Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Facilitated trehalose transporter Tret1.

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 g11243 g11243.t2 isoform g11243.t2 14871414 14872970
chr_1 g11243 g11243.t2 exon g11243.t2.exon1 14871414 14871776
chr_1 g11243 g11243.t2 exon g11243.t2.exon2 14871829 14872656
chr_1 g11243 g11243.t2 cds g11243.t2.CDS1 14872066 14872656
chr_1 g11243 g11243.t2 exon g11243.t2.exon3 14872722 14872970
chr_1 g11243 g11243.t2 cds g11243.t2.CDS2 14872722 14872970
chr_1 g11243 g11243.t2 TSS g11243.t2 NA NA
chr_1 g11243 g11243.t2 TTS g11243.t2 NA NA

Sequences

>g11243.t2 Gene=g11243 Length=1440
ATGAATAATTATAAAGTTTCAGCACAAGTTTTAGTGGCATCCATTGGTAAATTTAGAAAA
AATTTGAAAAAAAAAATTATAAAAAAATTATTTACAGCGAGTATTGGAAGTCTGCTCTAT
GGTATAGGTCTAGGATGGTCTTCTCCAAGTGGAGTAAAAATTTTAAATACTGAGAAAAAT
TTTGAGATAACATCAAGTCAATTTTCATGGGTTGTCGCAATGAATTCTATTGGTGGTTGT
ATTGGTTGTTTAGTAACTGGTCTCATTCGAAGTAATTATGGAACAAAAGTTTCTATTTTT
ATATTTACTATTCCTAGCTTTAGCGGCTGGATGTTATTGGCATTTGCACAAGCCTGGTGG
ATGTTGATTATAGGTAGATTGATGATTGGAATTGCAGCAGCAGGTTACAGTTTCAATGTT
TTAATTTACATTGGATAATGTTCATCGAAAGAAATTCGTGGTGTTTTGCTAAGCTTTTAT
GAAATTACTGTAAAATCAGGAATTTTGTTCAGTTATGCAATTGGTTCATTCACTCGACAG
TCAATAACGAATGCTATTTGTGGAGGAATTGTAGTTTTATATGCAATTGCATTCTTATTC
ATGCCTGAGAGTCCATTGTATCTGATGAAACAACATAAAACTGAAGAGGCAAAAAAATCA
TTGACATACCTTCGTGGAAGAAACTACAAAATGGATGATGAGTTAACTAGACTTCATTTG
GAAATCGATGAACTCGAGCGAAACACAAAACCCTTTTGGCAAGAAATCAGAACAAAAGCA
ACTCGCAAAGCATTCGTGATTGTGATGTCAATGTTTATTTTCTTTCAATTGTGCGGAATT
AATGCTATCATCTTCTATACAACAACAATTTTAATTGAGAGTGGCATAACGATTGATCCA
TTTATAGCTACATGCATGCTCGGTGTGATTCAAGTGATTGGAGTCTTGTGTTCTACAGCT
TTGGTTGATCACTATGGAAGAAAAATTTTACTTATTGCTTCAAATATTATTATGATTTTT
GGATTGTTAGGTGTTGGTATATATTTTCATTTGAAGGAAAAAACTACTGTAACTAGCATT
ACATGGCTTCCACTGGTATTATTTTGCATTTATTTCATTGGATTCTCAATTGGAGTTGGA
AGCGTAACATATGTCTTAATGGGAGAATTAATTTCACTCAATGCAAAGAGAGTGATCGGA
CCAATGGCGCAATTTTCAAACTTTCTAATGGCATTTCTGATTGCAATATTCTTTCCTAAA
ATTGCAAATTATATTGGAATGCATTATGCTTTCTATATTTTTGCAGCATTTTGTTTTATT
GCTATTATATTTATTATAGTTATGCTACCAGAGACAAAAGGAAAATCTCTTGTTGAAATT
CAAAATTTACTAACTAATGATAGAAAATGTGACACAAACAATTTTAAAAATAGATTTTAA

>g11243.t2 Gene=g11243 Length=279
MPESPLYLMKQHKTEEAKKSLTYLRGRNYKMDDELTRLHLEIDELERNTKPFWQEIRTKA
TRKAFVIVMSMFIFFQLCGINAIIFYTTTILIESGITIDPFIATCMLGVIQVIGVLCSTA
LVDHYGRKILLIASNIIMIFGLLGVGIYFHLKEKTTVTSITWLPLVLFCIYFIGFSIGVG
SVTYVLMGELISLNAKRVIGPMAQFSNFLMAFLIAIFFPKIANYIGMHYAFYIFAAFCFI
AIIFIIVMLPETKGKSLVEIQNLLTNDRKCDTNNFKNRF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11243.t2 Coils Coil Coil 28 48 -
5 g11243.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 1 267 2.8E-68
2 g11243.t2 PANTHER PTHR48021 - 1 264 9.0E-72
3 g11243.t2 PANTHER PTHR48021:SF27 FACILITATED TREHALOSE TRANSPORTER TRET1-1-LIKE PROTEIN 1 264 9.0E-72
1 g11243.t2 Pfam PF00083 Sugar (and other) transporter 1 263 2.7E-51
9 g11243.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 63 -
16 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 64 86 -
11 g11243.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 100 -
18 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 101 122 -
8 g11243.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 123 128 -
19 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 129 150 -
12 g11243.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 151 161 -
17 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 186 -
7 g11243.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 187 197 -
15 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 198 218 -
13 g11243.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 219 229 -
14 g11243.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 230 249 -
10 g11243.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 250 279 -
26 g11243.t2 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 1 253 16.78
4 g11243.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 1 259 2.35E-30
23 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 65 87 -
20 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 100 122 -
25 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
24 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 164 186 -
22 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 198 217 -
21 g11243.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -

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:0055085 transmembrane transport BP
GO:0016021 integral component of membrane CC
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. There were no conditions that were differentially expressed