General information for g4084.t10
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.t10 | TSS | g4084.t10 | 30504329 | 30504329 |
| chr_3 | g4084 | g4084.t10 | isoform | g4084.t10 | 30504338 | 30505824 |
| chr_3 | g4084 | g4084.t10 | exon | g4084.t10.exon1 | 30504338 | 30505285 |
| chr_3 | g4084 | g4084.t10 | cds | g4084.t10.CDS1 | 30504382 | 30505285 |
| chr_3 | g4084 | g4084.t10 | exon | g4084.t10.exon2 | 30505339 | 30505562 |
| chr_3 | g4084 | g4084.t10 | cds | g4084.t10.CDS2 | 30505339 | 30505562 |
| chr_3 | g4084 | g4084.t10 | exon | g4084.t10.exon3 | 30505621 | 30505824 |
| chr_3 | g4084 | g4084.t10 | cds | g4084.t10.CDS3 | 30505621 | 30505824 |
| chr_3 | g4084 | g4084.t10 | TTS | g4084.t10 | 30505973 | 30505973 |
Sequences
>g4084.t10 Gene=g4084 Length=1376
GCTCAGAAACCCCAAACGAAAGCAGTCAATTGATACGAAAACGAATGAGAATGAATTTAA
CGAAATTTCGGGCTGTCTTTGCTAATCGCAGTTTTTTGGTTGATACACTGACAATTTTCT
TCGGAATTGGTACATGGATTGGTGTGAATTCGCTCTGGATTCAATTGCCGCTGCTTGTAA
ATGTATTGCCTGAATCATGGTTTCTTGCATCTTATTTAGTAATAATTGTACAAGTAGCAA
ATCTTGGTCCTCTCACATACACACTTATTCAAAAATTATGCCCGATCAGAGACAGTTTCT
TTATTTATTGGCTTCTAACATTAGGAGTTGCAGCCGCTTTTGTTATGGCATTCTTTTATG
ATATTACTGCATATTTTTGGGGAGCAGAACGATCTATTGCATTTCTTGGTCTTGTTTTTT
GCTTTGCTCTTGTCGGATGCACATCTTCAGTGTTGTTCATGCCATATTGTGGGCGATTGC
GAGACATTTATTTAGTGACATATTTAATAGGAGAAGGACTTTCTGGTTTATTGCCTGGTG
TTTTAGGCTTAATTCAAGGTGTTGGAGGAAATGCTCAATGTATTCCTAATGAAGATTTAG
ATGACCCAAAATATGTACAATATTTTCCACCACCTCGTTTCTCAACACAGACCTTCTTCA
TCATCATTTCCTCACTCTTTATTGCAAGCTTAATTGCCTTCATTTTACTTGATCAATTAA
AATCAGTTAAAAAAGAATATGCAAATGTGACAATTTCACATGGTAACAAATATGAATACA
ATAGGAATGCTGAAAATGAAGAACATAAAGTGAATAATGAAACAGATAGAAAGAAGCCTG
AAGAGAAAATTAAGAAGCTATCGGTTGCAAATTATCATGGATTACTTGTGCTTCTTGGAA
CAATTTGTATGTTTACAAATGCAATTGTGCCCTCTATCATGCCTTTTGGTACATTACCTT
ACGGAAATGTGACTTATCATCTGAGTGTGACTTTATCCGCAATTGCAAATCCAGTGGCAT
GTTTTATAGCAGTTTTTCTCACTGGTACATCAATTCGAAATATAATAACGCTGTCTATTA
CTTCTTTGCCTTTTGTGATATATTCTATGACTACATCTGTAATGTCACCGTCACCTCCAA
TGATGGACACAATTTACGGTGAATTTTTTGTGATTTTAAGTTGGACACTTCTCATTGGAT
TTGGTTCATATATTCGTTTAAAAATTACAACAATCTTTCGTTATAATGATGGAAAAAGCC
TTGTGTGGGTTGGTGCATGGACACAAATTGGAAGTTTTGTGGGATCTGTTTTGTCTTTTA
TTGTGGTTAACTATACAGGCATCTTTCAACAATATAATCCATGCGAATCACTCTAA
>g4084.t10 Gene=g4084 Length=443
MRMNLTKFRAVFANRSFLVDTLTIFFGIGTWIGVNSLWIQLPLLVNVLPESWFLASYLVI
IVQVANLGPLTYTLIQKLCPIRDSFFIYWLLTLGVAAAFVMAFFYDITAYFWGAERSIAF
LGLVFCFALVGCTSSVLFMPYCGRLRDIYLVTYLIGEGLSGLLPGVLGLIQGVGGNAQCI
PNEDLDDPKYVQYFPPPRFSTQTFFIIISSLFIASLIAFILLDQLKSVKKEYANVTISHG
NKYEYNRNAENEEHKVNNETDRKKPEEKIKKLSVANYHGLLVLLGTICMFTNAIVPSIMP
FGTLPYGNVTYHLSVTLSAIANPVACFIAVFLTGTSIRNIITLSITSLPFVIYSMTTSVM
SPSPPMMDTIYGEFFVILSWTLLIGFGSYIRLKITTIFRYNDGKSLVWVGAWTQIGSFVG
SVLSFIVVNYTGIFQQYNPCESL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4084.t10 | PANTHER | PTHR12929:SF10 | RIBOFLAVIN TRANSPORTER RFT-2 | 14 | 440 | 2.4E-134 |
| 3 | g4084.t10 | PANTHER | PTHR12929 | SOLUTE CARRIER FAMILY 52 | 14 | 440 | 2.4E-134 |
| 1 | g4084.t10 | Pfam | PF06237 | Protein of unknown function (DUF1011) | 276 | 372 | 5.3E-28 |
| 15 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 31 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 26 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 35 | 53 | - |
| 32 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 75 | - |
| 19 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 76 | 86 | - |
| 34 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 112 | - |
| 25 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 113 | 117 | - |
| 28 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 118 | 138 | - |
| 18 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 139 | 149 | - |
| 37 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 150 | 170 | - |
| 22 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 171 | 202 | - |
| 29 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 222 | - |
| 20 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 223 | 276 | - |
| 36 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 277 | 299 | - |
| 24 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 300 | 310 | - |
| 27 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 311 | 333 | - |
| 17 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 334 | 339 | - |
| 35 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 362 | - |
| 23 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 363 | 373 | - |
| 30 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 374 | 394 | - |
| 16 | g4084.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 395 | 405 | - |
| 33 | g4084.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 428 | - |
| 21 | g4084.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 429 | 443 | - |
| 10 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 6 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 75 | - |
| 4 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 109 | - |
| 12 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 119 | 141 | - |
| 14 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 148 | 170 | - |
| 13 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 222 | - |
| 9 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 294 | - |
| 11 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 309 | 331 | - |
| 5 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 360 | - |
| 8 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 370 | 392 | - |
| 7 | g4084.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 405 | 427 | - |
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.
