General information for g4084.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Solute carrier family 52, riboflavin transporter, member 3-A.
Parent gene
- The parent gene g4084 is located on chr_3: 30504848..30505984 (+ strand)
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.t1 | TSS | g4084.t1 | 30503247 | 30503247 |
| chr_3 | g4084 | g4084.t1 | isoform | g4084.t1 | 30503762 | 30505824 |
| chr_3 | g4084 | g4084.t1 | exon | g4084.t1.exon1 | 30503762 | 30503871 |
| chr_3 | g4084 | g4084.t1 | cds | g4084.t1.CDS1 | 30503762 | 30503871 |
| chr_3 | g4084 | g4084.t1 | exon | g4084.t1.exon2 | 30504330 | 30505285 |
| chr_3 | g4084 | g4084.t1 | cds | g4084.t1.CDS2 | 30504330 | 30505285 |
| chr_3 | g4084 | g4084.t1 | exon | g4084.t1.exon3 | 30505339 | 30505562 |
| chr_3 | g4084 | g4084.t1 | cds | g4084.t1.CDS3 | 30505339 | 30505562 |
| chr_3 | g4084 | g4084.t1 | exon | g4084.t1.exon4 | 30505621 | 30505824 |
| chr_3 | g4084 | g4084.t1 | cds | g4084.t1.CDS4 | 30505621 | 30505824 |
| chr_3 | g4084 | g4084.t1 | TTS | g4084.t1 | 30505973 | 30505973 |
Sequences
>g4084.t1 Gene=g4084 Length=1494
ATGGAAAGTGAACCTGATTTCGTGATAAATGATCAAGGAGAGAATGAGAGATTTTCAGTA
CATAATCATCACCAATTTCAACAAGACGTTGCATTTTTTGATCAAAAAAGAAGATTACGC
TCAGAAACCCCAAACGAAAGCAGTCAATTGATACGAAAACGAATGAGAATGAATTTAACG
AAATTTCGGGCTGTCTTTGCTAATCGCAGTTTTTTGGTTGATACACTGACAATTTTCTTC
GGAATTGGTACATGGATTGGTGTGAATTCGCTCTGGATTCAATTGCCGCTGCTTGTAAAT
GTATTGCCTGAATCATGGTTTCTTGCATCTTATTTAGTAATAATTGTACAAGTAGCAAAT
CTTGGTCCTCTCACATACACACTTATTCAAAAATTATGCCCGATCAGAGACAGTTTCTTT
ATTTATTGGCTTCTAACATTAGGAGTTGCAGCCGCTTTTGTTATGGCATTCTTTTATGAT
ATTACTGCATATTTTTGGGGAGCAGAACGATCTATTGCATTTCTTGGTCTTGTTTTTTGC
TTTGCTCTTGTCGGATGCACATCTTCAGTGTTGTTCATGCCATATTGTGGGCGATTGCGA
GACATTTATTTAGTGACATATTTAATAGGAGAAGGACTTTCTGGTTTATTGCCTGGTGTT
TTAGGCTTAATTCAAGGTGTTGGAGGAAATGCTCAATGTATTCCTAATGAAGATTTAGAT
GACCCAAAATATGTACAATATTTTCCACCACCTCGTTTCTCAACACAGACCTTCTTCATC
ATCATTTCCTCACTCTTTATTGCAAGCTTAATTGCCTTCATTTTACTTGATCAATTAAAA
TCAGTTAAAAAAGAATATGCAAATGTGACAATTTCACATGGTAACAAATATGAATACAAT
AGGAATGCTGAAAATGAAGAACATAAAGTGAATAATGAAACAGATAGAAAGAAGCCTGAA
GAGAAAATTAAGAAGCTATCGGTTGCAAATTATCATGGATTACTTGTGCTTCTTGGAACA
ATTTGTATGTTTACAAATGCAATTGTGCCCTCTATCATGCCTTTTGGTACATTACCTTAC
GGAAATGTGACTTATCATCTGAGTGTGACTTTATCCGCAATTGCAAATCCAGTGGCATGT
TTTATAGCAGTTTTTCTCACTGGTACATCAATTCGAAATATAATAACGCTGTCTATTACT
TCTTTGCCTTTTGTGATATATTCTATGACTACATCTGTAATGTCACCGTCACCTCCAATG
ATGGACACAATTTACGGTGAATTTTTTGTGATTTTAAGTTGGACACTTCTCATTGGATTT
GGTTCATATATTCGTTTAAAAATTACAACAATCTTTCGTTATAATGATGGAAAAAGCCTT
GTGTGGGTTGGTGCATGGACACAAATTGGAAGTTTTGTGGGATCTGTTTTGTCTTTTATT
GTGGTTAACTATACAGGCATCTTTCAACAATATAATCCATGCGAATCACTCTAA
>g4084.t1 Gene=g4084 Length=497
MESEPDFVINDQGENERFSVHNHHQFQQDVAFFDQKRRLRSETPNESSQLIRKRMRMNLT
KFRAVFANRSFLVDTLTIFFGIGTWIGVNSLWIQLPLLVNVLPESWFLASYLVIIVQVAN
LGPLTYTLIQKLCPIRDSFFIYWLLTLGVAAAFVMAFFYDITAYFWGAERSIAFLGLVFC
FALVGCTSSVLFMPYCGRLRDIYLVTYLIGEGLSGLLPGVLGLIQGVGGNAQCIPNEDLD
DPKYVQYFPPPRFSTQTFFIIISSLFIASLIAFILLDQLKSVKKEYANVTISHGNKYEYN
RNAENEEHKVNNETDRKKPEEKIKKLSVANYHGLLVLLGTICMFTNAIVPSIMPFGTLPY
GNVTYHLSVTLSAIANPVACFIAVFLTGTSIRNIITLSITSLPFVIYSMTTSVMSPSPPM
