Gene loci information

Transcript annotation

  • This transcript has been annotated as Thiamine transporter 1.

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_4 g16613 g16613.t3 TSS g16613.t3 10230871 10230871
chr_4 g16613 g16613.t3 isoform g16613.t3 10231068 10232236
chr_4 g16613 g16613.t3 exon g16613.t3.exon1 10231068 10231222
chr_4 g16613 g16613.t3 cds g16613.t3.CDS1 10231068 10231222
chr_4 g16613 g16613.t3 exon g16613.t3.exon2 10231276 10231577
chr_4 g16613 g16613.t3 cds g16613.t3.CDS2 10231276 10231577
chr_4 g16613 g16613.t3 exon g16613.t3.exon3 10231632 10232236
chr_4 g16613 g16613.t3 cds g16613.t3.CDS3 10231632 10232236
chr_4 g16613 g16613.t3 TTS g16613.t3 10232508 10232508

Sequences

>g16613.t3 Gene=g16613 Length=1062
ATGAGACCAAGTGAGCCGTTCGTCACTGAATTTCTAACAAATGGCAAATGGAAAAATATT
ACATCGGATCAAGTTAATAGAGAAATTTATCCATTTGGGACTTATTCGTATTTGATTCAA
CTTTGCATTGTTTTTCTTATTACTGATATTTTGAGATATAAGCCAATTATTATTGCATCT
TCATGTGTTGGATTGATATTATGGTCACTTTTATTGTGGACAACTGGTATGACTGGAATG
TATTTAGTACAAATATGTTATGGATTTTTCATGGCAAGCGAAGTGGCTTATTACACTTAT
ATTTATGCAAAAATAAGTAAAGAAAATTATCAAAAAGCAACTGGATATACTCGTGCATCG
CTCTTAAGTGGCAAAGCACTAGGCTGTGTTCTTGCACAAATATTTATATCCCAAAATTTA
TTAAATGAACGTGATTTAAATTATATTTCATTAGGAGCACAAGGTGTTTCATTTATTGTC
GCAATATTTTTACCATCAGTTTCGGTTAGTTTGTACATGTGGAAAATTGATAAAAATGAT
AATGATTTAGAAAATGAAAATTTTCAAAATAGTCAAAAAGAAGCTAAACCTAAACTTTCA
TTTAAAAGAGCTTCAAAATTACTTTGGATTCATTTTAAGGAATCATATTCAAATAGAACA
GTTTTAATTTGGAGTTTATGGTGGGCTGCGAACACTACTGGTTTTTATTTAATAATCAAT
TATATTCAATTATTGTGGCAGCAAGTTGATCAAGAAAAAGAAAATTATTTTAATGGATAT
GTTGAGTTTCTGATAACAACTTTTGGTTCAATTACAGCCACAATTGCTGGTTATTCTTTT
AAAAATTCTTTTGCTAAATACGATATGTATCTTCTTACTTTATGTTCACTGTTACAAGGT
GGCTTTACAATCATAGCGGCAAAAACTCAATCAATTTGGGTTTGTTATGCTATGTATATT
TTAACAGGCTCTGTCTATCATTTTATTATCACATTGGTCACTGCATTTGTCGCAAAATTT
TTATCCGATGATTCTTTTGCTTTAGTTTTTGGAATTAATACA

>g16613.t3 Gene=g16613 Length=354
MRPSEPFVTEFLTNGKWKNITSDQVNREIYPFGTYSYLIQLCIVFLITDILRYKPIIIAS
SCVGLILWSLLLWTTGMTGMYLVQICYGFFMASEVAYYTYIYAKISKENYQKATGYTRAS
LLSGKALGCVLAQIFISQNLLNERDLNYISLGAQGVSFIVAIFLPSVSVSLYMWKIDKND
NDLENENFQNSQKEAKPKLSFKRASKLLWIHFKESYSNRTVLIWSLWWAANTTGFYLIIN
YIQLLWQQVDQEKENYFNGYVEFLITTFGSITATIAGYSFKNSFAKYDMYLLTLCSLLQG
GFTIIAAKTQSIWVCYAMYILTGSVYHFIITLVTAFVAKFLSDDSFALVFGINT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g16613.t3 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 33 354 7.7E-21
2 g16613.t3 PANTHER PTHR10686:SF36 AGAP006349-PA 1 354 1.1E-121
3 g16613.t3 PANTHER PTHR10686 FOLATE TRANSPORTER 1 354 1.1E-121
25 g16613.t3 PIRSF PIRSF028739 Folate/thiamine_transporter 1 354 1.4E-117
1 g16613.t3 Pfam PF01770 Reduced folate carrier 1 354 1.2E-118
15 g16613.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 28 -
23 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 29 48 -
10 g16613.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 49 54 -
22 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 75 -
12 g16613.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 76 80 -
17 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -
8 g16613.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 104 114 -
21 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 136 -
13 g16613.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 137 147 -
16 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 148 174 -
7 g16613.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 220 -
20 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 221 239 -
14 g16613.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 240 258 -
18 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 278 -
6 g16613.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 279 289 -
24 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 290 310 -
11 g16613.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 311 315 -
19 g16613.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 316 338 -
9 g16613.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 339 354 -
4 g16613.t3 SUPERFAMILY SSF103473 MFS general substrate transporter 37 353 4.58E-22
34 g16613.t3 TIGRFAM TIGR00806 rfc: reduced folate carrier 1 354 1.6E-80
33 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 48 -
26 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
28 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -
32 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 137 -
30 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 174 -
27 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 221 243 -
29 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 258 280 -
31 g16613.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 316 338 -

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:0090482 vitamin transmembrane transporter activity MF
GO:0051180 vitamin transport BP
GO:0016021 integral component of membrane CC

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