Gene loci information

Transcript annotation

  • This transcript has been annotated as Neuronal acetylcholine receptor subunit alpha-7.

Parent gene

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.t2 isoform g6291.t2 15951313 15977517
chr_2 g6291 g6291.t2 exon g6291.t2.exon1 15951313 15951466
chr_2 g6291 g6291.t2 cds g6291.t2.CDS1 15951313 15951466
chr_2 g6291 g6291.t2 exon g6291.t2.exon2 15955904 15956043
chr_2 g6291 g6291.t2 cds g6291.t2.CDS2 15955904 15956043
chr_2 g6291 g6291.t2 exon g6291.t2.exon3 15958703 15958747
chr_2 g6291 g6291.t2 cds g6291.t2.CDS3 15958703 15958747
chr_2 g6291 g6291.t2 exon g6291.t2.exon4 15966394 15966503
chr_2 g6291 g6291.t2 cds g6291.t2.CDS4 15966394 15966503
chr_2 g6291 g6291.t2 exon g6291.t2.exon5 15972342 15972522
chr_2 g6291 g6291.t2 cds g6291.t2.CDS5 15972342 15972522
chr_2 g6291 g6291.t2 exon g6291.t2.exon6 15974865 15974940
chr_2 g6291 g6291.t2 cds g6291.t2.CDS6 15974865 15974940
chr_2 g6291 g6291.t2 exon g6291.t2.exon7 15975686 15975730
chr_2 g6291 g6291.t2 cds g6291.t2.CDS7 15975686 15975730
chr_2 g6291 g6291.t2 exon g6291.t2.exon8 15975883 15975893
chr_2 g6291 g6291.t2 cds g6291.t2.CDS8 15975883 15975893
chr_2 g6291 g6291.t2 exon g6291.t2.exon9 15976126 15976264
chr_2 g6291 g6291.t2 cds g6291.t2.CDS9 15976126 15976264
chr_2 g6291 g6291.t2 exon g6291.t2.exon10 15977369 15977517
chr_2 g6291 g6291.t2 cds g6291.t2.CDS10 15977369 15977517
chr_2 g6291 g6291.t2 TSS g6291.t2 NA NA
chr_2 g6291 g6291.t2 TTS g6291.t2 NA NA

Sequences

>g6291.t2 Gene=g6291 Length=1050
ATGAAGTCTGACCTGAGAAATGTTGATTTTAAAATTTGCAATGAAAAATGTAAACAAAAA
AATGGCAACTTTGAGATGAAATATCTCGATAAATACGCAATTAAATCACTATTCCCTCGA
CCAATCGATGCATTAAAATGTGCTTTATCGATTGATAGTTTACAAGGTTATCACGAGAAG
CGACTTCTCAATAATTTATTGAATAATTATAATTTACTAGAACGACCAGTAGCAAATGAA
TCGGATCCATTAGAAGTAAGATTTGGATTAACGTTACAACAAATTATCGATGTGGATGAG
AAGAATCAGATTCTCACTACGAATGCGTGGTTAAATTTGGAATGGAATGACTACAATTTA
AAGTGGAATGAAACAGAGTATGGAGGTGTAAAAGACTTACGAATAACACCATCGAAGCTT
TGGAAGCCAGATGTCCTTATGTATAATAGTGCGGATGAGGGATTCGATGGAACGTATCAA
ACCAATGTAGTGGTCAAACATAACGGCAGTTGTCTGTACGTGCCCCCTGGCATCTTTAAA
AGCACATGCAAGATAGACATCACGTGGTTCCCCTTTGATGATCAACATTGCGATATGAAG
TTCGGTAGTTGGACTTACGACGGAAATCAGCTTGATTTGGTGCTAAATTCAGACGAAGGA
GGAGACTTATCAGATTTCATTACAAACGGAGAATGGTATCTAATAGGGATGCCAGGAAAA
AAGAATACAATAGTATATGCTTGTTGCCCAGAGCCATACGTGGACATTACATTTACGATA
CAAATACGAAGGCGAACTCTTTATTATTTTTTTAATTTAATCGTACCATGTGTCTTAATT
TCATCAATGGCTCTATTAGGATTTACATTGCCCCCCGATTCGGGTGAAAAGCTCACGTTA
GGCGTTACGATTCTTCTGTCGTTAACCGTATTTTTAAACTTAGTGGCAGAATCAATGCCA
ACGACATCCGATGCTGTTCCACTAATAGGTATATCTAGCAAAATAACACCCAAGAAATTC
TTTAAACACATGTATAGCTTGCCAAAATAA

>g6291.t2 Gene=g6291 Length=349
MKSDLRNVDFKICNEKCKQKNGNFEMKYLDKYAIKSLFPRPIDALKCALSIDSLQGYHEK
RLLNNLLNNYNLLERPVANESDPLEVRFGLTLQQIIDVDEKNQILTTNAWLNLEWNDYNL
KWNETEYGGVKDLRITPSKLWKPDVLMYNSADEGFDGTYQTNVVVKHNGSCLYVPPGIFK
STCKIDITWFPFDDQHCDMKFGSWTYDGNQLDLVLNSDEGGDLSDFITNGEWYLIGMPGK
KNTIVYACCPEPYVDITFTIQIRRRTLYYFFNLIVPCVLISSMALLGFTLPPDSGEKLTL
GVTILLSLTVFLNLVAESMPTTSDAVPLIGISSKITPKKFFKHMYSLPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g6291.t2 CDD cd18997 LGIC_ECD_nAChR 84 265 9.06801E-118
22 g6291.t2 CDD cd19051 LGIC_TM_cation 267 331 3.03445E-38
16 g6291.t2 Gene3D G3DSA:2.70.170.10 - 50 271 7.3E-94
15 g6291.t2 Gene3D G3DSA:1.20.58.390 Glr4197 protein 272 341 1.0E-28
3 g6291.t2 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 35 330 1.3E-183
4 g6291.t2 PANTHER PTHR18945:SF825 NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B 35 330 1.3E-183
9 g6291.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 93 109 7.1E-18
7 g6291.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 106 122 1.8E-14
11 g6291.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 127 141 7.1E-18
6 g6291.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 139 150 1.8E-14
12 g6291.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 145 157 7.1E-18
10 g6291.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 163 181 7.1E-18
5 g6291.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 183 197 1.8E-14
8 g6291.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 260 272 1.8E-14
1 g6291.t2 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 59 266 7.1E-77
2 g6291.t2 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 273 330 2.4E-20
18 g6291.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 266 -
21 g6291.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 267 286 -
19 g6291.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 287 297 -
20 g6291.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 298 316 -
17 g6291.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 317 349 -
26 g6291.t2 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 183 197 -
13 g6291.t2 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 58 265 6.02E-74
14 g6291.t2 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 266 331 1.06E-28
27 g6291.t2 TIGRFAM TIGR00860 LIC: cation transporter family protein 58 331 6.2E-98
24 g6291.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 267 289 -
25 g6291.t2 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. There were no conditions that were differentially expressed