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 g5603 g5603.t2 isoform g5603.t2 10518407 10545885
chr_2 g5603 g5603.t2 exon g5603.t2.exon1 10518407 10518566
chr_2 g5603 g5603.t2 cds g5603.t2.CDS1 10518407 10518566
chr_2 g5603 g5603.t2 exon g5603.t2.exon2 10528774 10528913
chr_2 g5603 g5603.t2 cds g5603.t2.CDS2 10528774 10528913
chr_2 g5603 g5603.t2 exon g5603.t2.exon3 10530174 10530218
chr_2 g5603 g5603.t2 cds g5603.t2.CDS3 10530174 10530218
chr_2 g5603 g5603.t2 exon g5603.t2.exon4 10531056 10531165
chr_2 g5603 g5603.t2 cds g5603.t2.CDS4 10531056 10531165
chr_2 g5603 g5603.t2 exon g5603.t2.exon5 10531276 10531407
chr_2 g5603 g5603.t2 cds g5603.t2.CDS5 10531276 10531407
chr_2 g5603 g5603.t2 exon g5603.t2.exon6 10531481 10531529
chr_2 g5603 g5603.t2 cds g5603.t2.CDS6 10531481 10531529
chr_2 g5603 g5603.t2 exon g5603.t2.exon7 10531857 10531904
chr_2 g5603 g5603.t2 cds g5603.t2.CDS7 10531857 10531904
chr_2 g5603 g5603.t2 exon g5603.t2.exon8 10532071 10532098
chr_2 g5603 g5603.t2 cds g5603.t2.CDS8 10532071 10532098
chr_2 g5603 g5603.t2 exon g5603.t2.exon9 10537561 10537605
chr_2 g5603 g5603.t2 cds g5603.t2.CDS9 10537561 10537605
chr_2 g5603 g5603.t2 exon g5603.t2.exon10 10537707 10537717
chr_2 g5603 g5603.t2 cds g5603.t2.CDS10 10537707 10537717
chr_2 g5603 g5603.t2 exon g5603.t2.exon11 10537952 10538090
chr_2 g5603 g5603.t2 cds g5603.t2.CDS11 10537952 10538090
chr_2 g5603 g5603.t2 exon g5603.t2.exon12 10538153 10538239
chr_2 g5603 g5603.t2 cds g5603.t2.CDS12 10538153 10538239
chr_2 g5603 g5603.t2 exon g5603.t2.exon13 10541275 10541384
chr_2 g5603 g5603.t2 cds g5603.t2.CDS13 10541275 10541384
chr_2 g5603 g5603.t2 exon g5603.t2.exon14 10544408 10544553
chr_2 g5603 g5603.t2 cds g5603.t2.CDS14 10544408 10544553
chr_2 g5603 g5603.t2 exon g5603.t2.exon15 10544688 10544813
chr_2 g5603 g5603.t2 cds g5603.t2.CDS15 10544688 10544813
chr_2 g5603 g5603.t2 exon g5603.t2.exon16 10545097 10545238
chr_2 g5603 g5603.t2 cds g5603.t2.CDS16 10545097 10545238
chr_2 g5603 g5603.t2 exon g5603.t2.exon17 10545733 10545885
chr_2 g5603 g5603.t2 cds g5603.t2.CDS17 10545733 10545885
chr_2 g5603 g5603.t2 TTS g5603.t2 10545988 10545988
chr_2 g5603 g5603.t2 TSS g5603.t2 NA NA

Sequences

>g5603.t2 Gene=g5603 Length=1671
ATGTTATCGCTAATAGTAAATAATAATTCGTTCAAAAATGTTGGAAAAATCAAATGTTTC
AGTAAATTTAATGTAAAATTTCAACAAATACACACCGACAACTTAATCGTATTAATCAAA
TGGATTACTTTGCTCATTTTTGTCACAACAGCGCCATTATTATGTTCAGCGGGATATAAT
GAAAAGCGATTACTACACGATCTTCTAGACCCTTACAATACGCTCGAACGACCAGTAGTG
AATGAATCCGATCCACTTCAAATAAGTTTTGGCTTAATGTTAATGCAAATCATCGATGTG
GACGAAAAGAATCAGTTGCTAGTAACAAATATTTGGTTAAAACTAGAATGGAATGATATG
AACTTGCGATGGAATGCAACAGAGTATGGCGGTGTAAAAGACCTTCGGATACCGCCACAT
CGAATATGGAAGCCAGATGTTCTCATGTACAATAGTGCTGACGAAGGATTTGATGGCACA
TATCCGACAAATGTTGTTGTTCGCAGTAATGGTTCATGCTTATATGTACCTCCCGGTATT
TTCAAGTCAACATGTAAAATTGATATTACGTGGTTTCCATTCGATGACCAACGTTGTGAG
ATGAAATTTGGCAGTTGGACATATGATGGATTTCAGCTCGATCTTCAACTGCAAGATGAA
GCGGGTGGTGATATTTCTAGCTTTGTTACGAATGGTGAATGGGATTTACTAGGTGTACCG
GGTAAAAGAAATGAGATCTATTACAATTGTTGTCCAGAGCCGTACGTGGACATCACATTC
GCTATAATCATAAGACGACGAACGTTGTACTATTTTTTTAATTTAATCGTCCCATGTGTA
CTGATTGCTTCTATGGCATTATTGGGATTTACATTGCCCCCCGATTCGGGTGAAAAACTA
TCATTAGGCGTAACAATTTTACTATCATTAACTGTATTTTTAAATATGGTCGCTGAGACA
ATGCCGGCAACATCCGATGCCGTTCCATTATTAGGTACATATTTCAATTGCATAATGTTC
ATGGTTGCCTCGTCAGTCGTCTCAACAATTTTAATATTAAATTACCATCATAGAAACGCC
GATACACATGAAATGTCTGATTGGGTGAAAATTGTTTTTCTGTACTGGCTGCCTTGTATT
CTTCGAATGAATCGACCTGAACGAGTTGCAATGGAATATCCACCAACACCGACGTCGGAT
GCGTCGGAACGTAAAGCGACAAATATTCAGGATGTTGAACTGAGAGAACGATCTTCAAAG
TCACTTTTAGCTAATGTACTAGACATCGATGATGATTTTCGGCATAATTGTAGACCGTTA
ACTCCTGGAGGTACACTGCCACATTCCAATCCACCTTATTTTAGAACTGTTTATAGACAT
GATGACAATTGTAGTATTGGCACAATTGGCGGTACTCGAATGCCTGATGCAATTGCACCG
CATGCCTGCAGTTTCACATCATCGGCAGACTACGAATTGGCACTGATATTGAAAGAAATA
CGATTTATAACGGATCAAATACGAAAAGAGGACGATGAATCGGGAGTGGCGAAAGATTGG
AAATATGCTGCTATGGTCGTTGATAGACTGTGCCTTATTATTTTTACATTCTTCACAATA
GTCGCTACGATCGCAGTACTAATGTCCGCTCCACATATCATCGTTTCGTAG

