Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicular glutamate transporter 2.2.

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_2 g6927 g6927.t2 TTS g6927.t2 20019090 20019090
chr_2 g6927 g6927.t2 isoform g6927.t2 20019163 20020231
chr_2 g6927 g6927.t2 exon g6927.t2.exon1 20019163 20019320
chr_2 g6927 g6927.t2 cds g6927.t2.CDS1 20019163 20019320
chr_2 g6927 g6927.t2 exon g6927.t2.exon2 20019372 20019408
chr_2 g6927 g6927.t2 cds g6927.t2.CDS2 20019372 20019408
chr_2 g6927 g6927.t2 exon g6927.t2.exon3 20019466 20019802
chr_2 g6927 g6927.t2 cds g6927.t2.CDS3 20019466 20019802
chr_2 g6927 g6927.t2 exon g6927.t2.exon4 20019862 20019988
chr_2 g6927 g6927.t2 cds g6927.t2.CDS4 20019862 20019988
chr_2 g6927 g6927.t2 exon g6927.t2.exon5 20020047 20020154
chr_2 g6927 g6927.t2 cds g6927.t2.CDS5 20020047 20020113
chr_2 g6927 g6927.t2 exon g6927.t2.exon6 20020228 20020231
chr_2 g6927 g6927.t2 TSS g6927.t2 NA NA

Sequences

>g6927.t2 Gene=g6927 Length=771
GCGGGTGAAAGAATATACATAGAGCAATCATTAAATAGACAATCTATGGATAAAGAAGTT
AAAATTCCATGGAAAGCTATTTTTAATTCGAGTGCTGTTTGGGCAATTATTGCTGCACAA
TTTAGTGAAGGTTGGGGCTTCTTTACTTTGCAAACTCAGCTCCCACAGTTCTTAAAAGAT
GCATTAAATTTTGATATTGCGAAATCTGGAATAATTTCGGCATTGCCTTATCTTTGCATG
GCTGTAATGTGTCAAATTGCTGGCTATCTTTCTGACTGGGTACGAATTAAAGGGTATTGG
ACAACAGGACAAACACGACGATATTTTAATTCAATGGCGTTTTTAACACAAATGGCTTGC
ATGTTACTTGCAGCTTTCTTTCTGCATCCTGTTTCATCGGTTACATTTATTACGATTGGT
GTGGCTATGGCATCATTTGCTTATGCCAGCTTTTCTGTAAATTATCTAGATATTGCACCA
CAATTTGCAGGCGTTTTAATGGGGCTTTGCAACAGTTTTGCAACAGTCGCAGGAATAATT
TCACCTATTTTGACTGGATATATTGTAACTGATGCTGATGCAGAACAATGGAAAATAATT
TTCTATATTGCTGCTGGAATTTATGTTTTTGGTTGTGTTATTTATTGGATTTGGGCACAA
GGAGAAATTCAACCATGGGCAGTTCAAGAATCGATTGAGTTTGAAGATGCTTCTGAAATG
CCAAAAATACAAAATGGAATTTCAAATCCTGCACTTGATGTAAAGAAATAA

>g6927.t2 Gene=g6927 Length=241
MDKEVKIPWKAIFNSSAVWAIIAAQFSEGWGFFTLQTQLPQFLKDALNFDIAKSGIISAL
PYLCMAVMCQIAGYLSDWVRIKGYWTTGQTRRYFNSMAFLTQMACMLLAAFFLHPVSSVT
FITIGVAMASFAYASFSVNYLDIAPQFAGVLMGLCNSFATVAGIISPILTGYIVTDADAE
QWKIIFYIAAGIYVFGCVIYWIWAQGEIQPWAVQESIEFEDASEMPKIQNGISNPALDVK
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6927.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 4 209 6.9E-36
2 g6927.t2 PANTHER PTHR11662 SOLUTE CARRIER FAMILY 17 3 218 8.9E-78
3 g6927.t2 PANTHER PTHR11662:SF437 GH23975P 3 218 8.9E-78
1 g6927.t2 Pfam PF07690 Major Facilitator Superfamily 6 167 2.0E-16
13 g6927.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
24 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
18 g6927.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
21 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 75 -
14 g6927.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 95 -
22 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 113 -
19 g6927.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 118 -
20 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 141 -
15 g6927.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 142 147 -
23 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 148 172 -
17 g6927.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 173 183 -
25 g6927.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 184 203 -
16 g6927.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 204 241 -
12 g6927.t2 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 17 241 8.506
10 g6927.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 4 212 1.96E-32
7 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
4 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
5 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 113 -
9 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -
6 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
8 g6927.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 184 203 -

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