General information for g5446.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 g5446 is located on chr_2: 9633075..9651645 (- 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 | g5446 | g5446.t1 | isoform | g5446.t1 | 9633075 | 9651645 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon1 | 9633075 | 9633320 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS1 | 9633075 | 9633320 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon2 | 9633377 | 9633553 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS2 | 9633377 | 9633553 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon3 | 9634209 | 9634394 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS3 | 9634209 | 9634394 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon4 | 9634451 | 9634636 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS4 | 9634451 | 9634636 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon5 | 9634696 | 9635048 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS5 | 9634696 | 9635048 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon6 | 9635401 | 9635488 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS6 | 9635401 | 9635488 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon7 | 9635584 | 9635607 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS7 | 9635584 | 9635607 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon8 | 9635854 | 9636168 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS8 | 9635854 | 9636168 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon9 | 9637311 | 9637602 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS9 | 9637311 | 9637602 |
| chr_2 | g5446 | g5446.t1 | exon | g5446.t1.exon10 | 9651569 | 9651645 |
| chr_2 | g5446 | g5446.t1 | cds | g5446.t1.CDS10 | 9651569 | 9651645 |
| chr_2 | g5446 | g5446.t1 | TSS | g5446.t1 | 9652017 | 9652017 |
| chr_2 | g5446 | g5446.t1 | TTS | g5446.t1 | NA | NA |
Sequences
>g5446.t1 Gene=g5446 Length=1944
ATGGACGGTTTTCGTGATGGATTTCGTGAAAATTTTAAAGAAGGTCTCAAAGATAAAGTC
GGGAATGTATTTTCTGGAGTTAAACGTGAACAATTTTCGATGCCTAAACCGGGTGGCTAT
GAACAAATGGGTGGAACAGACGGTGATGGAGGTGGAGGACGAATGTATGATGACAATCTT
CCTGAATCACCTATGTCATTTGAAGAGATTGAACGTCCACCTCTACGGCATATCGACAAA
TATACAAAGGCTGAATGTCCATGTCTTTCACAACGATACACAATTGCATTAATGGCATGT
CTAGGCTTCATTATCTCATTTGGAATGCGATGTAATATGGGAATGGCAAAATTGCAGCTC
GAACATCATGAGAACAAAACAGCAAATGCATCTTCTCATCATGAAGGAGCTGTAAATGTA
ACTTCTCATAAAGTAACTGCTCTAGGTCCAAATGAAATACAATTTAAATGGAGCGTTGCT
ATGGAAAGCGCTGTCGATTCTTCCTTCTTTTGGGGCTATCTTGTGACGCAAATTCCAGGT
GGTTTTCTCGCATCAATCTATCCAGCTAATCGAATCTTTGGAACTGCCATTGCCTGTTCG
GCTTTTCTTAATCTATTTTTACCAGGAGCTTTCGAGTTTCCGGGTATCATTATTTGTATA
AGAGTACTACAAGGACTCGTTGAAGGCGTCACTTATCCAGCTTGTCATGGTATTTGGAGA
TTTTGGGCTCCACCACTTGAAAGAAGTAGATTAGCGACTATGGCATTTAGTGGATCTTAT
GCCGGAATTGTTATAGGTATGCCTCTATGTGGAATTTTAACAAGTTGGATTAGTTGGAAA
GCGGCATTCTTTTTCTATGGAGTTATGGGTGTCATCTGGTACATGTTTTGGTTATGGTTG
ACATTTGAAAAACCTCGAAATCATCCAGCAATTAGTATACAAGAATTAAAATATATTGAA
AAATCATTAGGAGAGTCAGTAAATTTACAAATGCCAACAATTGCTACAACGCCATGGCAT
GAAATTTCTCGCTCAATGCCAGTTTATGCCATTATTGTTGCCAACTTTTGTCGTTCATGG
AACTTTTATTTACTTGTACTGTATCAAAGCAAATTCTTGAGACATAGGTTTAATTATGAG
CTTGCTGAAGCTGGTATTCTTGGTGCATTGCCTCATTTGTTGATGACAATTATAGTACCA
TTAGGCGGAATGCTGGCTGATCATTTACGCAAAAATGGAATAATGACGACAACAAATGTT
CGTAAACTATTTAATTGTGGCGGATTTGGATTAGAAGGATTATTCTTCTTATTTGTAGCA
CATGCATCTACTAAAGGAGGTGCTGTAACAGCCCTGACATTAGGTGTTGCATTTAGCGGA
TTCGCCATATCAGGCTACAATGTCAATCATTTAGATATTGCACCAAGATATGCAAGTATT
TTGATGGGTATGTCAAATGGCATTGGTACTATTGCTGGTCTTCTATGCCCAATATTTATT
GACTACGTAACCAGCGATCAGAATGATAAAAGTTGCTGGACGATTGTTTTCACGATGGCA
GCATGTGTTCATTTAACGGGAATTACATTTTATGGAATATTTGCATCAGGTGAATTGCAG
CCATGGGCAGAACCAAGTATAGCAGAACAAAAAGCATGGGATCCTGTGGCTGCAGGAGCA
ATTAAAGAAACTTCCTTTAATGATCCTAATACAAATATTCAAATAAATCATACAAATGTT
TCATCTTACGGAGCGACTGAACACGTAACTGGTAATCCGTTTGCAGCAAGTGGTGGTACA
GGTTTTCCAAATCCAAATCCTAGCAATCCATTTGCTCAAAATACAATGACAGCTCAACCT
GTTCAACCATATCCTACAGACTCATATATGCATGGTAGCTCTCAAGATCGTGACTTTACT
AATCAATATTCTACCAATTACTAA
