General information for g6292.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Acetylcholine receptor subunit alpha-type acr-16.
Parent gene
- The parent gene g6292 is located on chr_2: 16005376..16006580 (+ 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_2 | g6292 | g6292.t1 | isoform | g6292.t1 | 16005376 | 16006580 |
| chr_2 | g6292 | g6292.t1 | exon | g6292.t1.exon1 | 16005376 | 16005465 |
| chr_2 | g6292 | g6292.t1 | cds | g6292.t1.CDS1 | 16005376 | 16005465 |
| chr_2 | g6292 | g6292.t1 | exon | g6292.t1.exon2 | 16005897 | 16006117 |
| chr_2 | g6292 | g6292.t1 | cds | g6292.t1.CDS2 | 16005897 | 16006117 |
| chr_2 | g6292 | g6292.t1 | exon | g6292.t1.exon3 | 16006184 | 16006357 |
| chr_2 | g6292 | g6292.t1 | cds | g6292.t1.CDS3 | 16006184 | 16006357 |
| chr_2 | g6292 | g6292.t1 | exon | g6292.t1.exon4 | 16006496 | 16006580 |
| chr_2 | g6292 | g6292.t1 | cds | g6292.t1.CDS4 | 16006496 | 16006580 |
| chr_2 | g6292 | g6292.t1 | TSS | g6292.t1 | NA | NA |
| chr_2 | g6292 | g6292.t1 | TTS | g6292.t1 | NA | NA |
Sequences
>g6292.t1 Gene=g6292 Length=570
ATGTTTATGGTTGCATCATCAGTCGTACTGACAGTAGTTGTTTTAAATTATCATCATCGA
ACTGCCGATATTCACGAGATGCCACAATGGATAAAATCGGTGTTTCTTCAATGGCTTCCA
TGGATTTTAAGAATGAGTCGACCGGGTAGAAAAATAACTAGAAAAACAATTATGCTTAGT
AATCGTATGAAAGAGCTCGAGTTGAAAGAGCGTTCATCAAAATCACTGTTAGCTAATGTG
TTAGATATAGACGATGATTTTCGACATGTAAGTGGTATGACTGGTTCAACCACAGCGATA
GGGTCAACGGCATTTACCCGACCCACAACAATAGATGATCACAATTCGATATCAGGAGGT
TGTACGCATAAAGATCTTCATTATATACTTAAGGAATTGCAATTTATTACAAATCGCATG
AAACGGGCAGATGACGAAGCTGAGATAGTCAGCGACTGGAAATTTGCTGCCATGGTCGTA
GACCGATTTTGTCTATTCGTGTTTACGTTATTTACAATAATTGCTACAGTTACCGTTCTA
CTGTCAGCGCCACACATAATCGTTCAATAA
>g6292.t1 Gene=g6292 Length=189
MFMVASSVVLTVVVLNYHHRTADIHEMPQWIKSVFLQWLPWILRMSRPGRKITRKTIMLS
NRMKELELKERSSKSLLANVLDIDDDFRHVSGMTGSTTAIGSTAFTRPTTIDDHNSISGG
CTHKDLHYILKELQFITNRMKRADDEAEIVSDWKFAAMVVDRFCLFVFTLFTIIATVTVL
LSAPHIIVQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6292.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 1 | 48 | 9.2E-8 |
| 9 | g6292.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 116 | 189 | 3.3E-13 |
| 3 | g6292.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 1 | 69 | 1.1E-42 |
| 5 | g6292.t1 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 1 | 69 | 1.1E-42 |
| 2 | g6292.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 94 | 179 | 1.1E-42 |
| 4 | g6292.t1 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 94 | 179 | 1.1E-42 |
| 1 | g6292.t1 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 1 | 179 | 4.2E-28 |
| 13 | g6292.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 14 | g6292.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g6292.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 18 | g6292.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 12 | g6292.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 29 | - |
| 17 | g6292.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 46 | - |
| 10 | g6292.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 47 | 162 | - |
| 16 | g6292.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 163 | 187 | - |
| 11 | g6292.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 188 | 189 | - |
| 7 | g6292.t1 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 1 | 188 | 1.02E-38 |
| 6 | g6292.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 187 | - |
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: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