General information for g1788.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vesicular acetylcholine transporter.
Parent gene
- The parent gene g1788 is located on chr_3: 12998617..13000338 (- 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 | g1788 | g1788.t1 | isoform | g1788.t1 | 12998617 | 13000338 |
| chr_3 | g1788 | g1788.t1 | exon | g1788.t1.exon1 | 12998617 | 13000338 |
| chr_3 | g1788 | g1788.t1 | cds | g1788.t1.CDS1 | 12998617 | 13000338 |
| chr_3 | g1788 | g1788.t1 | TSS | g1788.t1 | NA | NA |
| chr_3 | g1788 | g1788.t1 | TTS | g1788.t1 | NA | NA |
Sequences
>g1788.t1 Gene=g1788 Length=1722
ATGGCGCCACTACCGATTATCAACATGGAATATGCCGAGGCAAAAGAAGTGCTTTGGACA
AAAATTCAGGAGCCAATGATGCAACGTAAATTAATTCTTGTCATTGTATCAATAGCATTG
CTGTTAGACAATATGTTATATATGGTTATTGTTCCCATTATTCCCGATTATTTGCGTTAT
GTTGGTGCATGGGGTGATGAGGACCAGCAAGAATATTTCGAATCATTAAAACCACACAAT
ACGACTGGCACAACTATAAAAACTCCAAGAGATCATCATGGTCAAGATTCAGCAACTGGT
TTACTTTTTGCATCGAAAGCTATCGTACAATTAATGGTAAATCCTTTCTCAGGCGCAATT
ATCGACAGAATTGGTTATGATATTCCTATGATGATCGGACTTATTATCATGTTCTTCTCT
ACATCGCTATTTGCATGCGGTCGCAGCTACTCAGGACTCTTCTTTGCACGTGCATTGCAA
GGTGTGGGGTCAGCATTCGCTGATACATCTGGTCTTGCAATGATTGCTGATCGTTTCACA
GAAGAAGCAGAACGAACAAAAGCTCTCGGTATTGCACTTGCATTTATTAGTTTCGGTTGT
CTCGTTGCACCGCCATTTGGTGGCGCATTATATCAATTTGCCGGCAAGGAAGTTCCATTT
TTAATTTTAGCATTAATTTCACTTCTTGATGGCTTTATGCTGCTACTCGTAATGAAACCA
ATTAAGCAACAAATTCGTGAAAGTCAATCGGAAACGCGACCCGAAACAATTCCAATTTGG
CAACTCATGATGGATCCATACATTGCAGTTTGTGCTGGTGCATTAATGATGTCAAATGTT
CCACTTGCTTTTCTTGAACCAACGATATCGCTTTGGATGGAAGACACAATGACAACTGAT
AATTGGAAAATTGGTATGATTTGGCTGCCAGCTTTCTTTCCTCATGTGTTCGGTGTAATT
ATTACTGTAAAAATGGCTCGTCGTTATCCCCATCATCAATGGAGAATGGCCGCAGTTGGT
CTTGCACTAGAAGGAGTCAGTTGTCTTTTTCTGCCATTCATAACATCTTACAAAGTACTT
ACAATTCCCATTTGTGTTATTTGCTTTGGTATTGCACTTATCGATACAGCATTACTGCCA
ACACTCGGTTATTTGGTGGATACACGTTATGTATCAGTTTATGGAAGTATTTATGCAATT
GCTGATATCTCATATTCATTAGCATATGCAGTTGGACCAATTATTGCTGGTGGAATAGTT
GAATTGATCGGTTTCGTAGCATTAAATTTGATCATTGCAATTATCTGTCTCGCATATGCA
CCAATAATGCGATACCTTAGAAATGTTTATGACTTTAAGCCTTTCGAAAGTGAAGCAAAT
ATTCTAATGAGTGATCCACCTGCAAAAGAATATCAAACTTATACAATGCAAAATCAGCAA
CCAGCTGGTGATTATAAGAATCATTTAGAATATGGAAAATATCAAGATGAAAGTGGTGGT
GTACAAGAGACAAACATCGATCAACAATATGATTATTCACAGCAGCAGTATCAGCAGCAG
GATTATAATTATCAACAGCAAGGATATCAGGATCAAGGAGGAGCTTATAATCAGCGAAAT
CTTCCACAACAGCCTGTCGCAAATCCATTTAGACAGCAGCAGCCACAACAACAACAAGGT
CAACCACCAGTCGCTAATCCTTTCCGATCTGGCTTCAATTAA
>g1788.t1 Gene=g1788 Length=573
MAPLPIINMEYAEAKEVLWTKIQEPMMQRKLILVIVSIALLLDNMLYMVIVPIIPDYLRY
VGAWGDEDQQEYFESLKPHNTTGTTIKTPRDHHGQDSATGLLFASKAIVQLMVNPFSGAI
IDRIGYDIPMMIGLIIMFFSTSLFACGRSYSGLFFARALQGVGSAFADTSGLAMIADRFT
EEAERTKALGIALAFISFGCLVAPPFGGALYQFAGKEVPFLILALISLLDGFMLLLVMKP
IKQQIRESQSETRPETIPIWQLMMDPYIAVCAGALMMSNVPLAFLEPTISLWMEDTMTTD
NWKIGMIWLPAFFPHVFGVIITVKMARRYPHHQWRMAAVGLALEGVSCLFLPFITSYKVL
TIPICVICFGIALIDTALLPTLGYLVDTRYVSVYGSIYAIADISYSLAYAVGPIIAGGIV
ELIGFVALNLIIAIICLAYAPIMRYLRNVYDFKPFESEANILMSDPPAKEYQTYTMQNQQ
PAGDYKNHLEYGKYQDESGGVQETNIDQQYDYSQQQYQQQDYNYQQQGYQDQGGAYNQRN
LPQQPVANPFRQQQPQQQQGQPPVANPFRSGFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g1788.t1 | CDD | cd17383 | MFS_SLC18A3_VAChT | 33 | 447 | 0.0 |
| 37 | g1788.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 548 | 573 | - |
| 38 | g1788.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 548 | 566 | - |
| 2 | g1788.t1 | PANTHER | PTHR23506 | - | 4 | 483 | 7.6E-250 |
