Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Synaptic vesicular amine transporter.

Parent gene

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.t2 isoform g11715.t2 18035356 18037324
chr_1 g11715 g11715.t2 exon g11715.t2.exon1 18035356 18035563
chr_1 g11715 g11715.t2 exon g11715.t2.exon2 18035702 18035758
chr_1 g11715 g11715.t2 exon g11715.t2.exon3 18035820 18035966
chr_1 g11715 g11715.t2 exon g11715.t2.exon4 18036090 18036518
chr_1 g11715 g11715.t2 cds g11715.t2.CDS1 18036136 18036518
chr_1 g11715 g11715.t2 exon g11715.t2.exon5 18036589 18036785
chr_1 g11715 g11715.t2 cds g11715.t2.CDS2 18036589 18036622
chr_1 g11715 g11715.t2 exon g11715.t2.exon6 18036871 18037324
chr_1 g11715 g11715.t2 TSS g11715.t2 NA NA
chr_1 g11715 g11715.t2 TTS g11715.t2 NA NA

Sequences

>g11715.t2 Gene=g11715 Length=1492
GGTTAGAAATATATTTATTTCTAAAATAAAATATCTTTATTAAAAAGAATAATTTTAATT
TTATATTAGATAATGTTAGTTGGTTTGCAGAACGTGAAGAACGTCATAAAGAGTTGGTTG
ATGAAACAGCTGAAGTTGGTTTAATGTTTGCATCTAAAGCTTTTGTGCAGCTCATATCAA
ATCCTTTTGTAGGACCATTAACTCACAAATTTGCACAGCATCCCAATGTTTGCAGGATTT
GTCATTATGTTTTTATCAACATTAATTTTTGCCTTTGGTAGAACTTATCCAGTTCTGTTT
ATAGCACGTGCATTACAAGGTATTGGTTCGTCGTGTTCTTCAGTTTCTGGAATGGGAATG
CTTGCTGATCGATATACTGATGATAAGGAAAGAGGAAATGCTATGGGAATAGAAATTATA
ACTAACATTTCTTCATAGGTCCACCATTTGGAGGCTTTATGTATGAATTCGTGGGGAAAA
CAGCACCTTTTTTAGTTCTTTCTATTCTTGCATTAGGTGATGGAATGCTTCAGCTATTTA
TGTTGCAACCATCAGTAGCACGATCAGAAGCAGATGCGCCTTCATTAAAAGCTCTTGTTA
TGGATCCATATATTTTAATAGCAGCTGGAGCAATTACATTTGCTAATATGGGTATCGCTA
TGCTTGAACCTTCCCTTCCAATTTGGATGATAGATCGTATGGATGCATCAAGATGGGAGC
AAGGTGTTACATTCTTACCAGCTTCTATTAGTTACTTAATTGGAACAAATTTATTTGGAC
CACTTGGACATCGTATTGGAAGATGGCGAGCAGCATTAATTGGACTTGTTATCATAGGCA
CATTCCTTCTGCAACATCAATGTATCATCTCATAATTCCAAATGCCGGTCTTGGTTTCGC
TATCGGTATGGTTGATTCATGTATGATGCCAGAACTTGGTTATCTAGTAGATATACGTCA
TTCTGCTGTTTATGGAAGTGTATATGCGCTAGGTGATGTAGCATTTTGTGTAGGATTTGC
TGTAGGACCTGCTTTAAGTGGAACATTAGTAAAGAATATTGGGTTCGAATGGATGATGTT
TGGAATTGGAGTTTTGTGTTTTGTATATGCACCATTACTGCTATTTCTAAAAGCACCTCC
AACTAAAGAAGAGAAAAAGGTGGGTGATGATGAGACTTATTCAAATAATGCAATTGATTT
ATGTGATGAAAATGGAAATAATAACGGCAATAAAATCACTGCCAATACTTTAAAAACAAA
AATTTAAGTTTATTTAGGTTATAATTTATATAATAATTAAATATTATTTGTTGTAAAATA
TGTTAATAAATTTTATTTTGAAAATTTATTATATGGTTTTTATTTTTAAAAACATGTTTC
AAAAAAAATTTAGAATTCAATTTTACAAACTTTTTTCATTTAGCAATTAATTACTGGAGA
TCGGTCATCTGTACGATACGTCGCTTATCAAAATGATGACGATGAAGAGTAA

>g11715.t2 Gene=g11715 Length=138
MYEFVGKTAPFLVLSILALGDGMLQLFMLQPSVARSEADAPSLKALVMDPYILIAAGAIT
FANMGIAMLEPSLPIWMIDRMDASRWEQGVTFLPASISYLIGTNLFGPLGHRIGRWRAAL
IGLVIIGTFLLQHQCIIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11715.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 46 134 1.9E-10
2 g11715.t2 PANTHER PTHR23506:SF30 SYNAPTIC VESICULAR AMINE TRANSPORTER 1 131 2.2E-52
3 g11715.t2 PANTHER PTHR23506 - 1 131 2.2E-52
1 g11715.t2 Pfam PF07690 Major Facilitator Superfamily 2 130 1.1E-8
14 g11715.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 36 -
15 g11715.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
16 g11715.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 18 -
20 g11715.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 36 -
12 g11715.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 51 -
18 g11715.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
10 g11715.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 70 89 -
17 g11715.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 107 -
13 g11715.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 108 112 -
19 g11715.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 131 -
11 g11715.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 132 138 -
8 g11715.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 3 131 2.22E-15
5 g11715.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 29 -
6 g11715.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 69 -
4 g11715.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
7 g11715.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 137 -

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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