Gene loci information

Transcript annotation

  • This transcript has been annotated as Solute carrier family 52, riboflavin transporter, member 3-A.

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_3 g4084 g4084.t9 TSS g4084.t9 30503247 30503247
chr_3 g4084 g4084.t9 isoform g4084.t9 30503669 30505824
chr_3 g4084 g4084.t9 exon g4084.t9.exon1 30503669 30503871
chr_3 g4084 g4084.t9 cds g4084.t9.CDS1 30503762 30503871
chr_3 g4084 g4084.t9 exon g4084.t9.exon2 30504330 30505285
chr_3 g4084 g4084.t9 cds g4084.t9.CDS2 30504330 30505285
chr_3 g4084 g4084.t9 exon g4084.t9.exon3 30505339 30505559
chr_3 g4084 g4084.t9 cds g4084.t9.CDS3 30505339 30505559
chr_3 g4084 g4084.t9 exon g4084.t9.exon4 30505621 30505824
chr_3 g4084 g4084.t9 cds g4084.t9.CDS4 30505621 30505824
chr_3 g4084 g4084.t9 TTS g4084.t9 30505973 30505973

Sequences

>g4084.t9 Gene=g4084 Length=1584
AGCTACTACTCATTTATTCTCTTAAGTGTTGATTACACGCAAGATAAGATTGAGCTATTT
ATCAGCTTGAGAGACATATAAACAAGAACTGAAATGGAAAGTGAACCTGATTTCGTGATA
AATGATCAAGGAGAGAATGAGAGATTTTCAGTACATAATCATCACCAATTTCAACAAGAC
GTTGCATTTTTTGATCAAAAAAGAAGATTACGCTCAGAAACCCCAAACGAAAGCAGTCAA
TTGATACGAAAACGAATGAGAATGAATTTAACGAAATTTCGGGCTGTCTTTGCTAATCGC
AGTTTTTTGGTTGATACACTGACAATTTTCTTCGGAATTGGTACATGGATTGGTGTGAAT
TCGCTCTGGATTCAATTGCCGCTGCTTGTAAATGTATTGCCTGAATCATGGTTTCTTGCA
TCTTATTTAGTAATAATTGTACAAGTAGCAAATCTTGGTCCTCTCACATACACACTTATT
CAAAAATTATGCCCGATCAGAGACAGTTTCTTTATTTATTGGCTTCTAACATTAGGAGTT
GCAGCCGCTTTTGTTATGGCATTCTTTTATGATATTACTGCATATTTTTGGGGAGCAGAA
CGATCTATTGCATTTCTTGGTCTTGTTTTTTGCTTTGCTCTTGTCGGATGCACATCTTCA
GTGTTGTTCATGCCATATTGTGGGCGATTGCGAGACATTTATTTAGTGACATATTTAATA
GGAGAAGGACTTTCTGGTTTATTGCCTGGTGTTTTAGGCTTAATTCAAGGTGTTGGAGGA
AATGCTCAATGTATTCCTAATGAAGATTTAGATGACCCAAAATATGTACAATATTTTCCA
CCACCTCGTTTCTCAACACAGACCTTCTTCATCATCATTTCCTCACTCTTTATTGCAAGC
TTAATTGCCTTCATTTTACTTGATCAATTAAAATCAGTTAAAAAAGAATATGCAAATGTG
ACAATTTCACATGGTAACAAATATGAATACAATAGGAATGCTGAAAATGAAGAACATAAA
GTGAATAATGAAACAGATAGAAAGAAGCCTGAAGAGAAAATTAAGAAGCTATCGGTTGCA
AATTATCATGGATTACTTGTGCTTCTTGGAACAATTTGTATGTTTACAAATGCAATTGTG
CCCTCTATCATGCCTTTTGGTACATTACCTTACGGAAATGTGACTTATCATCTGAGTGTG
ACTTTATCCGCAATTGCAAATCCAGTGGCATGTTTTATAGCAGTTTTTCTCACTGGTACA
TCAATTCGAAATATAATAACGCTGTCTATTACTTCTTTGCCTTTTGTGATATATTCTATG
ACTACATCTGTAATGTCACCGTCACCTCCAATGATGGACACAATTTACGGTGAATTTTTT
ATTTTAAGTTGGACACTTCTCATTGGATTTGGTTCATATATTCGTTTAAAAATTACAACA
ATCTTTCGTTATAATGATGGAAAAAGCCTTGTGTGGGTTGGTGCATGGACACAAATTGGA
AGTTTTGTGGGATCTGTTTTGTCTTTTATTGTGGTTAACTATACAGGCATCTTTCAACAA
TATAATCCATGCGAATCACTCTAA

>g4084.t9 Gene=g4084 Length=496
MESEPDFVINDQGENERFSVHNHHQFQQDVAFFDQKRRLRSETPNESSQLIRKRMRMNLT
KFRAVFANRSFLVDTLTIFFGIGTWIGVNSLWIQLPLLVNVLPESWFLASYLVIIVQVAN
LGPLTYTLIQKLCPIRDSFFIYWLLTLGVAAAFVMAFFYDITAYFWGAERSIAFLGLVFC
FALVGCTSSVLFMPYCGRLRDIYLVTYLIGEGLSGLLPGVLGLIQGVGGNAQCIPNEDLD
DPKYVQYFPPPRFSTQTFFIIISSLFIASLIAFILLDQLKSVKKEYANVTISHGNKYEYN
RNAENEEHKVNNETDRKKPEEKIKKLSVANYHGLLVLLGTICMFTNAIVPSIMPFGTLPY
GNVTYHLSVTLSAIANPVACFIAVFLTGTSIRNIITLSITSLPFVIYSMTTSVMSPSPPM
MDTIYGEFFILSWTLLIGFGSYIRLKITTIFRYNDGKSLVWVGAWTQIGSFVGSVLSFIV
VNYTGIFQQYNPCESL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4084.t9 PANTHER PTHR12929:SF10 RIBOFLAVIN TRANSPORTER RFT-2 68 493 3.2E-132
3 g4084.t9 PANTHER PTHR12929 SOLUTE CARRIER FAMILY 52 68 493 3.2E-132
1 g4084.t9 Pfam PF06237 Protein of unknown function (DUF1011) 330 426 6.4E-28
16 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 61 -
35 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 86 -
24 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 105 -
30 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 106 129 -
15 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 130 140 -
33 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 166 -
26 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 167 171 -
29 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 192 -
20 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
36 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 224 -
22 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 225 256 -
28 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 257 276 -
18 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 277 330 -
37 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 331 353 -
21 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 354 364 -
27 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 365 387 -
19 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 388 393 -
31 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 394 416 -
23 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 417 427 -
32 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 428 447 -
17 g4084.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 448 458 -
34 g4084.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 459 481 -
25 g4084.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 482 496 -
6 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 65 87 -
7 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 107 129 -
11 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -
5 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
8 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 202 224 -
13 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 254 276 -
14 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -
4 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 365 387 -
10 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 394 413 -
12 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 423 445 -
9 g4084.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 458 480 -

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:0005887 integral component of plasma membrane CC
GO:0032218 riboflavin transport BP
GO:0032217 riboflavin 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.

Raw TPM values