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.t2 TSS g13131.t2 28117161 28117161
chr_1 g13131 g13131.t2 isoform g13131.t2 28117241 28118803
chr_1 g13131 g13131.t2 exon g13131.t2.exon1 28117241 28117293
chr_1 g13131 g13131.t2 cds g13131.t2.CDS1 28117241 28117293
chr_1 g13131 g13131.t2 exon g13131.t2.exon2 28117441 28117517
chr_1 g13131 g13131.t2 cds g13131.t2.CDS2 28117441 28117517
chr_1 g13131 g13131.t2 exon g13131.t2.exon3 28117607 28117901
chr_1 g13131 g13131.t2 cds g13131.t2.CDS3 28117607 28117901
chr_1 g13131 g13131.t2 exon g13131.t2.exon4 28117991 28118073
chr_1 g13131 g13131.t2 cds g13131.t2.CDS4 28117991 28118073
chr_1 g13131 g13131.t2 exon g13131.t2.exon5 28118135 28118272
chr_1 g13131 g13131.t2 cds g13131.t2.CDS5 28118135 28118272
chr_1 g13131 g13131.t2 exon g13131.t2.exon6 28118332 28118803
chr_1 g13131 g13131.t2 cds g13131.t2.CDS6 28118332 28118657
chr_1 g13131 g13131.t2 TTS g13131.t2 28118985 28118985

Sequences

>g13131.t2 Gene=g13131 Length=1118
ATGTGGATACTAAAAGTTTTAATTGTAATAATCTTTATCGTGTCGTGTGCTAGCGCACAG
CAGAATGTGACAAAAATAATTGACTCGCTTACTGAAAACTATGATAAACGTTTGCGTCCA
AATTATGGAAAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCA
TTTTCTGAAGAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGAT
CCACGACTTCAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTT
GGACGAACTCTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCAT
ACGATAACAACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGT
GTAAGATTGAGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAATGGACACT
CAGTTATGTGCAATTCCTATTGAGAGCTATGCACATCGTTCAAATGAAATTACTTATTAC
TGGAAAGATGGAAATGATTCAGTTGGAATAGTGCCTGACATTGATTTGCCTTTAATAAAA
GTGAAGAATCTTGATTTAAAATCTCAAGTTATTAGCCTAGCACATGGCACTTACTCAAGA
ATGGAATTGACAGTTGCATTTGAACGCACAGTTGGTTATTATATTATTCAAATTTACATT
CCATGCACAATGATTGTAATTATAGCTTGGATAAGTTTCTTCTTGAACAAAAATGCTATG
AACATTCGTTGTGTGTTGTGCATTGCTGGTTTGCTGTCTTTGATCGTTGAATGCCAAGCT
ATCAATACTTTTATCCCGAAAACTTCTTATTCAAAGGCTTTAGATCTTTACACTGGAATT
TGTATGACTTTGGTTTTTATTGCTCTTGTTGGTAAGATTAAAACTTTTACAATTTTATTT
ATCTTTTTGTAAAATATTCTTTTTTAGAATTTGCATTCATTTCAAACACAGAGAGTTTTA
AAAATTCAACCAAAGCACCGTGTGCTGACAAAATTTTCCGCTTTTTATTCCCAATATTCT
TTATTGTTTTCAACATTTTCTATTGGATTTATTATTGA

>g13131.t2 Gene=g13131 Length=323
MWILKVLIVIIFIVSCASAQQNVTKIIDSLTENYDKRLRPNYGKMPVNVGVSAYILGIHS
FSEENMDFTMDFYFRQYWNDPRLQFKKQPGIEYITPGYEFGRTLWFPDTFFVNEKESFLH
TITTKNEFVKIYHNGDVVKSVRLSVTFSCPMNFVRYPMDTQLCAIPIESYAHRSNEITYY
WKDGNDSVGIVPDIDLPLIKVKNLDLKSQVISLAHGTYSRMELTVAFERTVGYYIIQIYI
PCTMIVIIAWISFFLNKNAMNIRCVLCIAGLLSLIVECQAINTFIPKTSYSKALDLYTGI
CMTLVFIALVGKIKTFTILFIFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13131.t2 Gene3D G3DSA:2.70.170.10 - 12 228 2.9E-70
15 g13131.t2 Gene3D G3DSA:1.20.58.390 Glr4197 protein 229 314 6.4E-26
3 g13131.t2 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 18 310 1.2E-85
4 g13131.t2 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 18 310 1.2E-85
5 g13131.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 69 85 7.9E-12
7 g13131.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 103 114 7.9E-12
8 g13131.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 149 163 7.9E-12
6 g13131.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 225 237 7.9E-12
10 g13131.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 234 254 7.6E-9
9 g13131.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 294 315 7.6E-9
1 g13131.t2 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 24 197 7.9E-46
2 g13131.t2 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 238 310 5.1E-18
21 g13131.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
22 g13131.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
23 g13131.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 14 -
27 g13131.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
20 g13131.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 230 -
26 g13131.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 231 255 -
17 g13131.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 256 261 -
25 g13131.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 262 285 -
19 g13131.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 286 296 -
24 g13131.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 297 322 -
18 g13131.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 323 323 -
32 g13131.t2 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 149 163 -
34 g13131.t2 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 16 5.0
11 g13131.t2 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 22 229 3.66E-51
12 g13131.t2 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 232 311 2.09E-24
14 g13131.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
28 g13131.t2 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 19 -
13 g13131.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -
33 g13131.t2 TIGRFAM TIGR00860 LIC: cation transporter family protein 6 311 3.5E-89
31 g13131.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 233 255 -
30 g13131.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 262 284 -
29 g13131.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 299 321 -

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