General information for g11715.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 g11715 is located on chr_1: 18035356..18037324 (+ 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_1 | g11715 | g11715.t1 | isoform | g11715.t1 | 18033135 | 18037324 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon1 | 18033135 | 18033417 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS1 | 18033135 | 18033417 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon2 | 18035222 | 18035356 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS2 | 18035222 | 18035356 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon3 | 18035425 | 18035563 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS3 | 18035425 | 18035563 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon4 | 18035641 | 18035652 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS4 | 18035641 | 18035652 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon5 | 18035712 | 18035758 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS5 | 18035712 | 18035758 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon6 | 18035820 | 18035966 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS6 | 18035820 | 18035966 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon7 | 18036032 | 18036064 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS7 | 18036032 | 18036064 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon8 | 18036116 | 18036531 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS8 | 18036116 | 18036531 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon9 | 18036589 | 18036785 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS9 | 18036589 | 18036785 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon10 | 18036871 | 18036991 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS10 | 18036871 | 18036991 |
| chr_1 | g11715 | g11715.t1 | exon | g11715.t1.exon11 | 18037256 | 18037324 |
| chr_1 | g11715 | g11715.t1 | cds | g11715.t1.CDS11 | 18037256 | 18037324 |
| chr_1 | g11715 | g11715.t1 | TSS | g11715.t1 | NA | NA |
| chr_1 | g11715 | g11715.t1 | TTS | g11715.t1 | NA | NA |
Sequences
>g11715.t1 Gene=g11715 Length=1599
ATGCAAACAACTGAAGAAGGCGTTCAACAGACTGAACTAAAGTCGAGTCCCAATAATCCA
TTCCGAAATCCACAAACACAACAATTACCACAACAACATTCAATTTATGCACAGCAATAT
CAGAGCGCCAGCATTGACAGCGGTAAAGGTAATAATAACGATTTTACAACATCATGGGAC
AAATTCAAAATGTGGATGATCAACTGGCGTGGTTCACGACAATTGGTGTTAGTAATCGTT
GCTATTGCTTTACTGTTGGATAATATGCTGTTAACTGTCGTTGTTCCCATCATACCCGAA
TTTCTTTATGATATAAGACATCAGGATGCTCCTCTATCTAGTTTTCAAAAAAATCCACCA
TCAATAAGCACACCCAATTATGACAATGAAGGACCAGATTTTACTACAGCTGGATATGAT
AATGTTAGTTGGTTTGCAGAACGTGAAGAACGTCATAAAGAGTTGGTTGATGAAACAGCT
GAAGTTGGTTTAATGTTTGCATCTAAAGCTTTTGTGCAGCTCATATCAAATCCTTTTGTA
GGACCATTAACTCACAAAATTGGTTACAGCATCCCAATGTTTGCAGGATTTGTCATTATG
TTTTTATCAACATTAATTTTTGCCTTTGGTAGAACTTATCCAGTTCTGTTTATAGCACGT
GCATTACAAGGTATTGGTTCGTCGTGTTCTTCAGTTTCTGGAATGGGAATGCTTGCTGAT
CGATATACTGATGATAAGGAAAGAGGAAATGCTATGGGAATAGCATTAGGTGGTTTAGCC
CTCGGTGTACTTATTGGTCCACCATTTGGAGGCTTTATGTATGAATTCGTGGGGAAAACA
GCACCTTTTTTAGTTCTTTCTATTCTTGCATTAGGTGATGGAATGCTTCAGCTATTTATG
TTGCAACCATCAGTAGCACGATCAGAAGCAGATGCGCCTTCATTAAAAGCTCTTGTTATG
GATCCATATATTTTAATAGCAGCTGGAGCAATTACATTTGCTAATATGGGTATCGCTATG
CTTGAACCTTCCCTTCCAATTTGGATGATAGATCGTATGGATGCATCAAGATGGGAGCAA
GGTGTTACATTCTTACCAGCTTCTATTAGTTACTTAATTGGAACAAATTTATTTGGACCA
CTTGGACATCGTATTGGAAGATGGCGAGCAGCATTAATTGGACTTGTTATCATAGGCACG
TGCTTAATTGCTATTCCTTCTGCAACATCAATGTATCATCTCATAATTCCAAATGCCGGT
CTTGGTTTCGCTATCGGTATGGTTGATTCATGTATGATGCCAGAACTTGGTTATCTAGTA
GATATACGTCATTCTGCTGTTTATGGAAGTGTATATGCGCTAGGTGATGTAGCATTTTGT
GTAGGATTTGCTGTAGGACCTGCTTTAAGTGGAACATTAGTAAAGAATATTGGGTTCGAA
TGGATGATGTTTGGAATTGGAGTTTTGTGTTTTGTATATGCACCATTACTGCTATTTCTA
AAAGCACCTCCAACTAAAGAAGAGAAAAAGCAATTAATTACTGGAGATCGGTCATCTGTA
CGATACGTCGCTTATCAAAATGATGACGATGAAGAGTAA
>g11715.t1 Gene=g11715 Length=532
MQTTEEGVQQTELKSSPNNPFRNPQTQQLPQQHSIYAQQYQSASIDSGKGNNNDFTTSWD
