General information for g5603.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 g5603 is located on chr_2: 10518407..10545885 (+ 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 | g5603 | g5603.t1 | isoform | g5603.t1 | 10518407 | 10545885 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon1 | 10518407 | 10518566 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS1 | 10518407 | 10518566 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon2 | 10528774 | 10528913 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS2 | 10528774 | 10528913 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon3 | 10530174 | 10530218 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS3 | 10530174 | 10530218 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon4 | 10531056 | 10531165 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS4 | 10531056 | 10531165 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon5 | 10531276 | 10531407 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS5 | 10531276 | 10531407 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon6 | 10531481 | 10531529 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS6 | 10531481 | 10531529 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon7 | 10531857 | 10531904 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS7 | 10531857 | 10531904 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon8 | 10532071 | 10532098 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS8 | 10532071 | 10532098 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon9 | 10537561 | 10537605 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS9 | 10537561 | 10537605 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon10 | 10537707 | 10537717 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS10 | 10537707 | 10537717 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon11 | 10537952 | 10538090 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS11 | 10537952 | 10538090 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon12 | 10538153 | 10538239 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS12 | 10538153 | 10538239 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon13 | 10541275 | 10541384 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS13 | 10541275 | 10541384 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon14 | 10544408 | 10544553 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS14 | 10544408 | 10544553 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon15 | 10544688 | 10544767 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS15 | 10544688 | 10544767 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon16 | 10545039 | 10545238 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS16 | 10545039 | 10545238 |
| chr_2 | g5603 | g5603.t1 | exon | g5603.t1.exon17 | 10545733 | 10545885 |
| chr_2 | g5603 | g5603.t1 | cds | g5603.t1.CDS17 | 10545733 | 10545885 |
| chr_2 | g5603 | g5603.t1 | TTS | g5603.t1 | 10545988 | 10545988 |
| chr_2 | g5603 | g5603.t1 | TSS | g5603.t1 | NA | NA |
Sequences
>g5603.t1 Gene=g5603 Length=1683
ATGTTATCGCTAATAGTAAATAATAATTCGTTCAAAAATGTTGGAAAAATCAAATGTTTC
AGTAAATTTAATGTAAAATTTCAACAAATACACACCGACAACTTAATCGTATTAATCAAA
TGGATTACTTTGCTCATTTTTGTCACAACAGCGCCATTATTATGTTCAGCGGGATATAAT
GAAAAGCGATTACTACACGATCTTCTAGACCCTTACAATACGCTCGAACGACCAGTAGTG
AATGAATCCGATCCACTTCAAATAAGTTTTGGCTTAATGTTAATGCAAATCATCGATGTG
GACGAAAAGAATCAGTTGCTAGTAACAAATATTTGGTTAAAACTAGAATGGAATGATATG
AACTTGCGATGGAATGCAACAGAGTATGGCGGTGTAAAAGACCTTCGGATACCGCCACAT
CGAATATGGAAGCCAGATGTTCTCATGTACAATAGTGCTGACGAAGGATTTGATGGCACA
TATCCGACAAATGTTGTTGTTCGCAGTAATGGTTCATGCTTATATGTACCTCCCGGTATT
TTCAAGTCAACATGTAAAATTGATATTACGTGGTTTCCATTCGATGACCAACGTTGTGAG
ATGAAATTTGGCAGTTGGACATATGATGGATTTCAGCTCGATCTTCAACTGCAAGATGAA
GCGGGTGGTGATATTTCTAGCTTTGTTACGAATGGTGAATGGGATTTACTAGGTGTACCG
GGTAAAAGAAATGAGATCTATTACAATTGTTGTCCAGAGCCGTACGTGGACATCACATTC
GCTATAATCATAAGACGACGAACGTTGTACTATTTTTTTAATTTAATCGTCCCATGTGTA
CTGATTGCTTCTATGGCATTATTGGGATTTACATTGCCCCCCGATTCGGGTGAAAAACTA
TCATTAGGCGTAACAATTTTACTATCATTAACTGTATTTTTAAATATGGTCGCTGAGACA
ATGCCGGCAACATCCGATGCCGTTCCATTATTAGGTACATATTTCAATTGCATAATGTTC
ATGGTTGCCTCGTCAGTCGTCTCAACAATTTTAATATTAAATTACCATCATAGAAACGCC
GATACACATGAAATGTCTGATTGGGTGAAAATTGTTTTTCTGTACTGGCTGCCTTGTATT
CTTCGAATGAATCGACCTGAACGAGTTGCAATGGAATATCCACCAACACCGACGTCGGAT
GCGTCGGAACGTAAAGCGACAAATATTCAGGATGTTGAACTGAGAGAACGATCTTCAAAG
TCACTTTTAGCTAATGTACTAGACATCGATGATGATTTTCGGCATAATTGTAGACCGTTA
ACTCCTGGAGCAGACAAACTAAGTCAATCTCTAAATGTTCTGGTACTTCCTTTACCTCCT
