General information for g6291.t3
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 g6291 is located on chr_2: 15951313..15982765 (+ 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 | g6291 | g6291.t3 | isoform | g6291.t3 | 15951313 | 15982765 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon1 | 15951313 | 15951466 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS1 | 15951313 | 15951466 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon2 | 15955904 | 15956043 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS2 | 15955904 | 15956043 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon3 | 15958703 | 15958747 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS3 | 15958703 | 15958747 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon4 | 15966394 | 15966503 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS4 | 15966394 | 15966503 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon5 | 15972342 | 15972522 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS5 | 15972342 | 15972522 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon6 | 15974865 | 15974940 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS6 | 15974865 | 15974940 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon7 | 15975686 | 15975730 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS7 | 15975686 | 15975730 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon8 | 15975883 | 15975893 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS8 | 15975883 | 15975893 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon9 | 15976126 | 15976264 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS9 | 15976126 | 15976264 |
| chr_2 | g6291 | g6291.t3 | exon | g6291.t3.exon10 | 15982620 | 15982765 |
| chr_2 | g6291 | g6291.t3 | cds | g6291.t3.CDS10 | 15982620 | 15982765 |
| chr_2 | g6291 | g6291.t3 | TSS | g6291.t3 | NA | NA |
| chr_2 | g6291 | g6291.t3 | TTS | g6291.t3 | NA | NA |
Sequences
>g6291.t3 Gene=g6291 Length=1047
ATGAAGTCTGACCTGAGAAATGTTGATTTTAAAATTTGCAATGAAAAATGTAAACAAAAA
AATGGCAACTTTGAGATGAAATATCTCGATAAATACGCAATTAAATCACTATTCCCTCGA
CCAATCGATGCATTAAAATGTGCTTTATCGATTGATAGTTTACAAGGTTATCACGAGAAG
CGACTTCTCAATAATTTATTGAATAATTATAATTTACTAGAACGACCAGTAGCAAATGAA
TCGGATCCATTAGAAGTAAGATTTGGATTAACGTTACAACAAATTATCGATGTGGATGAG
AAGAATCAGATTCTCACTACGAATGCGTGGTTAAATTTGGAATGGAATGACTACAATTTA
AAGTGGAATGAAACAGAGTATGGAGGTGTAAAAGACTTACGAATAACACCATCGAAGCTT
TGGAAGCCAGATGTCCTTATGTATAATAGTGCGGATGAGGGATTCGATGGAACGTATCAA
ACCAATGTAGTGGTCAAACATAACGGCAGTTGTCTGTACGTGCCCCCTGGCATCTTTAAA
AGCACATGCAAGATAGACATCACGTGGTTCCCCTTTGATGATCAACATTGCGATATGAAG
TTCGGTAGTTGGACTTACGACGGAAATCAGCTTGATTTGGTGCTAAATTCAGACGAAGGA
GGAGACTTATCAGATTTCATTACAAACGGAGAATGGTATCTAATAGGGATGCCAGGAAAA
AAGAATACAATAGTATATGCTTGTTGCCCAGAGCCATACGTGGACATTACATTTACGATA
CAAATACGAAGGCGAACTCTTTATTATTTTTTTAATTTAATCGTACCATGTGTCTTAATT
TCATCAATGGCTCTATTAGGATTTACATTGCCCCCCGATTCGGGTGAAAAGCTCACGTTA
GGAGTCACGATTCTTCTATCACTAACCGTATTTCTCAACTTAGTGGCTGAGACATTACCA
CAAGTGTCTGATGCAATTCCATTGTTAGGTAGCGATGCAATTCTACTCTCTCTTGTCTTG
TTGCAAACAAAAAATTATCAAAAATGA
>g6291.t3 Gene=g6291 Length=348
MKSDLRNVDFKICNEKCKQKNGNFEMKYLDKYAIKSLFPRPIDALKCALSIDSLQGYHEK
RLLNNLLNNYNLLERPVANESDPLEVRFGLTLQQIIDVDEKNQILTTNAWLNLEWNDYNL
KWNETEYGGVKDLRITPSKLWKPDVLMYNSADEGFDGTYQTNVVVKHNGSCLYVPPGIFK
STCKIDITWFPFDDQHCDMKFGSWTYDGNQLDLVLNSDEGGDLSDFITNGEWYLIGMPGK
KNTIVYACCPEPYVDITFTIQIRRRTLYYFFNLIVPCVLISSMALLGFTLPPDSGEKLTL
GVTILLSLTVFLNLVAETLPQVSDAIPLLGSDAILLSLVLLQTKNYQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g6291.t3 | CDD | cd18997 | LGIC_ECD_nAChR | 84 | 265 | 5.58717E-118 |
| 24 | g6291.t3 | CDD | cd19051 | LGIC_TM_cation | 267 | 343 | 1.53173E-35 |
| 16 | g6291.t3 | Gene3D | G3DSA:2.70.170.10 | - | 50 | 271 | 7.3E-94 |
| 15 | g6291.t3 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 272 | 343 | 5.2E-27 |
| 3 | g6291.t3 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 35 | 331 | 2.0E-182 |
| 4 | g6291.t3 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 35 | 331 | 2.0E-182 |
| 9 | g6291.t3 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 93 | 109 | 7.0E-18 |
| 7 | g6291.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 106 | 122 | 1.8E-14 |
| 11 | g6291.t3 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 127 | 141 | 7.0E-18 |
| 6 | g6291.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 139 | 150 | 1.8E-14 |
| 12 | g6291.t3 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 145 | 157 | 7.0E-18 |
| 10 | g6291.t3 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 163 | 181 | 7.0E-18 |
| 5 | g6291.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 183 | 197 | 1.8E-14 |
| 8 | g6291.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 260 | 272 | 1.8E-14 |
| 1 | g6291.t3 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 59 | 266 | 7.0E-77 |
| 2 | g6291.t3 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 273 | 330 | 6.8E-20 |
| 19 | g6291.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 266 | - |
| 23 | g6291.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 267 | 286 | - |
| 17 | g6291.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 287 | 297 | - |
| 22 | g6291.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 316 | - |
| 20 | g6291.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 317 | 321 | - |
| 21 | g6291.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 322 | 341 | - |
| 18 | g6291.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 342 | 348 | - |
| 28 | g6291.t3 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 183 | 197 | - |
| 13 | g6291.t3 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 58 | 265 | 6.02E-74 |
| 14 | g6291.t3 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 266 | 330 | 1.7E-27 |
| 29 | g6291.t3 | TIGRFAM | TIGR00860 | LIC: cation transporter family protein | 58 | 330 | 5.0E-97 |
| 26 | g6291.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 267 | 289 | - |
| 27 | g6291.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 299 | 316 | - |
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.
