Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Proton-coupled amino acid transporter 2.

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_2 g7356 g7356.t4 TTS g7356.t4 23362322 23362322
chr_2 g7356 g7356.t4 isoform g7356.t4 23363342 23364685
chr_2 g7356 g7356.t4 exon g7356.t4.exon1 23363342 23363675
chr_2 g7356 g7356.t4 cds g7356.t4.CDS1 23363342 23363675
chr_2 g7356 g7356.t4 exon g7356.t4.exon2 23363753 23363855
chr_2 g7356 g7356.t4 cds g7356.t4.CDS2 23363753 23363855
chr_2 g7356 g7356.t4 exon g7356.t4.exon3 23363919 23364063
chr_2 g7356 g7356.t4 cds g7356.t4.CDS3 23363919 23364054
chr_2 g7356 g7356.t4 exon g7356.t4.exon4 23364605 23364685
chr_2 g7356 g7356.t4 TSS g7356.t4 23364669 23364669

Sequences

>g7356.t4 Gene=g7356 Length=663
GTGTACGTATATATCAACATCTCTTTTCTTTTATCCGTCTAACACTTTTTTGTACATTTA
CTCAATCTCGCTCAAAAGTAATCTGATGAGATGAGTAACGAACGACAACCTCTGCTTATA
AGCGACACTGAGCAGCACAGTGTATCACCACCAAGACCAGATATTCGAAATTCACCTGAA
AATATCATCGTAGACGGAAATGAAGATGACAAGAGTGTTGATGAGGACCTTTATGACCCT
TACAAAAATCGTCAACTAGAACACCCGACGAGTAATTTAGAGACGATGATTTTGTTAATA
AAAGGCAATATCGGTACTGGAATACTTGCTATGGGTGATGCATTTAAGAACTCTGGCTTG
TACGTTGGACTGTTTGGAACTTTTATTCTTGGATTCGTCTGTACACACTGCATGCATATG
CTAGTAAAATGTTCTCATGAGCTTTGCGTTAGAGTGCAAGTACCATCAATGAATTTCTCC
TCAGTCGTTTATGCGAGCTTTGAAACTGGACCTGTGGCATTGAGAAAATATTCACATCTT
GCCAAAAATTTAATTAATCTTTTTCTCATTATCACTCAAATTGGATTTTGCTGCGTATAT
TTTGTATTTGTTGCAGTAAATTTACAAGAAATTGTTGCTCATTATTGGATTAAATTGGAC
ACT

>g7356.t4 Gene=g7356 Length=191
MSNERQPLLISDTEQHSVSPPRPDIRNSPENIIVDGNEDDKSVDEDLYDPYKNRQLEHPT
SNLETMILLIKGNIGTGILAMGDAFKNSGLYVGLFGTFILGFVCTHCMHMLVKCSHELCV
RVQVPSMNFSSVVYASFETGPVALRKYSHLAKNLINLFLIITQIGFCCVYFVFVAVNLQE
IVAHYWIKLDT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7356.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 39 -
7 g7356.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
2 g7356.t4 PANTHER PTHR22950 AMINO ACID TRANSPORTER 33 184 2.4E-45
3 g7356.t4 PANTHER PTHR22950:SF460 PROTON-COUPLED AMINO ACID TRANSPORTER 4-LIKE PROTEIN 33 184 2.4E-45
1 g7356.t4 Pfam PF01490 Transmembrane amino acid transporter protein 58 184 1.3E-19
10 g7356.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 89 -
11 g7356.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
8 g7356.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 153 -
12 g7356.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 176 -
9 g7356.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 177 191 -
4 g7356.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
5 g7356.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 176 -

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