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.t28 isoform g3681.t28 27388722 27393342
chr_3 g3681 g3681.t28 exon g3681.t28.exon1 27388722 27388931
chr_3 g3681 g3681.t28 exon g3681.t28.exon2 27390194 27390227
chr_3 g3681 g3681.t28 cds g3681.t28.CDS1 27390219 27390227
chr_3 g3681 g3681.t28 exon g3681.t28.exon3 27390295 27390365
chr_3 g3681 g3681.t28 cds g3681.t28.CDS2 27390295 27390365
chr_3 g3681 g3681.t28 exon g3681.t28.exon4 27391844 27391988
chr_3 g3681 g3681.t28 cds g3681.t28.CDS3 27391844 27391988
chr_3 g3681 g3681.t28 exon g3681.t28.exon5 27392559 27393108
chr_3 g3681 g3681.t28 cds g3681.t28.CDS4 27392559 27393108
chr_3 g3681 g3681.t28 exon g3681.t28.exon6 27393228 27393342
chr_3 g3681 g3681.t28 cds g3681.t28.CDS5 27393228 27393250
chr_3 g3681 g3681.t28 TSS g3681.t28 NA NA
chr_3 g3681 g3681.t28 TTS g3681.t28 NA NA

Sequences

>g3681.t28 Gene=g3681 Length=1125
ATTAAAATAAACAGAGATTTTTTTTTCATTCTCATCGCGACTCATTGCTTTTTTTATCTT
ATTGTTCACTAGTTCTCCACTACTGTAAATTGTCAATGCGTAAAACAAAAAGATATAACA
AATTAAAACATCACGCTGTCTATGGGTGTATAGTTTTTTTTCTTTAGTTTTCAAGTTGCG
CTCTTAGACTAGAGACGAAAATTAAGCAAGATTAATTTAAAAAAGCAACGCTAAAATGGT
AAATGAATATACTGGTCCCCCACCTCAAGAACTCGAAACATTTATATCAAAAGACCAAAA
GAATGGATCTTCAACGTACAAAATTGCACCCGCAACAAATGTCGAGAAAGGAATTTTATC
GGATTATGATCCTTTCAAAGAAAGGAAAGTAGATCATCCTACGTCAGATATGGATACATT
GACTCATTTATTGAAAGCATCACTTGGCACTGGAATATTGGCAATGCCATTGGCATTTAG
CTATTCTGGTTTAGTGACAGGTATTTTTGCAACTATTCTGACGGCGCTTATATGTACTCA
CTGCGCCTATATCCTTGTTAAATGCAGTCATTCATTATATTACCGCACTCGAAGGTCAAC
AATGAACTTTTCTGAAGTAGCAGAAGCAGCTTGTTTAAATGGACCTGCGTGGGCACGTCC
ATGGGCACAATTTCTAAAGCATTTCATCAATTATGGTCTCTTCATTACATATTTTGGAAC
ATGTTCCGTATATACAGTGATTATTGCTGAAAATTTTCAACAAATTATTCAACATTACAC
TGAATGGAATGTCGATGTTCGTGTTTATATTGCAATTTTATTAATCCCATTGATTTTATT
GTCATGGGTACCAAATCTCAAGTATCTTGCACCATTCTCTTCTGTGGCTAACATATTCAT
GGGAATTGGATTATTGATAACATTTTACTATTGCGTAACAGATATGCCAAACATTAGTGA
ACGTGAAATGCATACATCATTATTGCAAATCCCGCCATTCTTTGGAATAACTATATTTAA
ATTAAGGCAATAGGAGTTGTAATGCCGCTTGAAAATTCTATGAAAACACCTAAGCACTTC
ATTGGAATCTGTGGTGTATTAAATCAAGGTGATTGTTAATAAAAT

>g3681.t28 Gene=g3681 Length=265
MVNEYTGPPPQELETFISKDQKNGSSTYKIAPATNVEKGILSDYDPFKERKVDHPTSDMD
TLTHLLKASLGTGILAMPLAFSYSGLVTGIFATILTALICTHCAYILVKCSHSLYYRTRR
STMNFSEVAEAACLNGPAWARPWAQFLKHFINYGLFITYFGTCSVYTVIIAENFQQIIQH
YTEWNVDVRVYIAILLIPLILLSWVPNLKYLAPFSSVANIFMGIGLLITFYYCVTDMPNI
SEREMHTSLLQIPPFFGITIFKLRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t28 PANTHER PTHR22950 AMINO ACID TRANSPORTER 9 263 3.7E-105
3 g3681.t28 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 9 263 3.7E-105
1 g3681.t28 Pfam PF01490 Transmembrane amino acid transporter protein 55 261 4.3E-31
10 g3681.t28 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 85 -
16 g3681.t28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -
11 g3681.t28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 149 -
15 g3681.t28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 174 -
9 g3681.t28 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 185 -
13 g3681.t28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 205 -
12 g3681.t28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 210 -
14 g3681.t28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 234 -
8 g3681.t28 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 235 265 -
5 g3681.t28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -
6 g3681.t28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 149 171 -
4 g3681.t28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 205 -
7 g3681.t28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 210 232 -

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