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 g12354 g12354.t2 TSS g12354.t2 22809937 22809937
chr_1 g12354 g12354.t2 isoform g12354.t2 22809938 22811662
chr_1 g12354 g12354.t2 exon g12354.t2.exon1 22809938 22810051
chr_1 g12354 g12354.t2 exon g12354.t2.exon2 22810242 22810507
chr_1 g12354 g12354.t2 cds g12354.t2.CDS1 22810331 22810507
chr_1 g12354 g12354.t2 exon g12354.t2.exon3 22810573 22811400
chr_1 g12354 g12354.t2 cds g12354.t2.CDS2 22810573 22811400
chr_1 g12354 g12354.t2 exon g12354.t2.exon4 22811456 22811662
chr_1 g12354 g12354.t2 cds g12354.t2.CDS3 22811456 22811662
chr_1 g12354 g12354.t2 TTS g12354.t2 22811723 22811723

Sequences

>g12354.t2 Gene=g12354 Length=1415
CAGTATTTTTCAGTCTGTGCATCAAATTGAAAGTCATGAAAATTTCGCAAAATTTTTTTC
AAGTTTTTGCTGCATTAATTGGTAAAATTTAGTTAGATTTTCTTAAAAATTTGGCCAGCA
TTGGAAGTTTTCTCTACGGTATAGGAATTGGTTGGTCTGCAACAAGTGCAGTAAAAATCT
TGGAAATTGAAAAACCTTTTGAAATGTCACAAAATCAATTTTCATGGGCTGTAGCAGCAA
ATTTAATTGGTGGATGTTTTGGTTGCTTAATCACAGGCTTAATTCGCAATAAATTTGGAA
CAAAAATTTCAATTTATATTTTTTGTGTTCCAAGCTTTTGTGGCTGGATTTTGTTGACAT
TTTCATTTAATTGGTGGATGGTAATTTTAGGAAGATTTATAATTGGTATTGCAGCATCAT
CTTTTAATTTCAATGTTTTGGTTTACATTGGTGAATGTGCATCAAAAGAAATTCGTGGAA
TTTTATTAAGTTTCTTTGAAATGAGTTTAAAATTTGGAATTTTATTCAGTTATGTTATTG
GCTCATTTACTAAGCAACAAGTGACAAACGCTGTTTGTGCATCAATCGTAATTTTTTATG
CAATTTCTTTCTCATTTTTACCAGAAAGTCCGCTTTATTTAATGAAGCAGCACAAAGCAG
AAAAAGCCAAAAAATCCTTAATTCGTCTTCGCGGAAGTAATTTCAAAATTGACGACGAAA
TGACAAATTTAAAGGAAGAAATTGAAGAACTTGAAAGAACAAAAAAGCCATTTTGGCAAG
AACTTTCCATAAAAGCGACTCGAAAAGCTTTTTTTATTTTAATTGCAATGTTTTTCTTTT
TCCAAATGTGCGGCATAAATGCAATAGTTTACTATACAACAATAATTTTCATTGAAAGTG
GTTTGACAATTGATCCATTCATAGCGACGTGCATACTTGGCATAATTCAAGTTGTTTCAA
TTTCATGCACTTTAGCATTTGTTGATCGATGTGGAAGAAAGCCTTTGTTAATTATTTCAA
ATGCAGTTATGATTTTTGGATTGTTTGGATTTGGAATTTATTTTCATATAAAAGAGAACA
TAAATGTTAGTGGATTTGAATTGCTGCCATTGTTTATGCTTGGTATTTTTATGATTGGAT
TTTCTATTGGAGTTGGAAATGTAACTTTTGTACTTATGGGTGAAATGTTTTCGCTTAATG
CTAAAAGATTTTTTGGACCATTAACACAGTTTATGAATTATCTCACATCATTTTCTATTG
CAATTTTCTTTCCTTTAGTTGCAAATTCAATTGGAATGCATTTTGCTTTTTACTTTTTTG
GACTTTGTTGTATATTTGCAATTATTTTTATTATTTTCATTCTTCCAGAAACGAAAGGAA
AAACTCTAGTTGAAATTCAAAAATTATTATCATAA

>g12354.t2 Gene=g12354 Length=403
MSQNQFSWAVAANLIGGCFGCLITGLIRNKFGTKISIYIFCVPSFCGWILLTFSFNWWMV
ILGRFIIGIAASSFNFNVLVYIGECASKEIRGILLSFFEMSLKFGILFSYVIGSFTKQQV
TNAVCASIVIFYAISFSFLPESPLYLMKQHKAEKAKKSLIRLRGSNFKIDDEMTNLKEEI
EELERTKKPFWQELSIKATRKAFFILIAMFFFFQMCGINAIVYYTTIIFIESGLTIDPFI
ATCILGIIQVVSISCTLAFVDRCGRKPLLIISNAVMIFGLFGFGIYFHIKENINVSGFEL
LPLFMLGIFMIGFSIGVGNVTFVLMGEMFSLNAKRFFGPLTQFMNYLTSFSIAIFFPLVA
NSIGMHFAFYFFGLCCIFAIIFIIFILPETKGKTLVEIQKLLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12354.t2 Coils Coil Coil 166 186 -
5 g12354.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 1 403 6.1E-98
2 g12354.t2 PANTHER PTHR48021:SF63 GH07001P-RELATED 2 401 2.9E-98
3 g12354.t2 PANTHER PTHR48021 - 2 401 2.9E-98
1 g12354.t2 Pfam PF00083 Sugar (and other) transporter 4 401 4.9E-79
16 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
20 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
8 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 29 34 -
25 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 55 -
15 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 56 60 -
22 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 82 -
9 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 83 93 -
28 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 94 113 -
18 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 118 -
21 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 139 -
11 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 140 201 -
27 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 202 227 -
17 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 228 238 -
26 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 239 260 -
12 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 261 266 -
19 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 267 289 -
14 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 290 300 -
24 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 301 324 -
7 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 325 335 -
23 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 336 356 -
13 g12354.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 357 367 -
29 g12354.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 368 387 -
10 g12354.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 388 403 -
41 g12354.t2 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 1 391 25.266
4 g12354.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 1 397 1.83E-51
42 g12354.t2 TIGRFAM TIGR00879 SP: MFS transporter, sugar porter (SP) family 4 398 2.5E-72
40 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
39 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 34 53 -
36 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -
37 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 114 -
34 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 146 -
32 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 206 228 -
35 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 238 260 -
31 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 267 289 -
38 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 304 326 -
33 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 338 360 -
30 g12354.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 365 387 -

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:0016021 integral component of membrane CC
GO:0022857 transmembrane transporter activity MF

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. There were no conditions that were differentially expressed