>g5603.t2 Gene=g5603 Length=556
MLSLIVNNNSFKNVGKIKCFSKFNVKFQQIHTDNLIVLIKWITLLIFVTTAPLLCSAGYN
EKRLLHDLLDPYNTLERPVVNESDPLQISFGLMLMQIIDVDEKNQLLVTNIWLKLEWNDM
NLRWNATEYGGVKDLRIPPHRIWKPDVLMYNSADEGFDGTYPTNVVVRSNGSCLYVPPGI
FKSTCKIDITWFPFDDQRCEMKFGSWTYDGFQLDLQLQDEAGGDISSFVTNGEWDLLGVP
GKRNEIYYNCCPEPYVDITFAIIIRRRTLYYFFNLIVPCVLIASMALLGFTLPPDSGEKL
SLGVTILLSLTVFLNMVAETMPATSDAVPLLGTYFNCIMFMVASSVVSTILILNYHHRNA
DTHEMSDWVKIVFLYWLPCILRMNRPERVAMEYPPTPTSDASERKATNIQDVELRERSSK
SLLANVLDIDDDFRHNCRPLTPGGTLPHSNPPYFRTVYRHDDNCSIGTIGGTRMPDAIAP
HACSFTSSADYELALILKEIRFITDQIRKEDDESGVAKDWKYAAMVVDRLCLIIFTFFTI
VATIAVLMSAPHIIVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g5603.t2 CDD cd18997 LGIC_ECD_nAChR 86 267 2.26895E-113
31 g5603.t2 CDD cd19051 LGIC_TM_cation 269 358 4.73576E-45
17 g5603.t2 Gene3D G3DSA:2.70.170.10 - 55 273 7.1E-91
15 g5603.t2 Gene3D G3DSA:1.20.58.390 Glr4197 protein 274 376 2.4E-43
16 g5603.t2 Gene3D G3DSA:1.20.58.390 Glr4197 protein 484 556 7.4E-13
3 g5603.t2 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 36 546 0.0
4 g5603.t2 PANTHER PTHR18945:SF825 NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B 36 546 0.0
10 g5603.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 95 111 1.2E-17
7 g5603.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 108 124 1.3E-13
12 g5603.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 129 143 1.2E-17
6 g5603.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 141 152 1.3E-13
11 g5603.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 147 159 1.2E-17
9 g5603.t2 PRINTS PR00254 Nicotinic acetylcholine receptor signature 165 183 1.2E-17
8 g5603.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 185 199 1.3E-13
5 g5603.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 262 274 1.3E-13
1 g5603.t2 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 61 268 3.3E-73
2 g5603.t2 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 275 546 1.2E-56
22 g5603.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 34 -
27 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 55 -
20 g5603.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 56 268 -
28 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 269 288 -
23 g5603.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 289 299 -
25 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 300 318 -
19 g5603.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 319 329 -
26 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 330 353 -
21 g5603.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 354 364 -
30 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 365 381 -
18 g5603.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 382 529 -
29 g5603.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 530 554 -
24 g5603.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 555 556 -
37 g5603.t2 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 185 199 -
13 g5603.t2 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 60 267 2.09E-72
14 g5603.t2 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 268 555 2.62E-75
38 g5603.t2 TIGRFAM TIGR00860 LIC: cation transporter family protein 56 549 1.9E-119
36 g5603.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 35 57 -
33 g5603.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 270 292 -
35 g5603.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 331 353 -
34 g5603.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 532 554 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5603/g5603.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5603.t2.fa.iupred3.txt does not exist

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

Pathway

This gene does not belong to any 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