACGTCCATGGGCACAATTTCTAAAGCATTTCAT
CAATTATGGTCTCTTCATTACATATTTTGGAACATGTTCCGTATATACAGTGATTATTGC
TGAAAATTTTCAACAAATTATTCAACATTACACTGAATGGAATGTCGATGTTCGTGTTTA
TATTGCAATTTTATTAATCCCATTGATTTTATTGTCATGGGTACCAAATCTCAAGTATCT
TGCACCATTCTCTTCTGTGGCTAACATATTCATGGGAATTGGATTATTGATAACATTTTA
CTATTGCGTAACAGATATGCCAAACATTAGTGAACGTGAAATGCATACATCATTATTGCA
AATCCCGCCATTCTTTGGAATAACTATATTTAAATTAAGGCAATAGGAGTTGTAATGCCG
CTTGAAAATTCTATGAAAACACCTAAGCACTTCATTGGAATCTGTGGTGTATTAAATCAA
GGTATGAGCGGTGTAACTTTGGTTTATATTCTACTCGGTTTCGTTGGTTATGTAAAATAT
GGAAATGAAGCAAAAGGATCAATAACATTGAATTTACCTATAGAGGATTTAGCAGCACAA
ACTGTGAAAATTTTAATTGCATTAGCTGTTTATTGTACATTTGGTCTTCAATTTTATGTC
TGCCTTGAAATTGGATGGGATTTTATTAAAGATAAATTTAGAAAACGTCCTTTGCTAGTT
AACTACATGATGAGAACAGTTCTTGTTACTGCCGCTGTCTTACTTGCTGTCGCTGTGCCT
ACAATTGGACCTTTTGTTGGCTTACTCGGTGCCTTCTGTTTCTCAATTCTGGGATTACTC
GTGCCTGTACTTATTGAAATGATTACATACTGGGATGAAGGATTTGGAAAATTGAACTGG
ATAATTTGGAAAAATGTAATTGTTTGCATTTTTGGAATTCTTGCTCTTGTTTTTGGTTCA
AAGGATGCAATAGCTGATATTATGAAAATGTATAATGAAAACCCAAGTGCTGATAATGCA
ACAACAATATTAGCTATCACAAATATGAATGAAATAGTAGAAGAACTCACCACACTATTA
CCAACTACTACAGGTGTTTGAAAAAAAGCAAGTCATAAACTCCGGCATCATTTAACGTAT
TTGAATTTTTTTCTCAATATAAATTTTCATCATATGCAGCGAATATTCTTTAAATAACAT
ATTGTAGTTAAAATTAAGATGCTGCCTAGATAGGTAGATATAGGCTTTAGTTATTTTAAA
AAACTGCTTTTACAACTATAAAATGTTCAGGTTCAGCACAGAAAGTGTTAGGTTTTTGTG
ATTTTCTAAGCTGATCAAAAACAAAAGTAAAAATGAATTAAAAGACTTGTTAAATTTTAT
ATTTTTCTTCTTATTTTAGTAAAATTAAAGTAGTTTATCAGTTTATTATTATATCAATAA
ATCACTTGATTTCGAAATCCCATTAAAATTTTTTGATATAACTTTTAAAACTATCGGTTC
TAACATTTGAAAGAATAAAACAAAACTTTATAGAAATGAATTAAGAACTGTATTTTTGTG
AAATTTCAGATTCGATTTAAAACATCAAATTATCATAGTAGATTTTTTTTATACTTGATA
AATCTGTCTCTATAGTTAATACTATGGAATGAACAATTTTTTTATATATTTAATTCATTT

>g3681.t5 Gene=g3681 Length=228
MPLENSMKTPKHFIGICGVLNQGMSGVTLVYILLGFVGYVKYGNEAKGSITLNLPIEDLA
AQTVKILIALAVYCTFGLQFYVCLEIGWDFIKDKFRKRPLLVNYMMRTVLVTAAVLLAVA
VPTIGPFVGLLGAFCFSILGLLVPVLIEMITYWDEGFGKLNWIIWKNVIVCIFGILALVF
GSKDAIADIMKMYNENPSADNATTILAITNMNEIVEELTTLLPTTTGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t5 PANTHER PTHR22950 AMINO ACID TRANSPORTER 1 193 5.8E-99
3 g3681.t5 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 1 193 5.8E-99
1 g3681.t5 Pfam PF01490 Transmembrane amino acid transporter protein 2 183 1.9E-32
8 g3681.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g3681.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 39 -
11 g3681.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 40 58 -
18 g3681.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 84 -
10 g3681.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 85 103 -
14 g3681.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 124 -
13 g3681.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 125 129 -
17 g3681.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 150 -
9 g3681.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 151 161 -
16 g3681.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 181 -
12 g3681.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 182 228 -
6 g3681.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
5 g3681.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
7 g3681.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 143 -
4 g3681.t5 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