General information for g227.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Synaptic vesicular amine transporter.
Parent gene
- The parent gene g227 is located on chr_3: 1876965..1879049 (+ 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 | g227 | g227.t1 | TSS | g227.t1 | 1874945 | 1874945 |
| chr_3 | g227 | g227.t1 | isoform | g227.t1 | 1875228 | 1876965 |
| chr_3 | g227 | g227.t1 | exon | g227.t1.exon1 | 1875228 | 1875318 |
| chr_3 | g227 | g227.t1 | cds | g227.t1.CDS1 | 1875228 | 1875318 |
| chr_3 | g227 | g227.t1 | exon | g227.t1.exon2 | 1875379 | 1875714 |
| chr_3 | g227 | g227.t1 | cds | g227.t1.CDS2 | 1875379 | 1875714 |
| chr_3 | g227 | g227.t1 | exon | g227.t1.exon3 | 1875776 | 1876080 |
| chr_3 | g227 | g227.t1 | cds | g227.t1.CDS3 | 1875776 | 1876080 |
| chr_3 | g227 | g227.t1 | exon | g227.t1.exon4 | 1876161 | 1876823 |
| chr_3 | g227 | g227.t1 | cds | g227.t1.CDS4 | 1876161 | 1876823 |
| chr_3 | g227 | g227.t1 | exon | g227.t1.exon5 | 1876882 | 1876965 |
| chr_3 | g227 | g227.t1 | cds | g227.t1.CDS5 | 1876882 | 1876965 |
| chr_3 | g227 | g227.t1 | TTS | g227.t1 | 1877074 | 1877074 |
Sequences
>g227.t1 Gene=g227 Length=1479
ATGGAAAGTGAATTTAATAAGAATCGATTTGCAATAACGTCTATCATCTATGCAACACTT
TTATTGGATAATATTTTACTTACAGTTATCGTTCCAATTCTACCAGACTATCTAGCATCA
TTTGCAACTAAAAATGATTCAAATGGTCTCTATAAAAATTTTGATCATTACATTCCCAAT
TCTATGCTTAACAAGCATCCTCTTGCTGGTAATTCAATAAAAAATGTGACAAAAGAAATT
CAACAACAGATGCATTATGGAAATGAATTCAATGTTGAAATGGAGAATGGAAAAGTTGGA
TTTTTACTTGCAATAAAAGCTTTTGTACAATTGTTCTTTAATCCTGTTTGTGGTAATTTA
AGCAAAAAATTTGGATACAAAAATATCATTTTTTTCGGTACTATCAACTTGCTTTTAGCC
TCTCTATTTTTTGCAATGGGAACTTCTTTTCTCATGTTGCTTTTAGCACGAGCAATTGAA
GGAATTGGATCAAGTTGCATAAATGTCTGTGGAATGAGTTTAATTGCTTCACTATATCTT
GAAGATCAGAAACGTTCAAAAGTAATGGGCATCATTTTAGGAAGCATTGCACTTGGTGTT
CTCTTTGGTTATCCTCTAGGCAGTCTTCTCTATGATTTTGTCAGTGAATCAGCGCCCTTC
ATCATCATTTCTGCATTTCTCATCACTGATCTTGCTTTCCAACTAACGTTCTTTAATTTG
ATGCGAAATGAGAATGAACTCAATGATGAGGAAAATCGAATGGTGGATGGAAATTCACAA
TGGTTACAACTGCTATCAAACAAAATGATTTTCTCCATCACTCTCGCAATTTTTATGTCA
ACTGCTGCTATGGCAATTCTAGAGCCTCTTTTGCCCATTTGGCTAATTTCTCATTTAAGA
CCTAAGAAATGGCAATTAGGTACAGTCTTTATTCCCGATTCTATGGGATATTTTATTGGA
ACAAATTTCTTCGGTTCATTCTCATTCAAAGTTGGACAAATTAAAATGTCTGTTTTGGCA
CTTATGTGTGTTGGAATATCTTCTACTATAATTCCTGAAGCAAAAACCGTCTCAAGCTTG
ATCATTCCACATTTCTGTCTTGGTTTGGGCATAGGAATTTTAGATACGTCATTAGTACCA
TATCTTGCACGATTAACTGACTCAATCACACAGAAATGTGATGAATCATGCGAAGAAAAT
GATATTCCATCAAATTATGGCAGTGTCTATGCAATTCAACAAACTGCTGTGAGTTTAGCT
TATTCGATTGTACCATTCATGGCTGGTGAAATGGTTGAGAGTATGGGATTCAAAACTATT
ATGAGATTACTTGGTATTTGTAATTTCATCTATGGACCACTTTTACTATTTATCACAATC
AAACATAATCTTAATAATACGGCAGCAAAACAACCTGATTTGCTACTTAAAGAAACAAAT
CCATCAGATTATAGACGATTTTATAATTCTATCGAGTGA
>g227.t1 Gene=g227 Length=492
MESEFNKNRFAITSIIYATLLLDNILLTVIVPILPDYLASFATKNDSNGLYKNFDHYIPN
SMLNKHPLAGNSIKNVTKEIQQQMHYGNEFNVEMENGKVGFLLAIKAFVQLFFNPVCGNL
SKKFGYKNIIFFGTINLLLASLFFAMGTSFLMLLLARAIEGIGSSCINVCGMSLIASLYL
EDQKRSKVMGIILGSIALGVLFGYPLGSLLYDFVSESAPFIIISAFLITDLAFQLTFFNL
MRNENELNDEENRMVDGNSQWLQLLSNKMIFSITLAIFMSTAAMAILEPLLPIWLISHLR
PKKWQLGTVFIPDSMGYFIGTNFFGSFSFKVGQIKMSVLALMCVGISSTIIPEAKTVSSL
IIPHFCLGLGIGILDTSLVPYLARLTDSITQKCDESCEENDIPSNYGSVYAIQQTAVSLA
YSIVPFMAGEMVESMGFKTIMRLLGICNFIYGPLLLFITIKHNLNNTAAKQPDLLLKETN
PSDYRRFYNSIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 40 | g227.t1 | CDD | cd17384 | MFS_SLC18A1_2_VAT1_2 | 12 | 459 | 1.40895E-167 |
| 2 | g227.t1 | PANTHER | PTHR23506:SF4 | PORTABELLA | 5 | 491 | 2.3E-171 |
| 3 | g227.t1 | PANTHER | PTHR23506 | - | 5 | 491 | 2.3E-171 |
| 1 | g227.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 88 | 384 | 3.1E-35 |
| 19 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 35 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 24 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 35 | 98 | - |
| 34 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 99 | 117 | - |
| 22 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 118 | 128 | - |
| 36 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 129 | 156 | - |
| 26 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 157 | 161 | - |
| 39 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 181 | - |
| 21 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 182 | 187 | - |
| 30 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 206 | - |
| 25 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 207 | 217 | - |
| 32 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 218 | 240 | - |
| 18 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 241 | 260 | - |
| 33 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 286 | - |
| 28 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 287 | 305 | - |
| 29 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 306 | 324 | - |
| 17 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 325 | 335 | - |
| 38 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 354 | - |
| 23 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 355 | 359 | - |
| 31 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 360 | 382 | - |
| 20 | g227.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 383 | 439 | - |
| 37 | g227.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 440 | 460 | - |
| 27 | g227.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 461 | 492 | - |
| 16 | g227.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 12 | 463 | 13.292 |
| 15 | g227.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 11 | 461 | 1.01E-52 |
| 9 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 5 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 99 | 116 | - |
| 8 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 129 | 151 | - |
| 11 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 161 | 180 | - |
| 12 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 192 | 214 | - |
| 6 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 218 | 240 | - |
| 4 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 295 | - |
| 7 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 327 | - |
| 14 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 351 | - |
| 10 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 361 | 383 | - |
| 13 | g227.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 460 | - |
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 K08155 (MFS transporter, DHA1 family, solute carrier family 18 (vesicular amine transporter), member 1/2)
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.
