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.t9 TSS g3681.t9 27386206 27386206
chr_3 g3681 g3681.t9 isoform g3681.t9 27386221 27393319
chr_3 g3681 g3681.t9 exon g3681.t9.exon1 27386221 27386316
chr_3 g3681 g3681.t9 exon g3681.t9.exon2 27390194 27390227
chr_3 g3681 g3681.t9 cds g3681.t9.CDS1 27390219 27390227
chr_3 g3681 g3681.t9 exon g3681.t9.exon3 27390295 27390365
chr_3 g3681 g3681.t9 cds g3681.t9.CDS2 27390295 27390365
chr_3 g3681 g3681.t9 exon g3681.t9.exon4 27391844 27391988
chr_3 g3681 g3681.t9 cds g3681.t9.CDS3 27391844 27391988
chr_3 g3681 g3681.t9 exon g3681.t9.exon5 27392559 27393108
chr_3 g3681 g3681.t9 cds g3681.t9.CDS4 27392559 27393108
chr_3 g3681 g3681.t9 exon g3681.t9.exon6 27393228 27393319
chr_3 g3681 g3681.t9 cds g3681.t9.CDS5 27393228 27393250
chr_3 g3681 g3681.t9 TTS g3681.t9 NA NA

Sequences

>g3681.t9 Gene=g3681 Length=988
CGCCAACTGAAGTAGAAAGAAATTTATTCTGTTAATTATTTTCTCTCTTTATACCGTTTC
ATATCCATTTTTGTGATAAAAAATATAAAATAAAAAATTAATTTAAAAAAGCAACGCTAA
AATGGTAAATGAATATACTGGTCCCCCACCTCAAGAACTCGAAACATTTATATCAAAAGA
CCAAAAGAATGGATCTTCAACGTACAAAATTGCACCCGCAACAAATGTCGAGAAAGGAAT
TTTATCGGATTATGATCCTTTCAAAGAAAGGAAAGTAGATCATCCTACGTCAGATATGGA
TACATTGACTCATTTATTGAAAGCATCACTTGGCACTGGAATATTGGCAATGCCATTGGC
ATTTAGCTATTCTGGTTTAGTGACAGGTATTTTTGCAACTATTCTGACGGCGCTTATATG
TACTCACTGCGCCTATATCCTTGTTAAATGCAGTCATTCATTATATTACCGCACTCGAAG
GTCAACAATGAACTTTTCTGAAGTAGCAGAAGCAGCTTGTTTAAATGGACCTGCGTGGGC
ACGTCCATGGGCACAATTTCTAAAGCATTTCATCAATTATGGTCTCTTCATTACATATTT
TGGAACATGTTCCGTATATACAGTGATTATTGCTGAAAATTTTCAACAAATTATTCAACA
TTACACTGAATGGAATGTCGATGTTCGTGTTTATATTGCAATTTTATTAATCCCATTGAT
TTTATTGTCATGGGTACCAAATCTCAAGTATCTTGCACCATTCTCTTCTGTGGCTAACAT
ATTCATGGGAATTGGATTATTGATAACATTTTACTATTGCGTAACAGATATGCCAAACAT
TAGTGAACGTGAAATGCATACATCATTATTGCAAATCCCGCCATTCTTTGGAATAACTAT
ATTTAAATTAAGGCAATAGGAGTTGTAATGCCGCTTGAAAATTCTATGAAAACACCTAAG
CACTTCATTGGAATCTGTGGTGTATTAA

>g3681.t9 Gene=g3681 Length=265
MVNEYTGPPPQELETFISKDQKNGSSTYKIAPATNVEKGILSDYDPFKERKVDHPTSDMD
TLTHLLKASLGTGILAMPLAFSYSGLVTGIFATILTALICTHCAYILVKCSHSLYYRTRR
STMNFSEVAEAACLNGPAWARPWAQFLKHFINYGLFITYFGTCSVYTVIIAENFQQIIQH
YTEWNVDVRVYIAILLIPLILLSWVPNLKYLAPFSSVANIFMGIGLLITFYYCVTDMPNI
SEREMHTSLLQIPPFFGITIFKLRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3681.t9 PANTHER PTHR22950 AMINO ACID TRANSPORTER 9 263 3.7E-105
3 g3681.t9 PANTHER PTHR22950:SF154 PROTON-COUPLED AMINO ACID TRANSPORTER-LIKE PROTEIN PATHETIC 9 263 3.7E-105
1 g3681.t9 Pfam PF01490 Transmembrane amino acid transporter protein 55 261 4.3E-31
10 g3681.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 85 -
16 g3681.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -
11 g3681.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 149 -
15 g3681.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 174 -
9 g3681.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 185 -
13 g3681.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 205 -
12 g3681.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 210 -
14 g3681.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 234 -
8 g3681.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 235 265 -
5 g3681.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -
6 g3681.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 149 171 -
4 g3681.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 205 -
7 g3681.t9 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