Gene loci information

Transcript annotation

  • This transcript has been annotated as Sodium- and chloride-dependent GABA transporter 1.

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 g9869 g9869.t6 TSS g9869.t6 5770746 5770746
chr_1 g9869 g9869.t6 isoform g9869.t6 5771012 5776427
chr_1 g9869 g9869.t6 exon g9869.t6.exon1 5771012 5771160
chr_1 g9869 g9869.t6 exon g9869.t6.exon2 5771715 5771768
chr_1 g9869 g9869.t6 exon g9869.t6.exon3 5771825 5771970
chr_1 g9869 g9869.t6 exon g9869.t6.exon4 5774693 5774836
chr_1 g9869 g9869.t6 exon g9869.t6.exon5 5774898 5775057
chr_1 g9869 g9869.t6 exon g9869.t6.exon6 5775214 5775527
chr_1 g9869 g9869.t6 cds g9869.t6.CDS1 5775399 5775527
chr_1 g9869 g9869.t6 exon g9869.t6.exon7 5775591 5776427
chr_1 g9869 g9869.t6 cds g9869.t6.CDS2 5775591 5776427
chr_1 g9869 g9869.t6 TTS g9869.t6 5776568 5776568

Sequences

>g9869.t6 Gene=g9869 Length=1804
ATGGATGTGAAATCTTTTGATGTGCCAAATATTAGTGGCATAGAAAAATCCTCGAATAAT
GGAAGCAATGTTGAAATTTCAACGTCATCTACTGTCAATTTAATTGAAGATCGAACAAAT
TGGAGTCGACCAATTGAATTTATTTTATCATTGTCTTTCGAAGGATTGGGGAACATTTGG
AGATTTCCTCATCTTGCTTATAGGAATGGCGGTGGAGCTTTTTTACTGCCATATTTTCTT
GCAGCAGTTTTTATTGGTTTGCCAATATTTTTTGCTGAACTGATTACAGGACAATATAGT
GGACTTGGGCCGATTAAAGCTTATAGTTATCTTGCTCCGCTCTTTAAAGGCTTGGGCTAC
TGCACATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGATTATTGCGTGGGTC
TTATTTTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCACATGTGACAATGAT
TGGAATTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTCGTCAAGAAAATGTT
GGTAGTGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGATTAACGAAATTTGT
TCAATTCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATACAACAACTTGGTTA
TCCTCGATGGCAAATGGTCATTTTTCTATTTCTTGGTTGGACACTTACATATTTGTGTTT
AATCAAAGGCGTTCAGTCAATGGGAAAAGTCGTCTATTTTACTGCCACATTTCCTTATGT
CATTTTAACAGCTCTCTTAATTCGCTCATTAACATTAGAAGGTTCTTATGAAGGCATCAT
GTTTTATATTACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAG
CAGTCAAATTTTCTACTCATTTGGCTTAGCTTGTGGCAGTCTTGTGGCTTTAGCTTCGTA
TAATAAATTTAAAAATAATTGCCATTTTGATGCAGTATTTATATCAATCATAAATTTTGG
CACTGCTATTTTCGGTGGTTTTGTAGTTTTTGCGACTCTTGGATTTTTATCAAATTCAAT
GCAACAACCTATTGATAATGTCGTAACTGGTGGCCCTGGTTTAACATTTATTACATATCC
TGAAGCTATCCTATTGATGCCATTGCCAAACCTTTGGGCAATTTTGTTTTTCCTCATGAT
GCTCATTTTGGGTTTAGGTTCTCAATTCCCTGGTGTTCAAATGATTTCAACTTCAATTGT
TGATCATTGGCCACATTTGAGAAATAAGGAATGGAAAGTGACAGCTGGAGTATGCATGAG
TTGTTTTGTTCTCGGTTTACCAATGACTTGTCATGGTGGAATTTATCTTTTTACTCTTAT
GGAATGGCATACAGCAAGTTGGGCAATTTTATTAATTGGTGCAGCTGAAATTGTCATCTT
TTCATGGGTCTATGGAATAAATAACACACTCGATATGATTAAAGAGATGGGAATGAAATT
CGTAAAAGTTACGAGATATTTCTGGAAAGCAGTATGGGTTGTTATAACACCAATTGGATC
AGTTGCAATTTTCATCTTTATTTTAACTGATTTGGGACCAAGTGAATTTCGTGATTATGT
TTTTCCTCTTTGGGCTGATATCTTAGGTTGGATGTTTGGACTTGCAACGCTTGTTCCTTT
TATTGTTTTCGCTATTTATCAATTAATTGTTGTAAAAGATAAGAAAACACTACTCAAACC
AACAGATCTTTGGGGCCCACAAGAAATCGATGGACAAAGGATTGATAGAGCAGTATTAGC
TTAA

>g9869.t6 Gene=g9869 Length=321
MFYITPQWERLLSPGVWGDASSQIFYSFGLACGSLVALASYNKFKNNCHFDAVFISIINF
GTAIFGGFVVFATLGFLSNSMQQPIDNVVTGGPGLTFITYPEAILLMPLPNLWAILFFLM
MLILGLGSQFPGVQMISTSIVDHWPHLRNKEWKVTAGVCMSCFVLGLPMTCHGGIYLFTL
MEWHTASWAILLIGAAEIVIFSWVYGINNTLDMIKEMGMKFVKVTRYFWKAVWVVITPIG
SVAIFIFILTDLGPSEFRDYVFPLWADILGWMFGLATLVPFIVFAIYQLIVVKDKKTLLK
PTDLWGPQEIDGQRIDRAVLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9869.t6 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 308 1.1E-92
3 g9869.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 53 73 8.8E-23
6 g9869.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 107 126 8.8E-23
5 g9869.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 187 207 8.8E-23
4 g9869.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 230 250 8.8E-23
1 g9869.t6 Pfam PF00209 Sodium:neurotransmitter symporter family 2 290 1.1E-84
21 g9869.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
25 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 41 -
19 g9869.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 42 52 -
27 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 77 -
22 g9869.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 78 111 -
29 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 133 -
16 g9869.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 153 -
28 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 179 -
20 g9869.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 180 184 -
26 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 185 206 -
17 g9869.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 226 -
24 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 248 -
23 g9869.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 249 267 -
30 g9869.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 290 -
18 g9869.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 291 321 -
15 g9869.t6 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 294 46.647
14 g9869.t6 SUPERFAMILY SSF161070 SNF-like 2 289 1.29E-74
8 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
7 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
13 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
11 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 158 180 -
12 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 185 207 -
10 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -
9 g9869.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 269 291 -

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:0016021 integral component of membrane CC

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