>g5446.t1 Gene=g5446 Length=647
MDGFRDGFRENFKEGLKDKVGNVFSGVKREQFSMPKPGGYEQMGGTDGDGGGGRMYDDNL
PESPMSFEEIERPPLRHIDKYTKAECPCLSQRYTIALMACLGFIISFGMRCNMGMAKLQL
EHHENKTANASSHHEGAVNVTSHKVTALGPNEIQFKWSVAMESAVDSSFFWGYLVTQIPG
GFLASIYPANRIFGTAIACSAFLNLFLPGAFEFPGIIICIRVLQGLVEGVTYPACHGIWR
FWAPPLERSRLATMAFSGSYAGIVIGMPLCGILTSWISWKAAFFFYGVMGVIWYMFWLWL
TFEKPRNHPAISIQELKYIEKSLGESVNLQMPTIATTPWHEISRSMPVYAIIVANFCRSW
NFYLLVLYQSKFLRHRFNYELAEAGILGALPHLLMTIIVPLGGMLADHLRKNGIMTTTNV
RKLFNCGGFGLEGLFFLFVAHASTKGGAVTALTLGVAFSGFAISGYNVNHLDIAPRYASI
LMGMSNGIGTIAGLLCPIFIDYVTSDQNDKSCWTIVFTMAACVHLTGITFYGIFASGELQ
PWAEPSIAEQKAWDPVAAGAIKETSFNDPNTNIQINHTNVSSYGATEHVTGNPFAASGGT
GFPNPNPSNPFAQNTMTAQPVQPYPTDSYMHGSSQDRDFTNQYSTNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g5446.t1 | CDD | cd17382 | MFS_SLC17A6_7_8_VGluT | 96 | 535 | 0.0 |
| 5 | g5446.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 334 | 540 | 4.9E-23 |
| 2 | g5446.t1 | PANTHER | PTHR11662 | SOLUTE CARRIER FAMILY 17 | 80 | 554 | 1.4E-183 |
| 3 | g5446.t1 | PANTHER | PTHR11662:SF418 | VESICULAR GLUTAMATE TRANSPORTER, ISOFORM A | 80 | 554 | 1.4E-183 |
| 1 | g5446.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 99 | 496 | 1.9E-42 |
| 15 | g5446.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 92 | - |
| 17 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 111 | - |
| 9 | g5446.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 112 | 257 | - |
| 20 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 277 | - |
| 11 | g5446.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 278 | 282 | - |
| 18 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 302 | - |
| 6 | g5446.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 303 | 347 | - |
| 24 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 348 | 369 | - |
| 14 | g5446.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 370 | 380 | - |
| 21 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 381 | 402 | - |
| 8 | g5446.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 403 | 422 | - |
| 23 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 423 | 442 | - |
| 12 | g5446.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 443 | 447 | - |
| 22 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 448 | 468 | - |
| 7 | g5446.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 469 | 479 | - |
| 16 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 480 | 500 | - |
| 13 | g5446.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 501 | 511 | - |
| 19 | g5446.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 512 | 534 | - |
| 10 | g5446.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 535 | 647 | - |
| 36 | g5446.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 94 | 539 | 11.356 |
| 4 | g5446.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 86 | 542 | 1.2E-62 |
| 31 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 110 | - |
| 26 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 189 | - |
| 32 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
| 33 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 273 | - |
| 35 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 301 | - |
| 30 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 381 | 403 | - |
| 34 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 423 | 442 | - |
| 29 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 446 | 468 | - |
| 28 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 481 | 503 | - |
| 27 | g5446.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 513 | 535 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5446/g5446.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5446.t1.fa.iupred3.txt does not exist
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 K12302 (MFS transporter, ACS family, solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6/7/8)
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.