TCTTCCAGACATGATGACAATTGTAGTATTGGCACAATTGGCGGTACTCGAATGCCTGAT
GCAATTGCACCGCATGCCTGCAGTTTCACATCATCGGCAGACTACGAATTGGCACTGATA
TTGAAAGAAATACGATTTATAACGGATCAAATACGAAAAGAGGACGATGAATCGGGAGTG
GCGAAAGATTGGAAATATGCTGCTATGGTCGTTGATAGACTGTGCCTTATTATTTTTACA
TTCTTCACAATAGTCGCTACGATCGCAGTACTAATGTCCGCTCCACATATCATCGTTTCG
TAG
>g5603.t1 Gene=g5603 Length=560
MLSLIVNNNSFKNVGKIKCFSKFNVKFQQIHTDNLIVLIKWITLLIFVTTAPLLCSAGYN
EKRLLHDLLDPYNTLERPVVNESDPLQISFGLMLMQIIDVDEKNQLLVTNIWLKLEWNDM
NLRWNATEYGGVKDLRIPPHRIWKPDVLMYNSADEGFDGTYPTNVVVRSNGSCLYVPPGI
FKSTCKIDITWFPFDDQRCEMKFGSWTYDGFQLDLQLQDEAGGDISSFVTNGEWDLLGVP
GKRNEIYYNCCPEPYVDITFAIIIRRRTLYYFFNLIVPCVLIASMALLGFTLPPDSGEKL
SLGVTILLSLTVFLNMVAETMPATSDAVPLLGTYFNCIMFMVASSVVSTILILNYHHRNA
DTHEMSDWVKIVFLYWLPCILRMNRPERVAMEYPPTPTSDASERKATNIQDVELRERSSK
SLLANVLDIDDDFRHNCRPLTPGADKLSQSLNVLVLPLPPSSRHDDNCSIGTIGGTRMPD
AIAPHACSFTSSADYELALILKEIRFITDQIRKEDDESGVAKDWKYAAMVVDRLCLIIFT
FFTIVATIAVLMSAPHIIVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 32 | g5603.t1 | CDD | cd18997 | LGIC_ECD_nAChR | 86 | 267 | 1.37998E-113 |
| 31 | g5603.t1 | CDD | cd19051 | LGIC_TM_cation | 269 | 358 | 8.30725E-45 |
| 17 | g5603.t1 | Gene3D | G3DSA:2.70.170.10 | - | 55 | 273 | 7.2E-91 |
| 16 | g5603.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 274 | 376 | 2.4E-43 |
| 15 | g5603.t1 | Gene3D | G3DSA:1.20.58.390 | Glr4197 protein | 488 | 560 | 7.5E-13 |
| 3 | g5603.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 36 | 550 | 0.0 |
| 4 | g5603.t1 | PANTHER | PTHR18945:SF825 | NICOTINIC ACETYLCHOLINE RECEPTOR ALPHA5, ISOFORM B | 36 | 550 | 0.0 |
| 10 | g5603.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 95 | 111 | 1.2E-17 |
| 7 | g5603.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 108 | 124 | 1.4E-13 |
| 12 | g5603.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 129 | 143 | 1.2E-17 |
| 6 | g5603.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 141 | 152 | 1.4E-13 |
| 11 | g5603.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 147 | 159 | 1.2E-17 |
| 9 | g5603.t1 | PRINTS | PR00254 | Nicotinic acetylcholine receptor signature | 165 | 183 | 1.2E-17 |
| 8 | g5603.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 185 | 199 | 1.4E-13 |
| 5 | g5603.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 262 | 274 | 1.4E-13 |
| 1 | g5603.t1 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 61 | 268 | 3.4E-73 |
| 2 | g5603.t1 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 275 | 550 | 1.1E-56 |
| 22 | g5603.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 34 | - |
| 27 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 55 | - |
| 20 | g5603.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 56 | 268 | - |
| 28 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 269 | 288 | - |
| 24 | g5603.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 289 | 299 | - |
| 25 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 300 | 318 | - |
| 18 | g5603.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 319 | 329 | - |
| 26 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 330 | 353 | - |
| 21 | g5603.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 354 | 364 | - |
| 30 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 381 | - |
| 19 | g5603.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 382 | 533 | - |
| 29 | g5603.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 534 | 558 | - |
| 23 | g5603.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 559 | 560 | - |
| 37 | g5603.t1 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 185 | 199 | - |
| 13 | g5603.t1 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 60 | 267 | 2.09E-72 |
| 14 | g5603.t1 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 268 | 559 | 1.96E-75 |
| 38 | g5603.t1 | TIGRFAM | TIGR00860 | LIC: cation transporter family protein | 56 | 553 | 1.6E-119 |
| 36 | g5603.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 57 | - |
| 34 | g5603.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 270 | 292 | - |
| 35 | g5603.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 353 | - |
| 33 | g5603.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 536 | 558 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5603/g5603.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5603.t1.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
- This transcript has been annotated with K05312 (nicotinic acetylcholine receptor, invertebrate)
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