General information for g13489.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neuronal acetylcholine receptor subunit alpha-7.
Parent gene
- The parent gene g13489 is located on chr_1: 30426186..30441361 (+ 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 | g13489 | g13489.t1 | isoform | g13489.t1 | 30426186 | 30441361 |
| chr_1 | g13489 | g13489.t1 | exon | g13489.t1.exon1 | 30426186 | 30426261 |
| chr_1 | g13489 | g13489.t1 | cds | g13489.t1.CDS1 | 30426186 | 30426261 |
| chr_1 | g13489 | g13489.t1 | exon | g13489.t1.exon2 | 30427122 | 30427261 |
| chr_1 | g13489 | g13489.t1 | cds | g13489.t1.CDS2 | 30427122 | 30427261 |
| chr_1 | g13489 | g13489.t1 | exon | g13489.t1.exon3 | 30438765 | 30438809 |
| chr_1 | g13489 | g13489.t1 | cds | g13489.t1.CDS3 | 30438765 | 30438809 |
| chr_1 | g13489 | g13489.t1 | exon | g13489.t1.exon4 | 30440316 | 30440425 |
| chr_1 | g13489 | g13489.t1 | cds | g13489.t1.CDS4 | 30440316 | 30440425 |
| chr_1 | g13489 | g13489.t1 | exon | g13489.t1.exon5 | 30441166 | 30441361 |
| chr_1 | g13489 | g13489.t1 | cds | g13489.t1.CDS5 | 30441166 | 30441361 |
| chr_1 | g13489 | g13489.t1 | TSS | g13489.t1 | NA | NA |
| chr_1 | g13489 | g13489.t1 | TTS | g13489.t1 | NA | NA |
Sequences
>g13489.t1 Gene=g13489 Length=567
ATGCCCGCGATACCTTCAACCTTCTCTACAACACTCTTTTATGGAATAAGTTTACTTTTG
TCTATTCTTCCTATTGCTACTCATGCTGGTTCACATGAAAAACGTTTACTTCATCATCTG
TTAGATTCTTACAATGTCCTTGAACGACCTGTAATGAATGAATCAGATCCATTGCAGCTG
AGTTTTGGATTGACTTTAATGCAAATCATTGATGTTGATGAAAAAAATCAACTTCTTATC
ACAAATATATGGCTTAAGCTGGAATGGAATGATATGAATTTAAGATGGAATGCAAGTGAT
TTTGGCGGTGTAAAAGACCTTCGGATACCGCCTCATCGATTATGGAAGCCAGATGTTCTC
ATGTACAATAGTGCGGACGAGGGATTCGATGGAACATATCCAACAAACGTGGTCGTTCGT
AGTAATGGCTCATGCCTTTACGTTCCACCTGGTATTTTTAAATCAACTTGCAAAATTGAT
ATAACATGGTTTCCATTCGATGATCAACGCTGTGAAATGAAATTCGGCAGTTGGACATAC
GATGGCTTTCAGGTAAGAGAAAAATAA
>g13489.t1 Gene=g13489 Length=188
MPAIPSTFSTTLFYGISLLLSILPIATHAGSHEKRLLHHLLDSYNVLERPVMNESDPLQL
SFGLTLMQIIDVDEKNQLLITNIWLKLEWNDMNLRWNASDFGGVKDLRIPPHRLWKPDVL
MYNSADEGFDGTYPTNVVVRSNGSCLYVPPGIFKSTCKIDITWFPFDDQRCEMKFGSWTY
DGFQVREK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g13489.t1 | CDD | cd18997 | LGIC_ECD_nAChR | 61 | 185 | 6.23578E-83 |
| 13 | g13489.t1 | Gene3D | G3DSA:2.70.170.10 | - | 25 | 188 | 2.3E-67 |
| 2 | g13489.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 19 | 185 | 8.8E-122 |
| 3 | g13489.t1 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 19 | 185 | 8.8E-122 |
| 10 | g13489.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 67 | 83 | 2.4E-18 |
| 4 | g13489.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 80 | 96 | 3.1E-10 |
| 7 | g13489.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 101 | 115 | 2.4E-18 |
| 5 | g13489.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 113 | 124 | 3.1E-10 |
| 9 | g13489.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 119 | 131 | 2.4E-18 |
| 8 | g13489.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 137 | 155 | 2.4E-18 |
| 6 | g13489.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 157 | 171 | 3.1E-10 |
| 1 | g13489.t1 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 33 | 186 | 2.7E-59 |
| 15 | g13489.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 16 | g13489.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 30 | - |
| 14 | g13489.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 31 | 188 | - |
| 19 | g13489.t1 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 157 | 171 | - |
| 11 | g13489.t1 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 32 | 186 | 1.7E-55 |
| 12 | g13489.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 29 | - |
| 18 | g13489.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 31 | - |
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:0034220 | ion transmembrane transport | BP |
| GO:0006811 | ion transport | BP |
| GO:0022848 | acetylcholine-gated cation-selective channel activity | MF |
| GO:0005216 | ion channel activity | MF |
| GO:0004888 | transmembrane signaling receptor activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0045211 | postsynaptic membrane | CC |
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