Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_1 g12840 g12840.t6 TTS g12840.t6 26499912 26499912
chr_1 g12840 g12840.t6 isoform g12840.t6 26500001 26501395
chr_1 g12840 g12840.t6 exon g12840.t6.exon1 26500001 26500213
chr_1 g12840 g12840.t6 cds g12840.t6.CDS1 26500001 26500213
chr_1 g12840 g12840.t6 exon g12840.t6.exon2 26500283 26500322
chr_1 g12840 g12840.t6 cds g12840.t6.CDS2 26500283 26500322
chr_1 g12840 g12840.t6 exon g12840.t6.exon3 26500382 26500525
chr_1 g12840 g12840.t6 cds g12840.t6.CDS3 26500382 26500525
chr_1 g12840 g12840.t6 exon g12840.t6.exon4 26500583 26500839
chr_1 g12840 g12840.t6 cds g12840.t6.CDS4 26500583 26500824
chr_1 g12840 g12840.t6 exon g12840.t6.exon5 26501124 26501395
chr_1 g12840 g12840.t6 TSS g12840.t6 26501969 26501969

Sequences

>g12840.t6 Gene=g12840 Length=926
ATGAAAGTTTTGAGAGGATGCTTGCTGCTTGGATGGGATTTGAGCGTGAGGATTTACATT
CTTATCATACTCATTCCAATTCTTTTTATCGGACAAATCAGAAGTTTAAAGTTCCTTGTG
CCATTCTCAGGAAGTGCAAATGTTTTCATTGTTGTTGTGTTTGCAATTGTACTTTACTAT
ATCTTCAAGGAACCACTAGATATAAGTGATAAGCCAAGTATTGTTAGTTGGACTAAATGG
CCTGTTTTCTTCAGGTAAATTTATGGCTTTAAGGTATCGGTGCAGTCATGCCTGTTGAAA
ATTCTATGGAAAAACCACAACAATTTCTTGGTTATCCGTCCGTACTTCTAATTGCTATGA
TTATCGTCACTGTTATGTATGCTGTCATCGGTTTCCTCGGCTTTGTACGATTTGGTGATG
AAATAAGAGGATCAATTACACTCAATTTACCAACAGATGAATGGCCAGCAGTCACTGGAC
AATCACTCATTGGTATTGCTATTTTACTCACATTTGGTCTTCAATTTTACATTCCAATGG
ACATTCTATTGAGAAAACTTGAAAATAGAATTGCAAAGAAAAGAAATATTTCAGAAATTG
CAATTAGAACCGGTATTATGCTTGCGATGGGAGCAGTAGCAATAGCAGTTCCTGATCTTG
AACCTGTTATCAGTCTTGTCGGTGCTGTTTTCTTCAGCAGCTTGGGTATTTTCGTTCCTG
CTTTTATCGAGATTGTATTTTTGTCTTCATATGAAGGCTACGGAGCTTTGAAATGGAAAT
TATGGAAAAACATTTTGCTCATGATTTTTTCACTTGTCGCCATGTTTGCAGGAGCATTTG
TATCGATTTTAGATATCATTGAAACGTATACTGGTGGAAGTCATGAAGAAAAGAAATTAG
CCATTCTTTCCAGCCCTCTAGATTAA

>g12840.t6 Gene=g12840 Length=212
MPVENSMEKPQQFLGYPSVLLIAMIIVTVMYAVIGFLGFVRFGDEIRGSITLNLPTDEWP
AVTGQSLIGIAILLTFGLQFYIPMDILLRKLENRIAKKRNISEIAIRTGIMLAMGAVAIA
VPDLEPVISLVGAVFFSSLGIFVPAFIEIVFLSSYEGYGALKWKLWKNILLMIFSLVAMF
AGAFVSILDIIETYTGGSHEEKKLAILSSPLD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12840.t6 PANTHER PTHR22950:SF494 GH04538P 1 195 1.3E-64
3 g12840.t6 PANTHER PTHR22950 AMINO ACID TRANSPORTER 1 195 1.3E-64
1 g12840.t6 Pfam PF01490 Transmembrane amino acid transporter protein 2 187 1.3E-32
11 g12840.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
16 g12840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
13 g12840.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 43 61 -
15 g12840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 83 -
10 g12840.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 84 103 -
19 g12840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 121 -
12 g12840.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 122 126 -
18 g12840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 127 153 -
9 g12840.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 154 164 -
17 g12840.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 165 188 -
14 g12840.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 189 212 -
5 g12840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
7 g12840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
8 g12840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 104 121 -
4 g12840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 153 -
6 g12840.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 165 187 -

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. There were no conditions that were differentially expressed