General information for g16613.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Folate transporter 1.
Parent gene
- The parent gene g16613 is located on chr_4: 10232479..10234633 (+ 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_4 | g16613 | g16613.t1 | TSS | g16613.t1 | 10230871 | 10230871 |
| chr_4 | g16613 | g16613.t1 | isoform | g16613.t1 | 10231068 | 10232479 |
| chr_4 | g16613 | g16613.t1 | exon | g16613.t1.exon1 | 10231068 | 10231222 |
| chr_4 | g16613 | g16613.t1 | cds | g16613.t1.CDS1 | 10231068 | 10231222 |
| chr_4 | g16613 | g16613.t1 | exon | g16613.t1.exon2 | 10231276 | 10231577 |
| chr_4 | g16613 | g16613.t1 | cds | g16613.t1.CDS2 | 10231276 | 10231577 |
| chr_4 | g16613 | g16613.t1 | exon | g16613.t1.exon3 | 10231632 | 10232243 |
| chr_4 | g16613 | g16613.t1 | cds | g16613.t1.CDS3 | 10231632 | 10232243 |
| chr_4 | g16613 | g16613.t1 | exon | g16613.t1.exon4 | 10232322 | 10232479 |
| chr_4 | g16613 | g16613.t1 | cds | g16613.t1.CDS4 | 10232322 | 10232479 |
| chr_4 | g16613 | g16613.t1 | TTS | g16613.t1 | 10232508 | 10232508 |
Sequences
>g16613.t1 Gene=g16613 Length=1227
ATGAGACCAAGTGAGCCGTTCGTCACTGAATTTCTAACAAATGGCAAATGGAAAAATATT
ACATCGGATCAAGTTAATAGAGAAATTTATCCATTTGGGACTTATTCGTATTTGATTCAA
CTTTGCATTGTTTTTCTTATTACTGATATTTTGAGATATAAGCCAATTATTATTGCATCT
TCATGTGTTGGATTGATATTATGGTCACTTTTATTGTGGACAACTGGTATGACTGGAATG
TATTTAGTACAAATATGTTATGGATTTTTCATGGCAAGCGAAGTGGCTTATTACACTTAT
ATTTATGCAAAAATAAGTAAAGAAAATTATCAAAAAGCAACTGGATATACTCGTGCATCG
CTCTTAAGTGGCAAAGCACTAGGCTGTGTTCTTGCACAAATATTTATATCCCAAAATTTA
TTAAATGAACGTGATTTAAATTATATTTCATTAGGAGCACAAGGTGTTTCATTTATTGTC
GCAATATTTTTACCATCAGTTTCGGTTAGTTTGTACATGTGGAAAATTGATAAAAATGAT
AATGATTTAGAAAATGAAAATTTTCAAAATAGTCAAAAAGAAGCTAAACCTAAACTTTCA
TTTAAAAGAGCTTCAAAATTACTTTGGATTCATTTTAAGGAATCATATTCAAATAGAACA
GTTTTAATTTGGAGTTTATGGTGGGCTGCGAACACTACTGGTTTTTATTTAATAATCAAT
TATATTCAATTATTGTGGCAGCAAGTTGATCAAGAAAAAGAAAATTATTTTAATGGATAT
GTTGAGTTTCTGATAACAACTTTTGGTTCAATTACAGCCACAATTGCTGGTTATTCTTTT
AAAAATTCTTTTGCTAAATACGATATGTATCTTCTTACTTTATGTTCACTGTTACAAGGT
GGCTTTACAATCATAGCGGCAAAAACTCAATCAATTTGGGTTTGTTATGCTATGTATATT
TTAACAGGCTCTGTCTATCATTTTATTATCACATTGGTCACTGCATTTGTCGCAAAATTT
TTATCCGATGATTCTTTTGCTTTAGTTTTTGGAATTAATACACTGATAGCTCTTGTTGCT
CAAACTATTTTCACGGTAGTTTTTGTTACTGAAACAGCAAGTTTTTCACTTGATCCACGA
CAGCAATTCATGGTTTTTGGATTTTATTTTATTGTACTTTTTGCAATTTTTTTGATTTTT
TCTGTAGTGAAATTTTTTAGAAAATAA
>g16613.t1 Gene=g16613 Length=408
MRPSEPFVTEFLTNGKWKNITSDQVNREIYPFGTYSYLIQLCIVFLITDILRYKPIIIAS
SCVGLILWSLLLWTTGMTGMYLVQICYGFFMASEVAYYTYIYAKISKENYQKATGYTRAS
LLSGKALGCVLAQIFISQNLLNERDLNYISLGAQGVSFIVAIFLPSVSVSLYMWKIDKND
NDLENENFQNSQKEAKPKLSFKRASKLLWIHFKESYSNRTVLIWSLWWAANTTGFYLIIN
YIQLLWQQVDQEKENYFNGYVEFLITTFGSITATIAGYSFKNSFAKYDMYLLTLCSLLQG
GFTIIAAKTQSIWVCYAMYILTGSVYHFIITLVTAFVAKFLSDDSFALVFGINTLIALVA
QTIFTVVFVTETASFSLDPRQQFMVFGFYFIVLFAIFLIFSVVKFFRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16613.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 33 | 403 | 2.3E-22 |
| 2 | g16613.t1 | PANTHER | PTHR10686:SF36 | AGAP006349-PA | 1 | 403 | 1.0E-136 |
| 3 | g16613.t1 | PANTHER | PTHR10686 | FOLATE TRANSPORTER | 1 | 403 | 1.0E-136 |
| 29 | g16613.t1 | PIRSF | PIRSF028739 | Folate/thiamine_transporter | 1 | 407 | 1.3E-128 |
| 1 | g16613.t1 | Pfam | PF01770 | Reduced folate carrier | 1 | 385 | 2.4E-127 |
| 17 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 28 | - |
| 26 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 48 | - |
| 10 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 49 | 54 | - |
| 25 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 75 | - |
| 13 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 76 | 80 | - |
| 19 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 103 | - |
| 8 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 104 | 114 | - |
| 24 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 136 | - |
| 14 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 137 | 147 | - |
| 18 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 148 | 174 | - |
| 7 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 175 | 220 | - |
| 23 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 239 | - |
| 15 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 240 | 258 | - |
| 21 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 259 | 278 | - |
| 6 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 279 | 289 | - |
| 28 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 290 | 310 | - |
| 12 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 311 | 315 | - |
| 22 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 316 | 338 | - |
| 9 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 339 | 344 | - |
| 20 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 345 | 370 | - |
| 16 | g16613.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 371 | 381 | - |
| 27 | g16613.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 382 | 406 | - |
| 11 | g16613.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 407 | 408 | - |
| 4 | g16613.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 37 | 400 | 1.96E-24 |
| 41 | g16613.t1 | TIGRFAM | TIGR00806 | rfc: reduced folate carrier | 1 | 403 | 4.1E-89 |
| 40 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 48 | - |
| 30 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 77 | - |
| 33 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 103 | - |
| 39 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 137 | - |
| 35 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 152 | 174 | - |
| 32 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 243 | - |
| 34 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 280 | - |
| 37 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 306 | - |
| 38 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 316 | 338 | - |
| 36 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 347 | 369 | - |
| 31 | g16613.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 406 | - |
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 transcript has been annotated with K14610 (solute carrier family 19 (thiamine transporter), member 2/3)
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.
