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.t9 TTS g12840.t9 26499912 26499912
chr_1 g12840 g12840.t9 isoform g12840.t9 26500001 26501973
chr_1 g12840 g12840.t9 exon g12840.t9.exon1 26500001 26500239
chr_1 g12840 g12840.t9 cds g12840.t9.CDS1 26500173 26500239
chr_1 g12840 g12840.t9 exon g12840.t9.exon2 26500382 26500525
chr_1 g12840 g12840.t9 cds g12840.t9.CDS2 26500382 26500525
chr_1 g12840 g12840.t9 exon g12840.t9.exon3 26500583 26500839
chr_1 g12840 g12840.t9 cds g12840.t9.CDS3 26500583 26500839
chr_1 g12840 g12840.t9 exon g12840.t9.exon4 26500997 26501018
chr_1 g12840 g12840.t9 cds g12840.t9.CDS4 26500997 26501018
chr_1 g12840 g12840.t9 exon g12840.t9.exon5 26501142 26501427
chr_1 g12840 g12840.t9 cds g12840.t9.CDS5 26501142 26501395
chr_1 g12840 g12840.t9 exon g12840.t9.exon6 26501814 26501973
chr_1 g12840 g12840.t9 TSS g12840.t9 26501969 26501969

Sequences

>g12840.t9 Gene=g12840 Length=1108
TGGTATGTATCAAATTGTAAATATGGAAAAGATAGAAAAATAAATTATTATAAAAATTAA
ACAAAAATAAGTAAGGCTTATTAATAAAATGGTGATTATTAAAAGATTAATAGGGCTTCG
CTATATTAGCAATTATACAAATTCATCAATAAATCGTCAGTTAAAGTGTTCATTTTCTTG
CTGTTTTTTGTTATGAAAGTTTTGAGAGGATGCTTGCTGCTTGGATGGGATTTGAGCGTG
AGGATTTACATTCTTATCATACTCATTCCAATTCTTTTTATCGGACAAATCAGAAGTTTA
AAGTTCCTTGTGCCATTCTCAGGAAGTGCAAATGTTTTCATTGTTGTTGTGTTTGCAATT
GTACTTTACTATATCTTCAAGGAACCACTAGATATAAGTGATAAGCCAAGTATTGTTAGT
TGGACTAAATGGCCTGTTTTCTTCAGCACAGTAATTTTTGCTATGGAAGGTATCGGTGCA
GTCATGCCTGTTGAAAATTCTATGGAAAAACCACAACAATTTCTTGGTTATCCGTCCGTA
CTTCTAATTGCTATGATTATCGTCACTGTTATGTATGCTGTCATCGGTTTCCTCGGCTTT
GTACGATTTGGTGATGAAATAAGAGGATCAATTACACTCAATTTACCAACAGATGAATGG
CCAGCAGTCACTGGACAATCACTCATTGGTATTGCTATTTTACTCACATTTGGTCTTCAA
TTTTACATTCCAATGGACATTCTATTGAGAAAACTTGAAAATAGAATTGCAAAGAAAAGA
AATATTTCAGAAATTGCAATTAGAACCGGTATTATGCTTGCGATGGGAGCAGTAGCAATA
GCAGTTCCTGATCTTGAACCTGTTATCAGTAATTCATATTTATCTTTCCTAAAAGGTTCC
TGCTTTTATCGAGATTGTATTTTTGTCTTCATATGAAGGCTACGGAGCTTTGAAATGGAA
ATTATGGAAAAACATTTTGCTCATGATTTTTTCACTTGTCGCCATGTTTGCAGGAGCATT
TGTATCGATTTTAGATATCATTGAAACGTATACTGGTGGAAGTCATGAAGAAAAGAAATT
AGCCATTCTTTCCAGCCCTCTAGATTAA

>g12840.t9 Gene=g12840 Length=247
MKVLRGCLLLGWDLSVRIYILIILIPILFIGQIRSLKFLVPFSGSANVFIVVVFAIVLYY
IFKEPLDISDKPSIVSWTKWPVFFSTVIFAMEGIGAVMPVENSMEKPQQFLGYPSVLLIA
MIIVTVMYAVIGFLGFVRFGDEIRGSITLNLPTDEWPAVTGQSLIGIAILLTFGLQFYIP
MDILLRKLENRIAKKRNISEIAIRTGIMLAMGAVAIAVPDLEPVISNSYLSFLKGSCFYR
DCIFVFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12840.t9 PANTHER PTHR22950:SF494 GH04538P 10 226 2.8E-77
3 g12840.t9 PANTHER PTHR22950 AMINO ACID TRANSPORTER 10 226 2.8E-77
1 g12840.t9 Pfam PF01490 Transmembrane amino acid transporter protein 13 226 1.0E-35
16 g12840.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 13 -
19 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 14 31 -
10 g12840.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 37 -
21 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 62 -
15 g12840.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 63 81 -
18 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 82 100 -
11 g12840.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 101 111 -
22 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 136 -
14 g12840.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 137 155 -
17 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 156 180 -
12 g12840.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 181 200 -
20 g12840.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 201 218 -
13 g12840.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 219 247 -
8 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 33 -
5 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 62 -
4 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 82 104 -
7 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -
9 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 158 180 -
6 g12840.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 218 -

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