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_3 g227 g227.t2 TSS g227.t2 1874945 1874945
chr_3 g227 g227.t2 isoform g227.t2 1875228 1876965
chr_3 g227 g227.t2 exon g227.t2.exon1 1875228 1875318
chr_3 g227 g227.t2 cds g227.t2.CDS1 1875228 1875318
chr_3 g227 g227.t2 exon g227.t2.exon2 1875379 1875714
chr_3 g227 g227.t2 cds g227.t2.CDS2 1875379 1875714
chr_3 g227 g227.t2 exon g227.t2.exon3 1875776 1876082
chr_3 g227 g227.t2 cds g227.t2.CDS3 1875776 1876082
chr_3 g227 g227.t2 exon g227.t2.exon4 1876161 1876823
chr_3 g227 g227.t2 cds g227.t2.CDS4 1876161 1876236
chr_3 g227 g227.t2 exon g227.t2.exon5 1876882 1876965
chr_3 g227 g227.t2 TTS g227.t2 1877074 1877074

Sequences

>g227.t2 Gene=g227 Length=1481
ATGGAAAGTGAATTTAATAAGAATCGATTTGCAATAACGTCTATCATCTATGCAACACTT
TTATTGGATAATATTTTACTTACAGTTATCGTTCCAATTCTACCAGACTATCTAGCATCA
TTTGCAACTAAAAATGATTCAAATGGTCTCTATAAAAATTTTGATCATTACATTCCCAAT
TCTATGCTTAACAAGCATCCTCTTGCTGGTAATTCAATAAAAAATGTGACAAAAGAAATT
CAACAACAGATGCATTATGGAAATGAATTCAATGTTGAAATGGAGAATGGAAAAGTTGGA
TTTTTACTTGCAATAAAAGCTTTTGTACAATTGTTCTTTAATCCTGTTTGTGGTAATTTA
AGCAAAAAATTTGGATACAAAAATATCATTTTTTTCGGTACTATCAACTTGCTTTTAGCC
TCTCTATTTTTTGCAATGGGAACTTCTTTTCTCATGTTGCTTTTAGCACGAGCAATTGAA
GGAATTGGATCAAGTTGCATAAATGTCTGTGGAATGAGTTTAATTGCTTCACTATATCTT
GAAGATCAGAAACGTTCAAAAGTAATGGGCATCATTTTAGGAAGCATTGCACTTGGTGTT
CTCTTTGGTTATCCTCTAGGCAGTCTTCTCTATGATTTTGTCAGTGAATCAGCGCCCTTC
ATCATCATTTCTGCATTTCTCATCACTGATCTTGCTTTCCAACTAACGTTCTTTAATTTG
ATGCGAAATGAGGTAATGAACTCAATGATGAGGAAAATCGAATGGTGGATGGAAATTCAC
AATGGTTACAACTGCTATCAAACAAAATGATTTTCTCCATCACTCTCGCAATTTTTATGT
CAACTGCTGCTATGGCAATTCTAGAGCCTCTTTTGCCCATTTGGCTAATTTCTCATTTAA
GACCTAAGAAATGGCAATTAGGTACAGTCTTTATTCCCGATTCTATGGGATATTTTATTG
GAACAAATTTCTTCGGTTCATTCTCATTCAAAGTTGGACAAATTAAAATGTCTGTTTTGG
CACTTATGTGTGTTGGAATATCTTCTACTATAATTCCTGAAGCAAAAACCGTCTCAAGCT
TGATCATTCCACATTTCTGTCTTGGTTTGGGCATAGGAATTTTAGATACGTCATTAGTAC
CATATCTTGCACGATTAACTGACTCAATCACACAGAAATGTGATGAATCATGCGAAGAAA
ATGATATTCCATCAAATTATGGCAGTGTCTATGCAATTCAACAAACTGCTGTGAGTTTAG
CTTATTCGATTGTACCATTCATGGCTGGTGAAATGGTTGAGAGTATGGGATTCAAAACTA
TTATGAGATTACTTGGTATTTGTAATTTCATCTATGGACCACTTTTACTATTTATCACAA
TCAAACATAATCTTAATAATACGGCAGCAAAACAACCTGATTTGCTACTTAAAGAAACAA
ATCCATCAGATTATAGACGATTTTATAATTCTATCGAGTGA

>g227.t2 Gene=g227 Length=269
MESEFNKNRFAITSIIYATLLLDNILLTVIVPILPDYLASFATKNDSNGLYKNFDHYIPN
SMLNKHPLAGNSIKNVTKEIQQQMHYGNEFNVEMENGKVGFLLAIKAFVQLFFNPVCGNL
SKKFGYKNIIFFGTINLLLASLFFAMGTSFLMLLLARAIEGIGSSCINVCGMSLIASLYL
EDQKRSKVMGIILGSIALGVLFGYPLGSLLYDFVSESAPFIIISAFLITDLAFQLTFFNL
MRNEVMNSMMRKIEWWMEIHNGYNCYQTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g227.t2 PANTHER PTHR23506:SF4 PORTABELLA 5 257 1.7E-74
3 g227.t2 PANTHER PTHR23506 - 5 257 1.7E-74
1 g227.t2 Pfam PF07690 Major Facilitator Superfamily 87 233 3.0E-25
12 g227.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
24 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
16 g227.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 98 -
23 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 117 -
15 g227.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 118 128 -
19 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 129 156 -
18 g227.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 157 161 -
21 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 181 -
14 g227.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 182 187 -
20 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 188 206 -
17 g227.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 207 217 -
22 g227.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 241 -
13 g227.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 242 269 -
11 g227.t2 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 12 269 17.205
10 g227.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 11 239 7.85E-29
8 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
4 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 116 -
7 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
9 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 161 180 -
6 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 187 209 -
5 g227.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 219 241 -

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.

Raw TPM values