Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t2 TSS g16613.t2 10230871 10230871
chr_4 g16613 g16613.t2 isoform g16613.t2 10231068 10232232
chr_4 g16613 g16613.t2 exon g16613.t2.exon1 10231068 10231577
chr_4 g16613 g16613.t2 cds g16613.t2.CDS1 10231349 10231577
chr_4 g16613 g16613.t2 exon g16613.t2.exon2 10231632 10232232
chr_4 g16613 g16613.t2 cds g16613.t2.CDS2 10231632 10232230
chr_4 g16613 g16613.t2 TTS g16613.t2 10232508 10232508

Sequences

>g16613.t2 Gene=g16613 Length=1111
ATGAGACCAAGTGAGCCGTTCGTCACTGAATTTCTAACAAATGGCAAATGGAAAAATATT
ACATCGGATCAAGTTAATAGAGAAATTTATCCATTTGGGACTTATTCGTATTTGATTCAA
CTTTGCATTGTTTTTCTTATTACTGATATTTTGAGGTATGCAGCATGCTTTAATAACTCT
AAAAAATCACTTAATTGATTGATTTTAGATATAAGCCAATTATTATTGCATCTTCATGTG
TTGGATTGATATTATGGTCACTTTTATTGTGGACAACTGGTATGACTGGAATGTATTTAG
TACAAATATGTTATGGATTTTTCATGGCAAGCGAAGTGGCTTATTACACTTATATTTATG
CAAAAATAAGTAAAGAAAATTATCAAAAAGCAACTGGATATACTCGTGCATCGCTCTTAA
GTGGCAAAGCACTAGGCTGTGTTCTTGCACAAATATTTATATCCCAAAATTTATTAAATG
AACGTGATTTAAATTATATTTCATTAGGAGCACAAGGTGTTTCATTTATTGTCGCAATAT
TTTTACCATCAGTTTCGGTTAGTTTGTACATGTGGAAAATTGATAAAAATGATAATGATT
TAGAAAATGAAAATTTTCAAAATAGTCAAAAAGAAGCTAAACCTAAACTTTCATTTAAAA
GAGCTTCAAAATTACTTTGGATTCATTTTAAGGAATCATATTCAAATAGAACAGTTTTAA
TTTGGAGTTTATGGTGGGCTGCGAACACTACTGGTTTTTATTTAATAATCAATTATATTC
AATTATTGTGGCAGCAAGTTGATCAAGAAAAAGAAAATTATTTTAATGGATATGTTGAGT
TTCTGATAACAACTTTTGGTTCAATTACAGCCACAATTGCTGGTTATTCTTTTAAAAATT
CTTTTGCTAAATACGATATGTATCTTCTTACTTTATGTTCACTGTTACAAGGTGGCTTTA
CAATCATAGCGGCAAAAACTCAATCAATTTGGGTTTGTTATGCTATGTATATTTTAACAG
GCTCTGTCTATCATTTTATTATCACATTGGTCACTGCATTTGTCGCAAAATTTTTATCCG
ATGATTCTTTTGCTTTAGTTTTTGGAATTAA

>g16613.t2 Gene=g16613 Length=276
MTGMYLVQICYGFFMASEVAYYTYIYAKISKENYQKATGYTRASLLSGKALGCVLAQIFI
SQNLLNERDLNYISLGAQGVSFIVAIFLPSVSVSLYMWKIDKNDNDLENENFQNSQKEAK
PKLSFKRASKLLWIHFKESYSNRTVLIWSLWWAANTTGFYLIINYIQLLWQQVDQEKENY
FNGYVEFLITTFGSITATIAGYSFKNSFAKYDMYLLTLCSLLQGGFTIIAAKTQSIWVCY
AMYILTGSVYHFIITLVTAFVAKFLSDDSFALVFGI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16613.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 1 276 2.5E-16
2 g16613.t2 PANTHER PTHR10686:SF36 AGAP006349-PA 4 276 1.4E-82
3 g16613.t2 PANTHER PTHR10686 FOLATE TRANSPORTER 4 276 1.4E-82
1 g16613.t2 Pfam PF01770 Reduced folate carrier 3 276 1.4E-79
19 g16613.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
23 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 27 -
12 g16613.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 28 38 -
24 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 39 60 -
17 g16613.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 71 -
22 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 98 -
14 g16613.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 99 144 -
26 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 163 -
18 g16613.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 164 182 -
25 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 202 -
15 g16613.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 203 213 -
20 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 214 234 -
16 g16613.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 235 239 -
21 g16613.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 240 262 -
13 g16613.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 263 276 -
10 g16613.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 3 276 6.54E-18
7 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -
6 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
8 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 76 98 -
5 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 145 167 -
9 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 182 204 -
4 g16613.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 240 262 -

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