General information for g6716.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vesicular glutamate transporter 1.
Parent gene
- The parent gene g6716 is located on chr_2: 18279758..18280796 (+ 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_2 | g6716 | g6716.t1 | isoform | g6716.t1 | 18279123 | 18280796 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon1 | 18279123 | 18279133 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS1 | 18279123 | 18279133 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon2 | 18279190 | 18279469 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS2 | 18279190 | 18279469 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon3 | 18279524 | 18279694 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS3 | 18279524 | 18279694 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon4 | 18279747 | 18280419 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS4 | 18279747 | 18280419 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon5 | 18280488 | 18280588 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS5 | 18280488 | 18280588 |
| chr_2 | g6716 | g6716.t1 | exon | g6716.t1.exon6 | 18280644 | 18280796 |
| chr_2 | g6716 | g6716.t1 | cds | g6716.t1.CDS6 | 18280644 | 18280796 |
| chr_2 | g6716 | g6716.t1 | TSS | g6716.t1 | NA | NA |
| chr_2 | g6716 | g6716.t1 | TTS | g6716.t1 | NA | NA |
Sequences
>g6716.t1 Gene=g6716 Length=1389
ATGAATGATAATGATGATCAAACACCTTTCTATTTAAAGAAACGATATCTTATTGTGTTT
CTTGTTTTTTTGGGATATACAAATTTATATACAATGCGAGTAAATTTAAGTGTTGCTATT
GTTGCATTAACTGAAAATCGGACAATAACAGTAAATGGCACTAAAACATATGAACAACAA
TTTTCTTGGACCTCAAAAGAAAAAGGCTTTGCACTTGGAGCATTTTTCTATGGATATATA
CTTACTCAAATTCCAGGTGGAATTTTAGCGGCAAAAATTGGTGGTCACTTGGTTTTTGGG
TTTGGCATTTTTGCAACTGCCATTATGGGTCTTTTAACACCAATATTATGTTACCAAGGT
ATAACATATTTAATAGCTGCACGAGTTTTACAAGGAATTTTTAGTGGTTTATCATTTCCT
TCTGTAAATGCAATATATGCAAAATGGAGTCCTCCTTTAGAGAGATCAAGAACAGCAAGT
TACGGCATTTCTGGAATTTATGTGGGAACTGTTATTGCAAATCTCTTATCAGGATGGCTT
GGGGACACATTTGGGTGGGAGAGTATATTTTATGTGTTTGGATTTGCTACAATTATCTGG
AATGTAGTTTGGTTTGCAGTTGTACGAGAATCTCCTGAAAAAGATCCATGGATTACAACT
AGTGAAAAACGTTTTATAAAAGAGAGTTTGAAAAATCAAAAGGGACAAAGAAATATAATT
AAACCGCCTTGGAAAGCTATATTCACTTCCGGTCCATTATATGTAATAGCTGTGGCTCAT
TTTTCATATACTTACGGTTATTATACTTTATTAACACAACTTCCTATGTATATGAGAGAT
ATACTTGGTTTAGATCTTACAAAGAGTGGTATAGTGAGTGGAGTACCTTATATTTTACAA
ACTGTTTTGATATTTATTTCTGGATACTTTGCTGATTGGCTTTTGATGAAAAAATATTTT
ACATTAACACAAGTTCGCAAATATTTCAACAATTCTGCTTTATTTTTTCAAATGGTATTT
TTGCTCATAAGTGCTTTTGTTACAAATACTACAACAATCATTGTCTGCATTTCGTTTTCC
GTCGGATTGGGAAGTTTAGCAATGTCCGGATATTTGCCAAATACAATTGATATAGCCCCT
CAGTTCGGAAGTATCCTTTTAGGAATAACTAATACATTTGCAACAGTTTCTGGCTTAATT
TCACCACCATTATCTGGATACATTGCTGTCACTCCAACTGCTGCCGAATATCAAATAATA
TTTTTCATAACATGTGGTGTATATATTTTAGGAATTATCGTTTATGGAATTTTTGCAACT
GCTGAAGTACAACCTTGGGCTGTTGTTGATGCTGAAGATAATGAAAATATGAACGAATTA
AAGAAATAA
>g6716.t1 Gene=g6716 Length=462
MNDNDDQTPFYLKKRYLIVFLVFLGYTNLYTMRVNLSVAIVALTENRTITVNGTKTYEQQ
FSWTSKEKGFALGAFFYGYILTQIPGGILAAKIGGHLVFGFGIFATAIMGLLTPILCYQG
ITYLIAARVLQGIFSGLSFPSVNAIYAKWSPPLERSRTASYGISGIYVGTVIANLLSGWL
GDTFGWESIFYVFGFATIIWNVVWFAVVRESPEKDPWITTSEKRFIKESLKNQKGQRNII
KPPWKAIFTSGPLYVIAVAHFSYTYGYYTLLTQLPMYMRDILGLDLTKSGIVSGVPYILQ
TVLIFISGYFADWLLMKKYFTLTQVRKYFNNSALFFQMVFLLISAFVTNTTTIIVCISFS
VGLGSLAMSGYLPNTIDIAPQFGSILLGITNTFATVSGLISPPLSGYIAVTPTAAEYQII
FFITCGVYILGIIVYGIFATAEVQPWAVVDAEDNENMNELKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 33 | g6716.t1 | CDD | cd17318 | MFS_SLC17 | 20 | 439 | 5.15144E-134 |
| 7 | g6716.t1 | Coils | Coil | Coil | 454 | 462 | - |
| 6 | g6716.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 11 | 219 | 3.4E-39 |
| 5 | g6716.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 241 | 444 | 1.7E-24 |
| 2 | g6716.t1 | PANTHER | PTHR11662 | SOLUTE CARRIER FAMILY 17 | 13 | 455 | 1.8E-142 |
| 3 | g6716.t1 | PANTHER | PTHR11662:SF437 | GH23975P | 13 | 455 | 1.8E-142 |
| 1 | g6716.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 36 | 402 | 1.1E-54 |
| 12 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 15 | - |
| 23 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 16 | 43 | - |
| 20 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 44 | 69 | - |
| 31 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 90 | - |
| 14 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 91 | 96 | - |
| 32 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 115 | - |
| 16 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 116 | 120 | - |
| 26 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 146 | - |
| 10 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 147 | 157 | - |
| 22 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 176 | - |
| 15 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 177 | 187 | - |
| 25 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 208 | - |
| 9 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 209 | 245 | - |
| 29 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 268 | - |
| 18 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 269 | 296 | - |
| 30 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 316 | - |
| 8 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 317 | 327 | - |
| 24 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 328 | 346 | - |
| 17 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 347 | 351 | - |
| 21 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 352 | 372 | - |
| 11 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 373 | 383 | - |
| 28 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 405 | - |
| 19 | g6716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 406 | 416 | - |
| 27 | g6716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 417 | 438 | - |
| 13 | g6716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 439 | 462 | - |
| 44 | g6716.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 17 | 443 | 22.82 |
| 4 | g6716.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 4 | 440 | 2.62E-73 |
| 36 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 37 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 91 | - |
| 39 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 118 | - |
| 38 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 159 | 181 | - |
| 41 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 208 | - |
| 42 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 269 | - |
| 35 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 289 | 311 | - |
| 40 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 332 | 363 | - |
| 43 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 378 | 400 | - |
| 34 | g6716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 419 | 441 | - |
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:0055085 | transmembrane transport | BP |
| GO:0022857 | transmembrane transporter activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08193 (MFS transporter, ACS family, solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), other)
Pathway
This gene does not belong to any 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. There were no conditions that were differentially expressed