MDTIYGEFFVILSWTLLIGFGSYIRLKITTIFRYNDGKSLVWVGAWTQIGSFVGSVLSFI
VVNYTGIFQQYNPCESL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4084.t1 | PANTHER | PTHR12929:SF10 | RIBOFLAVIN TRANSPORTER RFT-2 | 68 | 494 | 3.6E-134 |
| 3 | g4084.t1 | PANTHER | PTHR12929 | SOLUTE CARRIER FAMILY 52 | 68 | 494 | 3.6E-134 |
| 1 | g4084.t1 | Pfam | PF06237 | Protein of unknown function (DUF1011) | 330 | 426 | 6.4E-28 |
| 16 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 61 | - |
| 35 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 86 | - |
| 25 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 87 | 105 | - |
| 30 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 129 | - |
| 15 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 130 | 140 | - |
| 32 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 166 | - |
| 26 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 167 | 171 | - |
| 29 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 172 | 192 | - |
| 20 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 193 | 203 | - |
| 36 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 224 | - |
| 23 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 225 | 256 | - |
| 28 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 257 | 276 | - |
| 17 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 277 | 330 | - |
| 37 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 353 | - |
| 21 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 354 | 364 | - |
| 27 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 387 | - |
| 19 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 388 | 393 | - |
| 31 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 394 | 416 | - |
| 24 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 417 | 427 | - |
| 34 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 428 | 448 | - |
| 18 | g4084.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 449 | 459 | - |
| 33 | g4084.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 482 | - |
| 22 | g4084.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 483 | 497 | - |
| 5 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 87 | - |
| 8 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 107 | 129 | - |
| 11 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 163 | - |
| 4 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 195 | - |
| 10 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
| 13 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 254 | 276 | - |
| 14 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 348 | - |
| 9 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 363 | 385 | - |
| 7 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 392 | 414 | - |
| 6 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 424 | 446 | - |
| 12 | g4084.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 481 | - |
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
- This transcript has been annotated with K14620 (riboflavin transporter 2)
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.
