General information for g13491.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 g13491 is located on chr_1: 30472800..30491860 (+ 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 | g13491 | g13491.t1 | isoform | g13491.t1 | 30472800 | 30491860 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon1 | 30472800 | 30472823 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS1 | 30472800 | 30472823 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon2 | 30479197 | 30479244 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS2 | 30479197 | 30479244 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon3 | 30479316 | 30479343 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS3 | 30479316 | 30479343 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon4 | 30483316 | 30483360 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS4 | 30483316 | 30483360 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon5 | 30483423 | 30483572 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS5 | 30483423 | 30483572 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon6 | 30486266 | 30486321 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS6 | 30486266 | 30486321 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon7 | 30486449 | 30486479 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS7 | 30486449 | 30486479 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon8 | 30487133 | 30487242 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS8 | 30487133 | 30487242 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon9 | 30488252 | 30488391 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS9 | 30488252 | 30488391 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon10 | 30489145 | 30489418 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS10 | 30489145 | 30489418 |
| chr_1 | g13491 | g13491.t1 | exon | g13491.t1.exon11 | 30491711 | 30491860 |
| chr_1 | g13491 | g13491.t1 | cds | g13491.t1.CDS11 | 30491711 | 30491860 |
| chr_1 | g13491 | g13491.t1 | TSS | g13491.t1 | NA | NA |
| chr_1 | g13491 | g13491.t1 | TTS | g13491.t1 | NA | NA |
Sequences
>g13491.t1 Gene=g13491 Length=1056
ATGCAAAGTAAGTCTCGAAATATACTAGATGTTCAGTTACAAGACGAAGCTGGTGGTGAT
ATTAGCAGTTTTATAACGAATGGTGAATGGGAATTATTGGGAGTGCCTGGACAAAGAAAT
GAAATTTATTATAATTGCTGTCCTGAGCCTTATATTGATATAACATTCGCAATATTGATT
CGACGTAAAACATTATACTATTTCTTCAACTTGATTGTGCCATGTGTCTTGATCGCATCA
ATGGCATTGTTGGGTTTCACATTGCCTCCTGACAGCGGTGAAAAACTGTCTTTAGGAGTT
ACAATTCTTTTGTCTCTTACCGTCTTCCTTAACATGGTGGCTGAAACAATGCCGGCCACT
TCTGATGCTGTGCCTCTTTTAGGAACGTATTTCAATTGCATTATGTTCATGGTTGCGTCG
TCAGTAGTTTCAACAATTTTAATATTAAATTATCATCATCGTAATTCTGATACACATGAA
ATGTCCGACTGGGTTCGAGTGGTTTTTCTCTATTGGCTACCATGTATTCTTCGAATGTCG
CGTCCTGGCCAAGAATCTTACGAATGTGGACCAGTTCCGATTGGGAATAATGAAAAAGCA
AACCAAATGAGCGAAGTTGAGCTACGAGAACGGTCATCAAAATCACTGTTAGCAAATGTT
CTCGATATTGATGATGACTTCCGATGCAATCATCGTTGTAACACATTGCCACATAATCCC
ACATACTATCGTACAGTATACAGACAAGGTGAGGATGGAAGTCTTGGGCCGGTTGGTGGT
GGACAAATGCCTCCTCCAACTGTTGGTGGTCGACTGCATGAAACCGTCTCGCATACATGT
TTGAGCTCATCAGCTGAATATGAACTAGCACTGATACTGAAAGAGCTACGAGTTATAACT
GATGCGTTACGAGATGAAGATCAGAAAAGTGAAGTAACAAAGGACTGGAGATTTGCAGCG
ATGGTAGTTGACCGACTGTGCCTTATCATATTTACATTATTTACAATAATTTCAACGGTA
GCAGTCTTATTTAGTGCACCCAATTTTCTCCTTTAA
>g13491.t1 Gene=g13491 Length=351
MQSKSRNILDVQLQDEAGGDISSFITNGEWELLGVPGQRNEIYYNCCPEPYIDITFAILI
RRKTLYYFFNLIVPCVLIASMALLGFTLPPDSGEKLSLGVTILLSLTVFLNMVAETMPAT
SDAVPLLGTYFNCIMFMVASSVVSTILILNYHHRNSDTHEMSDWVRVVFLYWLPCILRMS
RPGQESYECGPVPIGNNEKANQMSEVELRERSSKSLLANVLDIDDDFRCNHRCNTLPHNP
TYYRTVYRQGEDGSLGPVGGGQMPPPTVGGRLHETVSHTCLSSSAEYELALILKELRVIT
DALRDEDQKSEVTKDWRFAAMVVDRLCLIIFTLFTIISTVAVLFSAPNFLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g13491.t1 | CDD | cd19051 | LGIC_TM_cation | 65 | 154 | 2.64253E-46 |
| 12 | g13491.t1 | Gene3D | G3DSA:2.70.170.10 | - | 2 | 64 | 7.6E-16 |
| 10 | g13491.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 65 | 182 | 1.1E-45 |
| 11 | g13491.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 275 | 350 | 1.1E-11 |
| 3 | g13491.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 9 | 342 | 3.7E-168 |
| 4 | g13491.t1 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 9 | 342 | 3.7E-168 |
| 1 | g13491.t1 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 13 | 64 | 3.1E-7 |
| 2 | g13491.t1 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 71 | 342 | 4.2E-59 |
| 14 | g13491.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 64 | - |
| 22 | g13491.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 84 | - |
| 17 | g13491.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 95 | - |
| 21 | g13491.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 114 | - |
| 15 | g13491.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 115 | 125 | - |
| 23 | g13491.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 149 | - |
| 18 | g13491.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 150 | 160 | - |
| 19 | g13491.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 161 | 177 | - |
| 13 | g13491.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 178 | 325 | - |
| 20 | g13491.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 346 | - |
| 16 | g13491.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 347 | 351 | - |
| 8 | g13491.t1 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 6 | 63 | 5.75E-11 |
| 9 | g13491.t1 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 64 | 349 | 1.26E-77 |
| 5 | g13491.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 6 | g13491.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 149 | - |
| 7 | g13491.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 348 | - |
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 transcript has been annotated with K04809 (nicotinic acetylcholine receptor alpha-7)
Pathway
- This transcript belongs to the following pathways
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