General information for g13131.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g13131.t1 | 28117161 | 28117161 |
| chr_1 | g13131 | g13131.t1 | isoform | g13131.t1 | 28117241 | 28118803 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon1 | 28117241 | 28117293 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS1 | 28117241 | 28117293 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon2 | 28117441 | 28117517 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS2 | 28117441 | 28117517 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon3 | 28117607 | 28117901 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS3 | 28117607 | 28117901 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon4 | 28117991 | 28118073 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS4 | 28117991 | 28118073 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon5 | 28118135 | 28118272 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS5 | 28118135 | 28118272 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon6 | 28118332 | 28118616 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS6 | 28118332 | 28118616 |
| chr_1 | g13131 | g13131.t1 | exon | g13131.t1.exon7 | 28118673 | 28118803 |
| chr_1 | g13131 | g13131.t1 | cds | g13131.t1.CDS7 | 28118673 | 28118803 |
| chr_1 | g13131 | g13131.t1 | TTS | g13131.t1 | 28118985 | 28118985 |
Sequences
>g13131.t1 Gene=g13131 Length=1062
ATGTGGATACTAAAAGTTTTAATTGTAATAATCTTTATCGTGTCGTGTGCTAGCGCACAG
CAGAATGTGACAAAAATAATTGACTCGCTTACTGAAAACTATGATAAACGTTTGCGTCCA
AATTATGGAAAAATGCCAGTGAATGTCGGTGTATCAGCATACATTTTGGGAATTCATTCA
TTTTCTGAAGAAAATATGGATTTTACAATGGACTTTTATTTTCGTCAATATTGGAATGAT
CCACGACTTCAATTTAAGAAACAACCAGGAATTGAATATATCACACCAGGTTATGAATTT
GGACGAACTCTTTGGTTTCCTGATACATTTTTTGTCAATGAAAAAGAATCATTTTTGCAT
ACGATAACAACAAAAAATGAATTTGTGAAAATTTATCATAATGGTGATGTTGTTAAGAGT
GTAAGATTGAGCGTCACATTTTCATGCCCAATGAATTTCGTTCGTTATCCAATGGACACT
CAGTTATGTGCAATTCCTATTGAGAGCTATGCACATCGTTCAAATGAAATTACTTATTAC
TGGAAAGATGGAAATGATTCAGTTGGAATAGTGCCTGACATTGATTTGCCTTTAATAAAA
GTGAAGAATCTTGATTTAAAATCTCAAGTTATTAGCCTAGCACATGGCACTTACTCAAGA
ATGGAATTGACAGTTGCATTTGAACGCACAGTTGGTTATTATATTATTCAAATTTACATT
CCATGCACAATGATTGTAATTATAGCTTGGATAAGTTTCTTCTTGAACAAAAATGCTATG
AACATTCGTTGTGTGTTGTGCATTGCTGGTTTGCTGTCTTTGATCGTTGAATGCCAAGCT
ATCAATACTTTTATCCCGAAAACTTCTTATTCAAAGGCTTTAGATCTTTACACTGGAATT
TGTATGACTTTGGTTTTTATTGCTCTTGTTGAATTTGCATTCATTTCAAACACAGAGAGT
TTTAAAAATTCAACCAAAGCACCGTGTGCTGACAAAATTTTCCGCTTTTTATTCCCAATA
TTCTTTATTGTTTTCAACATTTTCTATTGGATTTATTATTGA
>g13131.t1 Gene=g13131 Length=353
MWILKVLIVIIFIVSCASAQQNVTKIIDSLTENYDKRLRPNYGKMPVNVGVSAYILGIHS
FSEENMDFTMDFYFRQYWNDPRLQFKKQPGIEYITPGYEFGRTLWFPDTFFVNEKESFLH
TITTKNEFVKIYHNGDVVKSVRLSVTFSCPMNFVRYPMDTQLCAIPIESYAHRSNEITYY
WKDGNDSVGIVPDIDLPLIKVKNLDLKSQVISLAHGTYSRMELTVAFERTVGYYIIQIYI
PCTMIVIIAWISFFLNKNAMNIRCVLCIAGLLSLIVECQAINTFIPKTSYSKALDLYTGI
CMTLVFIALVEFAFISNTESFKNSTKAPCADKIFRFLFPIFFIVFNIFYWIYY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 31 | g13131.t1 | CDD | cd19049 | LGIC_TM_anion | 233 | 350 | 1.31119E-37 |
| 17 | g13131.t1 | Gene3D | G3DSA:2.70.170.10 | - | 12 | 228 | 3.8E-70 |
| 16 | g13131.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 229 | 353 | 9.8E-38 |
| 3 | g13131.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 18 | 318 | 3.8E-88 |
| 4 | g13131.t1 | PANTHER | PTHR18945:SF856 | GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA | 18 | 318 | 3.8E-88 |
| 5 | g13131.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 69 | 85 | 1.1E-11 |
| 7 | g13131.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 103 | 114 | 1.1E-11 |
| 8 | g13131.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 149 | 163 | 1.1E-11 |
| 6 | g13131.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 225 | 237 | 1.1E-11 |
| 11 | g13131.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 234 | 254 | 2.8E-22 |
| 9 | g13131.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 294 | 315 | 2.8E-22 |
| 10 | g13131.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 333 | 353 | 2.8E-22 |
| 1 | g13131.t1 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 24 | 197 | 1.0E-45 |
| 2 | g13131.t1 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 238 | 325 | 1.3E-22 |
| 23 | g13131.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 24 | g13131.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 25 | g13131.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 14 | - |
| 30 | g13131.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 21 | g13131.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 230 | - |
| 29 | g13131.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 255 | - |
| 18 | g13131.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 256 | 261 | - |
| 28 | g13131.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 262 | 284 | - |
| 22 | g13131.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 285 | 295 | - |
| 27 | g13131.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 296 | 315 | - |
| 19 | g13131.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 316 | 335 | - |
| 26 | g13131.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 352 | - |
| 20 | g13131.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 353 | 353 | - |
| 37 | g13131.t1 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 149 | 163 | - |
| 39 | g13131.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 16 | 5.0 |
| 12 | g13131.t1 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 22 | 229 | 4.84E-51 |
| 13 | g13131.t1 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 232 | 353 | 1.57E-29 |
| 15 | g13131.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 32 | g13131.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 14 | g13131.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 38 | g13131.t1 | TIGRFAM | TIGR00860 | LIC: cation transporter family protein | 6 | 320 | 5.8E-93 |
| 36 | g13131.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 255 | - |
| 34 | g13131.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 262 | 284 | - |
| 33 | g13131.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 294 | 316 | - |
| 35 | g13131.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 352 | - |
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.
