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.t4 TSS g13131.t4 28117161 28117161
chr_1 g13131 g13131.t4 isoform g13131.t4 28117241 28118803
chr_1 g13131 g13131.t4 exon g13131.t4.exon1 28117241 28117293
chr_1 g13131 g13131.t4 cds g13131.t4.CDS1 28117241 28117293
chr_1 g13131 g13131.t4 exon g13131.t4.exon2 28117441 28117517
chr_1 g13131 g13131.t4 cds g13131.t4.CDS2 28117441 28117517
chr_1 g13131 g13131.t4 exon g13131.t4.exon3 28117607 28117901
chr_1 g13131 g13131.t4 cds g13131.t4.CDS3 28117607 28117901
chr_1 g13131 g13131.t4 exon g13131.t4.exon4 28117991 28118052
chr_1 g13131 g13131.t4 cds g13131.t4.CDS4 28117991 28118052
chr_1 g13131 g13131.t4 exon g13131.t4.exon5 28118135 28118272
chr_1 g13131 g13131.t4 cds g13131.t4.CDS5 28118135 28118272
chr_1 g13131 g13131.t4 exon g13131.t4.exon6 28118332 28118616
chr_1 g13131 g13131.t4 cds g13131.t4.CDS6 28118332 28118616
chr_1 g13131 g13131.t4 exon g13131.t4.exon7 28118673 28118803
chr_1 g13131 g13131.t4 cds g13131.t4.CDS7 28118673 28118803
chr_1 g13131 g13131.t4 TTS g13131.t4 28118985 28118985

Sequences

>g13131.t4 Gene=g13131 Length=1041
ATGTGGATACTAAAAGTTTTAATTGTAATAATCTTTATCGTGTCGTGTGCTAGCGCACAG
CAGAATGTGACAAAAATAATTGACTCGCTTACTGAAAACTATGATAAACGTTTGCGTCCA
AATTATGGAAAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCA
TTTTCTGAAGAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGAT
CCACGACTTCAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTT
GGACGAACTCTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCAT
ACGATAACAACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGT
GTAAGATTGAGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAATGGACACT
CAGTTATATGCACATCGTTCAAATGAAATTACTTATTACTGGAAAGATGGAAATGATTCA
GTTGGAATAGTGCCTGACATTGATTTGCCTTTAATAAAAGTGAAGAATCTTGATTTAAAA
TCTCAAGTTATTAGCCTAGCACATGGCACTTACTCAAGAATGGAATTGACAGTTGCATTT
GAACGCACAGTTGGTTATTATATTATTCAAATTTACATTCCATGCACAATGATTGTAATT
ATAGCTTGGATAAGTTTCTTCTTGAACAAAAATGCTATGAACATTCGTTGTGTGTTGTGC
ATTGCTGGTTTGCTGTCTTTGATCGTTGAATGCCAAGCTATCAATACTTTTATCCCGAAA
ACTTCTTATTCAAAGGCTTTAGATCTTTACACTGGAATTTGTATGACTTTGGTTTTTATT
GCTCTTGTTGAATTTGCATTCATTTCAAACACAGAGAGTTTTAAAAATTCAACCAAAGCA
CCGTGTGCTGACAAAATTTTCCGCTTTTTATTCCCAATATTCTTTATTGTTTTCAACATT
TTCTATTGGATTTATTATTGA

>g13131.t4 Gene=g13131 Length=346
MWILKVLIVIIFIVSCASAQQNVTKIIDSLTENYDKRLRPNYGKMPVNVGVSAYILGIHS
FSEENMDFTMDFYFRQYWNDPRLQFKKQPGIEYITPGYEFGRTLWFPDTFFVNEKESFLH
TITTKNEFVKIYHNGDVVKSVRLSVTFSCPMNFVRYPMDTQLYAHRSNEITYYWKDGNDS
VGIVPDIDLPLIKVKNLDLKSQVISLAHGTYSRMELTVAFERTVGYYIIQIYIPCTMIVI
IAWISFFLNKNAMNIRCVLCIAGLLSLIVECQAINTFIPKTSYSKALDLYTGICMTLVFI
ALVEFAFISNTESFKNSTKAPCADKIFRFLFPIFFIVFNIFYWIYY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
31 g13131.t4 CDD cd19049 LGIC_TM_anion 226 343 1.14795E-37
17 g13131.t4 Gene3D G3DSA:2.70.170.10 - 12 221 3.0E-62
16 g13131.t4 Gene3D G3DSA:1.20.58.390 Glr4197 protein 222 346 9.4E-38
3 g13131.t4 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 18 310 6.5E-80
4 g13131.t4 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 18 310 6.5E-80
6 g13131.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 69 85 5.7E-10
7 g13131.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 103 114 5.7E-10
8 g13131.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 149 163 5.7E-10
5 g13131.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 218 230 5.7E-10
10 g13131.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 227 247 2.7E-22
11 g13131.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 287 308 2.7E-22
9 g13131.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 326 346 2.7E-22
1 g13131.t4 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 24 181 3.8E-38
2 g13131.t4 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 231 318 1.2E-22
23 g13131.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
24 g13131.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
25 g13131.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 14 -
30 g13131.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
22 g13131.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 223 -
29 g13131.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 224 248 -
19 g13131.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 249 254 -
27 g13131.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 255 277 -
20 g13131.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 278 288 -
26 g13131.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 289 308 -
18 g13131.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 309 328 -
28 g13131.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 329 345 -
21 g13131.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 346 346 -
38 g13131.t4 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 16 5.0
12 g13131.t4 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 22 222 3.79E-45
13 g13131.t4 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 225 346 1.57E-29
15 g13131.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
32 g13131.t4 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 19 -
14 g13131.t4 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -
37 g13131.t4 TIGRFAM TIGR00860 LIC: cation transporter family protein 6 313 8.6E-85
35 g13131.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 226 248 -
34 g13131.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 255 277 -
33 g13131.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 287 309 -
36 g13131.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 326 345 -

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. There were no conditions that were differentially expressed