Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t5 TSS g13131.t5 28117161 28117161
chr_1 g13131 g13131.t5 isoform g13131.t5 28117241 28118803
chr_1 g13131 g13131.t5 exon g13131.t5.exon1 28117241 28117293
chr_1 g13131 g13131.t5 cds g13131.t5.CDS1 28117241 28117293
chr_1 g13131 g13131.t5 exon g13131.t5.exon2 28117441 28117517
chr_1 g13131 g13131.t5 cds g13131.t5.CDS2 28117441 28117517
chr_1 g13131 g13131.t5 exon g13131.t5.exon3 28117607 28117896
chr_1 g13131 g13131.t5 cds g13131.t5.CDS3 28117607 28117896
chr_1 g13131 g13131.t5 exon g13131.t5.exon4 28117991 28118073
chr_1 g13131 g13131.t5 cds g13131.t5.CDS4 28117991 28118068
chr_1 g13131 g13131.t5 exon g13131.t5.exon5 28118135 28118272
chr_1 g13131 g13131.t5 exon g13131.t5.exon6 28118332 28118616
chr_1 g13131 g13131.t5 exon g13131.t5.exon7 28118673 28118803
chr_1 g13131 g13131.t5 TTS g13131.t5 28118985 28118985

Sequences

>g13131.t5 Gene=g13131 Length=1057
ATGTGGATACTAAAAGTTTTAATTGTAATAATCTTTATCGTGTCGTGTGCTAGCGCACAG
CAGAATGTGACAAAAATAATTGACTCGCTTACTGAAAACTATGATAAACGTTTGCGTCCA
AATTATGGAAAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCA
TTTTCTGAAGAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGAT
CCACGACTTCAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTT
GGACGAACTCTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCAT
ACGATAACAACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGT
ATTGAGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAATGGACACTCAGTT
ATGTGCAATTCCTATTGAGAGCTATGCACATCGTTCAAATGAAATTACTTATTACTGGAA
AGATGGAAATGATTCAGTTGGAATAGTGCCTGACATTGATTTGCCTTTAATAAAAGTGAA
GAATCTTGATTTAAAATCTCAAGTTATTAGCCTAGCACATGGCACTTACTCAAGAATGGA
ATTGACAGTTGCATTTGAACGCACAGTTGGTTATTATATTATTCAAATTTACATTCCATG
CACAATGATTGTAATTATAGCTTGGATAAGTTTCTTCTTGAACAAAAATGCTATGAACAT
TCGTTGTGTGTTGTGCATTGCTGGTTTGCTGTCTTTGATCGTTGAATGCCAAGCTATCAA
TACTTTTATCCCGAAAACTTCTTATTCAAAGGCTTTAGATCTTTACACTGGAATTTGTAT
GACTTTGGTTTTTATTGCTCTTGTTGAATTTGCATTCATTTCAAACACAGAGAGTTTTAA
AAATTCAACCAAAGCACCGTGTGCTGACAAAATTTTCCGCTTTTTATTCCCAATATTCTT
TATTGTTTTCAACATTTTCTATTGGATTTATTATTGA

>g13131.t5 Gene=g13131 Length=165
MWILKVLIVIIFIVSCASAQQNVTKIIDSLTENYDKRLRPNYGKMPVNVGVSAYILGIHS
FSEENMDFTMDFYFRQYWNDPRLQFKKQPGIEYITPGYEFGRTLWFPDTFFVNEKESFLH
TITTKNEFVKIYHNGDVVKSIERHIFMPNEFRSLSNGHSVMCNSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13131.t5 Gene3D G3DSA:2.70.170.10 - 12 150 6.7E-42
2 g13131.t5 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 18 142 1.7E-30
3 g13131.t5 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 18 142 1.7E-30
1 g13131.t5 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 24 141 2.9E-28
9 g13131.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
10 g13131.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
11 g13131.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 14 -
12 g13131.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
8 g13131.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 165 -
14 g13131.t5 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 16 5.0
4 g13131.t5 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 22 142 1.44E-30
6 g13131.t5 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
13 g13131.t5 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 19 -
5 g13131.t5 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -

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