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 g12621 g12621.t4 TSS g12621.t4 24819506 24819506
chr_1 g12621 g12621.t4 isoform g12621.t4 24819843 24822635
chr_1 g12621 g12621.t4 exon g12621.t4.exon1 24819843 24820201
chr_1 g12621 g12621.t4 cds g12621.t4.CDS1 24820199 24820201
chr_1 g12621 g12621.t4 exon g12621.t4.exon2 24821116 24821868
chr_1 g12621 g12621.t4 cds g12621.t4.CDS2 24821116 24821868
chr_1 g12621 g12621.t4 exon g12621.t4.exon3 24821926 24822635
chr_1 g12621 g12621.t4 cds g12621.t4.CDS3 24821926 24822183
chr_1 g12621 g12621.t4 TTS g12621.t4 24822639 24822639

Sequences

>g12621.t4 Gene=g12621 Length=1822
ATGTGGAGTGAAGTTCTACTTGCGATTTTCGGTAATAAATGAATAAATAAATAAAAATTT
AAAAGGCTAAAAAGTTTAATTTTTCTAAAGCAAATGTTGGGTCATTTTATTTTGGTGTCA
CAATTGCTTGGTCATCGCCAGCTGGTCCACAAGTTATTGAGAATGAAAATTATCCATTTT
GGGTGACAAAAAATCAATTTGGACTTATTGTTGCTTGCATTTCACTTGGCGGTATTACTT
CATGTATTCCATCGGGAATTATTAGGCATAAAATTGGAACAAAAAAGACAATTTTTTATT
TTTCATTTCCTGGTGTGATTGGATCAATTTTAATTACATTGGCAGATAATTTAGCTATGC
TACTAATAGGCAGATACTTAATTGGAATTTCACTCGGTTGTTTTATGTTTCTTGTGCAAA
TTTACGTAGGTGAAATCAGTAGCGATAAGAATCGTGGAAGTTTGTTGAACTTTATTCACA
TTCTGGTGCATTTAGGTGTACTTTTTGTCTATGTACTTGGACAAATTGTGAGTTTGAAAA
TGTTAAATATTATTTGTGGTGCTATTCCATTATTTTATGGTATTGGATTTTTACTTATGC
CAGAAACAAAGCCATATTTGATAAGTAAAGGAAAATACCAAAATGACATCAATGCAAATA
CAGCAGAACTCAGTAAATTGAAGCAGAATAATGATAAACCTGAAGTGAAAAAGAAAACAA
TTGTAGAATTGCTCCAAATGAGAGCGACGAGAAGAGCAATGATCATAATGGTTTTTCAGT
TCTTTTTCTTTCAAATGTCTGGCGCTGTTGCTGTCAATTTCTATGCAAAATTAATATTTA
TTGAAGCAAGTGTGAACATCAATCCAGGTTTAGCTTCAATCATCAATGTTTGTGTACTCT
GTTTGAGTGCCACAGTGTCTGTATTTTATGTACGAAAATTTGGACGCCGTATGATGCTTT
TTACATTCAATTCATTGAGTGTTGTGAGTTTGATTGGTCTTGGCATTTTTTTCTCACTAA
AAGACATGGGATATTCTATTGATAATATTAAATGGCTGCCGCTGGTGTCACTTTGTTTGA
ATTCTATTGCATTCTGTTTGGGAATCGCTCCAGTAACTTATGGACTTCTTGGTGAACTTT
TTACAATTGAAGCTAAGAAAATTCTTGCACCAATGGCACAAATTTTTAATCAGATAATGA
CATTTACTATTGGAATTTCTTTTCCATTTTTATCATCTGTGATTGGCACTGGTAGTGTAT
TCTTAATTTTTGCAATAACAACTTTTATTGATATTATATTTGGCTACTATTTTATTCCTG
AAACCAAAGGAAAATCTTTTGATGAGATTCAAGAAGCTTTATCAAAATAAGTAAAAGAAT
TTTAGCAAGGGAAAAATCACTTGGGCGATGACCTACATTTTTCTTGTCGCGCAACTTAAG
GCAACAAAAAACAAATGTCGCATGAAACAAAAAATGTTGCATGATTTTTGAATTTTATAA
AATTTTCTTTTATTCACATTTTGTTTAATAACAGTTTGATAAAGAATTAAATTTCAAATA
TTTTAATATAAATTTCAATACAATTGATCAAATATTTAACTTAGAAAATTTAATTATTTC
TAATTTTGTAAATGTTTTGTTTACAATTCACGTCATTGTTTACATTTTTTTATACATAAA
ATGTAAACAACGGGCAACAACGGGCAACAATGGCCAACAAAATGAACTTTCGCTGCTCCA
GTGATTTTCTCCTTGAATTTTAGTGTGAAAGTTCTTGTAAATAATTATTTATTAACTTAT
AAATCTAAGTAAAGAAAATTTT

>g12621.t4 Gene=g12621 Length=337
MLLIGRYLIGISLGCFMFLVQIYVGEISSDKNRGSLLNFIHILVHLGVLFVYVLGQIVSL
KMLNIICGAIPLFYGIGFLLMPETKPYLISKGKYQNDINANTAELSKLKQNNDKPEVKKK
TIVELLQMRATRRAMIIMVFQFFFFQMSGAVAVNFYAKLIFIEASVNINPGLASIINVCV
LCLSATVSVFYVRKFGRRMMLFTFNSLSVVSLIGLGIFFSLKDMGYSIDNIKWLPLVSLC
LNSIAFCLGIAPVTYGLLGELFTIEAKKILAPMAQIFNQIMTFTIGISFPFLSSVIGTGS
VFLIFAITTFIDIIFGYYFIPETKGKSFDEIQEALSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12621.t4 Coils Coil Coil 91 111 -
5 g12621.t4 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 1 337 4.5E-65
2 g12621.t4 PANTHER PTHR48021:SF63 GH07001P-RELATED 1 334 6.2E-70
3 g12621.t4 PANTHER PTHR48021 - 1 334 6.2E-70
1 g12621.t4 Pfam PF00083 Sugar (and other) transporter 1 334 2.7E-43
15 g12621.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
25 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
11 g12621.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 35 -
20 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 36 57 -
14 g12621.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 58 62 -
18 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 81 -
7 g12621.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 82 133 -
24 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 157 -
16 g12621.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 158 171 -
17 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 192 -
10 g12621.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 198 -
23 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 199 221 -
13 g12621.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 222 232 -
19 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 233 258 -
9 g12621.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 259 269 -
22 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 270 289 -
12 g12621.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 290 294 -
21 g12621.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 295 320 -
8 g12621.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 321 337 -
35 g12621.t4 ProSitePatterns PS00217 Sugar transport proteins signature 2. 8 33 -
36 g12621.t4 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 1 324 17.588
4 g12621.t4 SUPERFAMILY SSF103473 MFS general substrate transporter 1 333 3.66E-32
31 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 24 -
32 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 58 -
27 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 82 -
33 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 157 -
34 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 192 -
28 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 202 221 -
29 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 233 255 -
30 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 270 292 -
26 g12621.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 299 321 -

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.

Raw TPM values