Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative b-0,+–type amino acid transporter 1.

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 g2003 g2003.t5 TTS g2003.t5 14361323 14361323
chr_3 g2003 g2003.t5 isoform g2003.t5 14361973 14362953
chr_3 g2003 g2003.t5 exon g2003.t5.exon1 14361973 14362953
chr_3 g2003 g2003.t5 cds g2003.t5.CDS1 14362029 14362664
chr_3 g2003 g2003.t5 TSS g2003.t5 NA NA

Sequences

>g2003.t5 Gene=g2003 Length=981
TCTTTAGATTTTTTTCTTCAAAGGTTTAAAGTTTTTTATTAATTAAAAATGAATAGGAAA
CACACAACACTTGTCAAATGCTTTTGATAATCCAACACCATCTATGGGAGTAATTGCCAC
AGCATTTTATACAGGCTTATGGGCGTATGATGGTTGGAATAATTTAAATTATGTCACTGA
GGAAATACAAAATCCCAGCAAGTATGATCTATCACGTTCTTTTCATCAATTTCGTGCCTA
AAATGATTTTTCTAACTCATCTCACCCCAGAAATTTACCGAGATCAATTATGATTGCTAT
TCCATTGGTTACGCTCTGCTACGCTTTAATCAACATTTCCTATCTTGCCGCAATGTCGCC
GCAGGAGATGATCGAATCCGAAGCTGTTGCTGTCACGTTCGGAAATCGTATTTTAGGAAT
GTTTGCGTGGATAATGCCACTGAGTGTTACAATAAGCACTTTTGGCTCAGCAAATGGAAC
ATTATTTGCGGCAGGAAGACTTTGCTTTGCTGCTTCACGAGAGGGACATCTTCTTGATAT
TCTATCTTATGTTCATGTTCGTCGTTTAACTCCTGCACCAGGTCTAATTTTTCACTCTCT
TATTGCGTCTGCGATGGTGCTTCATGGCACTATTGACTCATTAATTGACTTCTTTAGCTT
TACGGCTTGGATATTTTATGGAGGTTCAATGTTTGCACTGATCGTCATGCGCTTCACAAA
ACCGAACTATCCGCGCCCTTATAAAGTGCCAATTATCATTCCTGTAATTGTTCTTGTGAT
TTCGGCTTATTTGGTCATTGGTCCGATCATCGATAAACCACAAATTGAGTATTTGTATAC
GGTTCTTTTTATTCTTCTTGGACTTGTTCTCTATTTGCCATTCGTTCGTTGGCGTATGCA
TCCTGTATTCATGAGTAAGTTTTAATTATTATCAAATCTATATTAATGTGACTAATTTAT
ATGTTTTATTCATTTATAGAT

>g2003.t5 Gene=g2003 Length=211
MIAIPLVTLCYALINISYLAAMSPQEMIESEAVAVTFGNRILGMFAWIMPLSVTISTFGS
ANGTLFAAGRLCFAASREGHLLDILSYVHVRRLTPAPGLIFHSLIASAMVLHGTIDSLID
FFSFTAWIFYGGSMFALIVMRFTKPNYPRPYKVPIIIPVIVLVISAYLVIGPIIDKPQIE
YLYTVLFILLGLVLYLPFVRWRMHPVFMSKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2003.t5 Gene3D G3DSA:1.20.1740.10 - 1 209 1.2E-29
2 g2003.t5 PANTHER PTHR11785:SF340 AROMATIC-PREFERRING AMINO ACID TRANSPORTER 1 209 1.5E-80
3 g2003.t5 PANTHER PTHR11785 AMINO ACID TRANSPORTER 1 209 1.5E-80
1 g2003.t5 Pfam PF13520 Amino acid permease 2 181 7.0E-18
16 g2003.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
17 g2003.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
18 g2003.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
24 g2003.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 21 -
14 g2003.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 44 -
21 g2003.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 73 -
10 g2003.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 92 -
20 g2003.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
13 g2003.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 116 120 -
22 g2003.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -
12 g2003.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 154 -
23 g2003.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 155 174 -
15 g2003.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 175 179 -
19 g2003.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 201 -
11 g2003.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 202 211 -
5 g2003.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 24 -
7 g2003.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
8 g2003.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -
6 g2003.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 155 174 -
4 g2003.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 181 203 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016020 membrane CC
GO:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter activity MF

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