| 3 | g1788.t1 | PANTHER | PTHR23506:SF13 | VESICULAR ACETYLCHOLINE TRANSPORTER | 4 | 483 | 7.6E-250 |
| 1 | g1788.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 37 | 396 | 2.3E-35 |
| 6 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 30 | - |
| 17 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 54 | - |
| 14 | g1788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 55 | 127 | - |
| 21 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 128 | 147 | - |
| 5 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 148 | 187 | - |
| 20 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 206 | - |
| 15 | g1788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 207 | 217 | - |
| 24 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 218 | 238 | - |
| 7 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 239 | 258 | - |
| 19 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 259 | 284 | - |
| 11 | g1788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 285 | 303 | - |
| 23 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 304 | 323 | - |
| 10 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 324 | 334 | - |
| 16 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 335 | 354 | - |
| 12 | g1788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 355 | 359 | - |
| 18 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 360 | 385 | - |
| 8 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 386 | 396 | - |
| 22 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 397 | 416 | - |
| 13 | g1788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 417 | 421 | - |
| 25 | g1788.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 422 | 442 | - |
| 9 | g1788.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 443 | 573 | - |
| 39 | g1788.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 32 | 451 | 18.843 |
| 4 | g1788.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 29 | 448 | 2.22E-59 |
| 40 | g1788.t1 | TIGRFAM | TIGR00880 | 2_A_01_02: multidrug resistance protein | 100 | 239 | 6.0E-40 |
| 34 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 53 | - |
| 31 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 124 | 146 | - |
| 29 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 210 | - |
| 35 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 237 | - |
| 27 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 267 | 289 | - |
| 33 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 304 | 323 | - |
| 36 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 355 | - |
| 30 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 360 | 382 | - |
| 32 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 394 | 416 | - |
| 28 | g1788.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 420 | 442 | - |
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:0016021 | integral component of membrane | CC |
| GO:0042908 | xenobiotic transport | BP |
| GO:0042910 | xenobiotic transmembrane transporter activity | MF |
| GO:0022857 | transmembrane transporter activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14636 (MFS transporter, DHA1 family, solute carrier family 18 (vesicular acetylcholine transporter), member 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. There were no conditions that were differentially expressed