General information for g13131.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Gamma-aminobutyric acid receptor subunit beta.
Parent gene
- The parent gene g13131 is located on chr_1: 28117606..28118803 (+ strand)
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.t3 | TSS | g13131.t3 | 28117161 | 28117161 |
| chr_1 | g13131 | g13131.t3 | isoform | g13131.t3 | 28117241 | 28118803 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon1 | 28117241 | 28117293 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon2 | 28117441 | 28117517 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon3 | 28117607 | 28117908 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon4 | 28117991 | 28118073 |
| chr_1 | g13131 | g13131.t3 | cds | g13131.t3.CDS1 | 28118016 | 28118073 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon5 | 28118135 | 28118272 |
| chr_1 | g13131 | g13131.t3 | cds | g13131.t3.CDS2 | 28118135 | 28118272 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon6 | 28118332 | 28118616 |
| chr_1 | g13131 | g13131.t3 | cds | g13131.t3.CDS3 | 28118332 | 28118616 |
| chr_1 | g13131 | g13131.t3 | exon | g13131.t3.exon7 | 28118673 | 28118803 |
| chr_1 | g13131 | g13131.t3 | cds | g13131.t3.CDS4 | 28118673 | 28118803 |
| chr_1 | g13131 | g13131.t3 | TTS | g13131.t3 | 28118985 | 28118985 |
Sequences
>g13131.t3 Gene=g13131 Length=1069
ATGTGGATACTAAAAGTTTTAATTGTAATAATCTTTATCGTGTCGTGTGCTAGCGCACAG
CAGAATGTGACAAAAATAATTGACTCGCTTACTGAAAACTATGATAAACGTTTGCGTCCA
AATTATGGAAAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCA
TTTTCTGAAGAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGAT
CCACGACTTCAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTT
GGACGAACTCTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCAT
ACGATAACAACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGT
GTAAGGTGAGAAATTGAGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAAT
GGACACTCAGTTATGTGCAATTCCTATTGAGAGCTATGCACATCGTTCAAATGAAATTAC
TTATTACTGGAAAGATGGAAATGATTCAGTTGGAATAGTGCCTGACATTGATTTGCCTTT
AATAAAAGTGAAGAATCTTGATTTAAAATCTCAAGTTATTAGCCTAGCACATGGCACTTA
CTCAAGAATGGAATTGACAGTTGCATTTGAACGCACAGTTGGTTATTATATTATTCAAAT
TTACATTCCATGCACAATGATTGTAATTATAGCTTGGATAAGTTTCTTCTTGAACAAAAA
TGCTATGAACATTCGTTGTGTGTTGTGCATTGCTGGTTTGCTGTCTTTGATCGTTGAATG
CCAAGCTATCAATACTTTTATCCCGAAAACTTCTTATTCAAAGGCTTTAGATCTTTACAC
TGGAATTTGTATGACTTTGGTTTTTATTGCTCTTGTTGAATTTGCATTCATTTCAAACAC
AGAGAGTTTTAAAAATTCAACCAAAGCACCGTGTGCTGACAAAATTTTCCGCTTTTTATT
CCCAATATTCTTTATTGTTTTCAACATTTTCTATTGGATTTATTATTGA
>g13131.t3 Gene=g13131 Length=203
MNFVRYPMDTQLCAIPIESYAHRSNEITYYWKDGNDSVGIVPDIDLPLIKVKNLDLKSQV
ISLAHGTYSRMELTVAFERTVGYYIIQIYIPCTMIVIIAWISFFLNKNAMNIRCVLCIAG
LLSLIVECQAINTFIPKTSYSKALDLYTGICMTLVFIALVEFAFISNTESFKNSTKAPCA
DKIFRFLFPIFFIVFNIFYWIYY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g13131.t3 | CDD | cd19049 | LGIC_TM_anion | 83 | 200 | 2.20896E-37 |
| 11 | g13131.t3 | Gene3D | G3DSA:2.70.170.10 | - | 1 | 78 | 6.9E-16 |
| 10 | g13131.t3 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 79 | 203 | 2.5E-38 |
| 3 | g13131.t3 | PANTHER | PTHR18945:SF853 | GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-LIKE | 1 | 200 | 2.1E-44 |
| 4 | g13131.t3 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 1 | 200 | 2.1E-44 |
| 7 | g13131.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 84 | 104 | 7.5E-23 |
| 6 | g13131.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 144 | 165 | 7.5E-23 |
| 5 | g13131.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 183 | 203 | 7.5E-23 |
| 1 | g13131.t3 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 1 | 47 | 1.2E-6 |
| 2 | g13131.t3 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 88 | 175 | 4.3E-23 |
| 14 | g13131.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 80 | - |
| 19 | g13131.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 105 | - |
| 13 | g13131.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 106 | 111 | - |
| 17 | g13131.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 134 | - |
| 15 | g13131.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 135 | 145 | - |
| 20 | g13131.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 165 | - |
| 12 | g13131.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 166 | 185 | - |
| 18 | g13131.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 202 | - |
| 16 | g13131.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 203 | 203 | - |
| 8 | g13131.t3 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 1 | 79 | 2.88E-11 |
| 9 | g13131.t3 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 82 | 203 | 7.06E-30 |
| 23 | g13131.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 83 | 105 | - |
| 22 | g13131.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 134 | - |
| 25 | g13131.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 144 | 166 | - |
| 24 | g13131.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 202 | - |
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.
