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.t7 TTS g12840.t7 26499912 26499912
chr_1 g12840 g12840.t7 isoform g12840.t7 26500001 26501973
chr_1 g12840 g12840.t7 exon g12840.t7.exon1 26500001 26500213
chr_1 g12840 g12840.t7 cds g12840.t7.CDS1 26500001 26500213
chr_1 g12840 g12840.t7 exon g12840.t7.exon2 26500283 26500322
chr_1 g12840 g12840.t7 cds g12840.t7.CDS2 26500283 26500322
chr_1 g12840 g12840.t7 exon g12840.t7.exon3 26500382 26500525
chr_1 g12840 g12840.t7 cds g12840.t7.CDS3 26500382 26500525
chr_1 g12840 g12840.t7 exon g12840.t7.exon4 26500583 26500839
chr_1 g12840 g12840.t7 cds g12840.t7.CDS4 26500583 26500839
chr_1 g12840 g12840.t7 exon g12840.t7.exon5 26500997 26501018
chr_1 g12840 g12840.t7 cds g12840.t7.CDS5 26500997 26501018
chr_1 g12840 g12840.t7 exon g12840.t7.exon6 26501142 26501427
chr_1 g12840 g12840.t7 cds g12840.t7.CDS6 26501142 26501395
chr_1 g12840 g12840.t7 exon g12840.t7.exon7 26501814 26501973
chr_1 g12840 g12840.t7 TSS g12840.t7 26501969 26501969

Sequences

>g12840.t7 Gene=g12840 Length=1122
TGGTATGTATCAAATTGTAAATATGGAAAAGATAGAAAAATAAATTATTATAAAAATTAA
ACAAAAATAAGTAAGGCTTATTAATAAAATGGTGATTATTAAAAGATTAATAGGGCTTCG
CTATATTAGCAATTATACAAATTCATCAATAAATCGTCAGTTAAAGTGTTCATTTTCTTG
CTGTTTTTTGTTATGAAAGTTTTGAGAGGATGCTTGCTGCTTGGATGGGATTTGAGCGTG
AGGATTTACATTCTTATCATACTCATTCCAATTCTTTTTATCGGACAAATCAGAAGTTTA
AAGTTCCTTGTGCCATTCTCAGGAAGTGCAAATGTTTTCATTGTTGTTGTGTTTGCAATT
GTACTTTACTATATCTTCAAGGAACCACTAGATATAAGTGATAAGCCAAGTATTGTTAGT
TGGACTAAATGGCCTGTTTTCTTCAGCACAGTAATTTTTGCTATGGAAGGTATCGGTGCA
GTCATGCCTGTTGAAAATTCTATGGAAAAACCACAACAATTTCTTGGTTATCCGTCCGTA
CTTCTAATTGCTATGATTATCGTCACTGTTATGTATGCTGTCATCGGTTTCCTCGGCTTT
GTACGATTTGGTGATGAAATAAGAGGATCAATTACACTCAATTTACCAACAGATGAATGG
CCAGCAGTCACTGGACAATCACTCATTGGTATTGCTATTTTACTCACATTTGGTCTTCAA
TTTTACATTCCAATGGACATTCTATTGAGAAAACTTGAAAATAGAATTGCAAAGAAAAGA
AATATTTCAGAAATTGCAATTAGAACCGGTATTATGCTTGCGATGGGAGCAGTAGCAATA
GCAGTTCCTGATCTTGAACCTGTTATCAGTCTTGTCGGTGCTGTTTTCTTCAGCAGCTTG
GGTATTTTCGTTCCTGCTTTTATCGAGATTGTATTTTTGTCTTCATATGAAGGCTACGGA
GCTTTGAAATGGAAATTATGGAAAAACATTTTGCTCATGATTTTTTCACTTGTCGCCATG
TTTGCAGGAGCATTTGTATCGATTTTAGATATCATTGAAACGTATACTGGTGGAAGTCAT
GAAGAAAAGAAATTAGCCATTCTTTCCAGCCCTCTAGATTAA

>g12840.t7 Gene=g12840 Length=309
MKVLRGCLLLGWDLSVRIYILIILIPILFIGQIRSLKFLVPFSGSANVFIVVVFAIVLYY
IFKEPLDISDKPSIVSWTKWPVFFSTVIFAMEGIGAVMPVENSMEKPQQFLGYPSVLLIA
MIIVTVMYAVIGFLGFVRFGDEIRGSITLNLPTDEWPAVTGQSLIGIAILLTFGLQFYIP
MDILLRKLENRIAKKRNISEIAIRTGIMLAMGAVAIAVPDLEPVISLVGAVFFSSLGIFV
PAFIEIVFLSSYEGYGALKWKLWKNILLMIFSLVAMFAGAFVSILDIIETYTGGSHEEKK
LAILSSPLD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12840.t7 PANTHER PTHR22950:SF494 GH04538P 10 292 3.5E-100
3 g12840.t7 PANTHER PTHR22950 AMINO ACID TRANSPORTER 10 292 3.5E-100
1 g12840.t7 Pfam PF01490 Transmembrane amino acid transporter protein 13 284 1.8E-41
20 g12840.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 13 -
26 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 14 31 -
12 g12840.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 37 -
28 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 62 -
19 g12840.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 63 81 -
27 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 82 100 -
14 g12840.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 101 111 -
25 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 136 -
18 g12840.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 137 155 -
22 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 156 180 -
15 g12840.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 181 200 -
23 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 201 218 -
17 g12840.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 219 223 -
21 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 224 250 -
13 g12840.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 251 261 -
24 g12840.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 262 285 -
16 g12840.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 286 309 -
7 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 33 -
4 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 62 -
9 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 82 104 -
11 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -
8 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 158 180 -
6 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 218 -
10 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 228 250 -
5 g12840.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 262 284 -

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

Pathway

  • This transcript belongs to the following pathways

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