Gene loci information

Transcript annotation

  • This transcript has been annotated as Gamma-aminobutyric acid receptor subunit beta.

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 g13131 g13131.t6 TSS g13131.t6 28117161 28117161
chr_1 g13131 g13131.t6 isoform g13131.t6 28117606 28118803
chr_1 g13131 g13131.t6 exon g13131.t6.exon1 28117606 28117901
chr_1 g13131 g13131.t6 cds g13131.t6.CDS1 28117609 28117901
chr_1 g13131 g13131.t6 exon g13131.t6.exon2 28117991 28118073
chr_1 g13131 g13131.t6 cds g13131.t6.CDS2 28117991 28118073
chr_1 g13131 g13131.t6 exon g13131.t6.exon3 28118135 28118272
chr_1 g13131 g13131.t6 cds g13131.t6.CDS3 28118135 28118272
chr_1 g13131 g13131.t6 exon g13131.t6.exon4 28118332 28118616
chr_1 g13131 g13131.t6 cds g13131.t6.CDS4 28118332 28118616
chr_1 g13131 g13131.t6 exon g13131.t6.exon5 28118673 28118803
chr_1 g13131 g13131.t6 cds g13131.t6.CDS5 28118673 28118803
chr_1 g13131 g13131.t6 TTS g13131.t6 28118985 28118985

Sequences

>g13131.t6 Gene=g13131 Length=933
GAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCATTTTCTGAA
GAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGATCCACGACTT
CAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTTGGACGAACT
CTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCATACGATAACA
ACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGTGTAAGATTG
AGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAATGGACACTCAGTTATGT
GCAATTCCTATTGAGAGCTATGCACATCGTTCAAATGAAATTACTTATTACTGGAAAGAT
GGAAATGATTCAGTTGGAATAGTGCCTGACATTGATTTGCCTTTAATAAAAGTGAAGAAT
CTTGATTTAAAATCTCAAGTTATTAGCCTAGCACATGGCACTTACTCAAGAATGGAATTG
ACAGTTGCATTTGAACGCACAGTTGGTTATTATATTATTCAAATTTACATTCCATGCACA
ATGATTGTAATTATAGCTTGGATAAGTTTCTTCTTGAACAAAAATGCTATGAACATTCGT
TGTGTGTTGTGCATTGCTGGTTTGCTGTCTTTGATCGTTGAATGCCAAGCTATCAATACT
TTTATCCCGAAAACTTCTTATTCAAAGGCTTTAGATCTTTACACTGGAATTTGTATGACT
TTGGTTTTTATTGCTCTTGTTGAATTTGCATTCATTTCAAACACAGAGAGTTTTAAAAAT
TCAACCAAAGCACCGTGTGCTGACAAAATTTTCCGCTTTTTATTCCCAATATTCTTTATT
GTTTTCAACATTTTCTATTGGATTTATTATTGA

>g13131.t6 Gene=g13131 Length=309
MPVNVGVSAYILGIHSFSEENMDFTMDFYFRQYWNDPRLQFKKQPGIEYITPGYEFGRTL
WFPDTFFVNEKESFLHTITTKNEFVKIYHNGDVVKSVRLSVTFSCPMNFVRYPMDTQLCA
IPIESYAHRSNEITYYWKDGNDSVGIVPDIDLPLIKVKNLDLKSQVISLAHGTYSRMELT
VAFERTVGYYIIQIYIPCTMIVIIAWISFFLNKNAMNIRCVLCIAGLLSLIVECQAINTF
IPKTSYSKALDLYTGICMTLVFIALVEFAFISNTESFKNSTKAPCADKIFRFLFPIFFIV
FNIFYWIYY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g13131.t6 CDD cd19049 LGIC_TM_anion 189 306 6.01662E-38
15 g13131.t6 Gene3D G3DSA:2.70.170.10 - 1 184 1.2E-59
14 g13131.t6 Gene3D G3DSA:1.20.58.390 Glr4197 protein 185 309 7.3E-38
3 g13131.t6 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 3 274 1.3E-78
4 g13131.t6 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 3 274 1.3E-78
6 g13131.t6 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 25 41 6.9E-12
5 g13131.t6 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 59 70 6.9E-12
7 g13131.t6 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 105 119 6.9E-12
8 g13131.t6 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 181 193 6.9E-12
10 g13131.t6 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 190 210 2.0E-22
11 g13131.t6 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 250 271 2.0E-22
9 g13131.t6 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 289 309 2.0E-22
1 g13131.t6 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 2 153 1.1E-38
2 g13131.t6 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 194 281 1.1E-22
20 g13131.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 186 -
22 g13131.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 187 211 -
17 g13131.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 212 217 -
21 g13131.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
18 g13131.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 241 251 -
24 g13131.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 252 271 -
16 g13131.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 272 291 -
23 g13131.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 292 308 -
19 g13131.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 309 309 -
30 g13131.t6 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 105 119 -
12 g13131.t6 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 2 185 4.58E-43
13 g13131.t6 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 188 309 1.09E-29
31 g13131.t6 TIGRFAM TIGR00860 LIC: cation transporter family protein 2 276 5.2E-84
27 g13131.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -
28 g13131.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
29 g13131.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 250 272 -
26 g13131.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 289 308 -

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:0005230 extracellular ligand-gated ion channel activity MF
GO:0005216 ion channel activity MF
GO:0034220 ion transmembrane transport BP
GO:0016021 integral component of membrane CC
GO:0004888 transmembrane signaling receptor activity MF
GO:0006811 ion transport BP

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