KFKMWMINWRGSRQLVLVIVAIALLLDNMLLTVVVPIIPEFLYDIRHQDAPLSSFQKNPP
SISTPNYDNEGPDFTTAGYDNVSWFAEREERHKELVDETAEVGLMFASKAFVQLISNPFV
GPLTHKIGYSIPMFAGFVIMFLSTLIFAFGRTYPVLFIARALQGIGSSCSSVSGMGMLAD
RYTDDKERGNAMGIALGGLALGVLIGPPFGGFMYEFVGKTAPFLVLSILALGDGMLQLFM
LQPSVARSEADAPSLKALVMDPYILIAAGAITFANMGIAMLEPSLPIWMIDRMDASRWEQ
GVTFLPASISYLIGTNLFGPLGHRIGRWRAALIGLVIIGTCLIAIPSATSMYHLIIPNAG
LGFAIGMVDSCMMPELGYLVDIRHSAVYGSVYALGDVAFCVGFAVGPALSGTLVKNIGFE
WMMFGIGVLCFVYAPLLLFLKAPPTKEEKKQLITGDRSSVRYVAYQNDDDEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 29 | g11715.t1 | CDD | cd17384 | MFS_SLC18A1_2_VAT1_2 | 76 | 501 | 0.0 |
| 7 | g11715.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 318 | 514 | 2.8E-24 |
| 40 | g11715.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 30 | - |
| 2 | g11715.t1 | PANTHER | PTHR23506:SF30 | SYNAPTIC VESICULAR AMINE TRANSPORTER | 64 | 118 | 3.1E-187 |
| 4 | g11715.t1 | PANTHER | PTHR23506 | - | 64 | 118 | 3.1E-187 |
| 3 | g11715.t1 | PANTHER | PTHR23506:SF30 | SYNAPTIC VESICULAR AMINE TRANSPORTER | 143 | 525 | 3.1E-187 |
| 5 | g11715.t1 | PANTHER | PTHR23506 | - | 143 | 525 | 3.1E-187 |
| 1 | g11715.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 158 | 436 | 1.5E-38 |
| 11 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 74 | - |
| 27 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 75 | 98 | - |
| 15 | g11715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 99 | 186 | - |
| 19 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 210 | - |
| 9 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 211 | 250 | - |
| 25 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 274 | - |
| 18 | g11715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 275 | 279 | - |
| 21 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 280 | 301 | - |
| 12 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 302 | 321 | - |
| 26 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 322 | 341 | - |
| 17 | g11715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 342 | 360 | - |
| 23 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 361 | 379 | - |
| 8 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 380 | 390 | - |
| 20 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 415 | - |
| 16 | g11715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 416 | 420 | - |
| 28 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 421 | 440 | - |
| 10 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 441 | 446 | - |
| 22 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 447 | 469 | - |
| 14 | g11715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 470 | 480 | - |
| 24 | g11715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 481 | 500 | - |
| 13 | g11715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 501 | 532 | - |
| 41 | g11715.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 76 | 506 | 20.502 |
| 6 | g11715.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 73 | 508 | 9.42E-66 |
| 31 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 98 | - |
| 38 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 209 | - |
| 37 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 273 | - |
| 32 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 301 | - |
| 34 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 322 | 341 | - |
| 33 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 361 | 383 | - |
| 39 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 390 | 412 | - |
| 35 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 417 | 439 | - |
| 30 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 446 | 468 | - |
| 36 | g11715.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 478 | 500 | - |
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. There were no conditions that were differentially expressed