General information for g7163.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Gamma-aminobutyric acid receptor subunit beta.
Parent gene
- The parent gene g7163 is located on chr_2: 21670596..21671820 (- 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 | g7163 | g7163.t3 | isoform | g7163.t3 | 21641630 | 21670596 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon1 | 21641630 | 21641794 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS1 | 21641630 | 21641794 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon2 | 21642140 | 21642630 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS2 | 21642140 | 21642630 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon3 | 21642935 | 21643219 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS3 | 21642935 | 21643219 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon4 | 21650289 | 21650426 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS4 | 21650289 | 21650426 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon5 | 21651387 | 21651524 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS5 | 21651387 | 21651524 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon6 | 21656880 | 21656962 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS6 | 21656880 | 21656962 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon7 | 21657053 | 21657279 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS7 | 21657053 | 21657279 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon8 | 21663949 | 21664016 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS8 | 21663949 | 21664016 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon9 | 21664534 | 21664634 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS9 | 21664534 | 21664634 |
| chr_2 | g7163 | g7163.t3 | exon | g7163.t3.exon10 | 21670484 | 21670596 |
| chr_2 | g7163 | g7163.t3 | cds | g7163.t3.CDS10 | 21670484 | 21670596 |
| chr_2 | g7163 | g7163.t3 | TSS | g7163.t3 | NA | NA |
| chr_2 | g7163 | g7163.t3 | TTS | g7163.t3 | NA | NA |
Sequences
>g7163.t3 Gene=g7163 Length=1809
ATGACTACACACATAGATAACATACAATTGCGAGTGCCATCTGTAGGTGCTCTTCTAGTA
GTCCTAGTATTCTTGCCACATCTTTTTAGCAAAGTACCATATGTGAATGCAGGGAGTGGT
TCTGGCGGAAGTATGCTAGGCGATGTTAATATATCAGCAATTTTAGATTCATTCAGTGTT
AGTTATGATAAAAGAGTAAGACCCAACTACGGAGGACCGCCAGTTGAAGTCGGTGTCACG
ATGTACGTCCTCAGTATCAGCTCGCTATCAGAAGTCAAAATGGACTTTACACTGGATTTT
TACTTTCGTCAATTTTGGACAGATCCTCGATTAGCTTATAGAAAGAGGCCTGGAGTCGAG
CAACTTTCAGTTGGTTCCGATTTCGTTAAGAGTATTTGGGTGCCGGATACATTCTTTGTG
AATGAAAAACAGTCTTACTTTCATATAGCCACAACTAGCAATGAGTTTATTAGAGTTCAC
CATTCAGGTTCAATCACTAGAAGTATGCGATTAACAATTACAGCCTCATGTCCTATGAAT
TTACAATACTTTCCTATGGATCGACAATTGTGTCATATCGAAATCGAAAGTTTTGGCTAC
ACAATGCGAGATATTCGATACTTCTGGAGAGATGGACTGAACTCTGTAGGAATGAGCAGC
GAAGTAGAGCTTCCACAATTTAGAGTACTGGGACACAGGCAGAGGGCGACCGAAATTAAC
CTAACTACAGTCGGATATACAATGAGAGATATCCGCTATAAATGGAATGAAGGTCCAAAT
TCCGTTGGAGTATCAGAAGATGTATCTCTACCGCAATTTAAGGTATTGGGGCATCGCCAA
CGAGCTATGGAAATCAGTCTCACAACAGGAAACTATTCGCGCTTAGCTTGTGAAATCCAG
TTTGTTAGATCAATGGGTTATTATTTAATTCAAATTTATATTCCATCTGGATTAATTGTA
ATCATATCGTGGGTATCATTTTGGCTTAATCGAAATGCAACTCCGGCTCGAGTTGCTCTC
GGTGTAACAACTGTATTGACAATGACAACACTTATGTCGTCCACAAATGCTGCCTTACCC
AAAATATCATACGTTAAATCGATTGACGTTTATTTGGGTACATGTTTCGTCATGGTGTTT
GCCAGTTTGCTCGAATATGCTACGGTTGGTTACATGGCTAAGCGAATTCAAATGCGAAAA
CAGCGTTTTATGGCAATACAAAAAATTGCTGAGCAGAAGAAAATACAAGTGGATAATGCC
CAACAGAACAATCCTCCGAGCGGTGGTGGTAGTGTAGTTGGTGGTCCACCAAGCGAGCAT
TCGCATTCACATGGACATAGCCACTCACATCACCCGCATGTACCAAAACAACAAATGGGC
ATGGGAAACCGTGGTCCACCTGGTATGTCGTTACAAGGTAATGTTGGCTCAAGAGGATGT
TCTATAGTTGGCCCCTTATTTCAAGAAGTTCGCTTCAAAGTTCACGATCCAAAAGCGCAC
TCGAAAGGTGGTACACTTGAGAACACAATTAATGGAGGGCGTGGTGGACAACAACAACAG
CAACCGCCACCACCAGCGCCTGCAGACGAAGAATCAGGTGGTGGCGGCGGAGGACCTCCA
CAACATTTAATTCATCCAGGGAAAAATATCAACACACTACTGGGAATTACTCCTTCCGAT
ATCGATAAATATTCACGAATTGTGTTCCCCGTTTGTTTTGTATGTTTCAACTTAATGTAT
TGGATAATTTATTTACATGTTAGTGATGTTGTAGCCGATGATTTAGTATTACTCGGCGAA
GATAAGTAG
>g7163.t3 Gene=g7163 Length=602
MTTHIDNIQLRVPSVGALLVVLVFLPHLFSKVPYVNAGSGSGGSMLGDVNISAILDSFSV
SYDKRVRPNYGGPPVEVGVTMYVLSISSLSEVKMDFTLDFYFRQFWTDPRLAYRKRPGVE
QLSVGSDFVKSIWVPDTFFVNEKQSYFHIATTSNEFIRVHHSGSITRSMRLTITASCPMN
LQYFPMDRQLCHIEIESFGYTMRDIRYFWRDGLNSVGMSSEVELPQFRVLGHRQRATEIN
LTTVGYTMRDIRYKWNEGPNSVGVSEDVSLPQFKVLGHRQRAMEISLTTGNYSRLACEIQ
FVRSMGYYLIQIYIPSGLIVIISWVSFWLNRNATPARVALGVTTVLTMTTLMSSTNAALP
KISYVKSIDVYLGTCFVMVFASLLEYATVGYMAKRIQMRKQRFMAIQKIAEQKKIQVDNA
QQNNPPSGGGSVVGGPPSEHSHSHGHSHSHHPHVPKQQMGMGNRGPPGMSLQGNVGSRGC
SIVGPLFQEVRFKVHDPKAHSKGGTLENTINGGRGGQQQQQPPPPAPADEESGGGGGGPP
QHLIHPGKNINTLLGITPSDIDKYSRIVFPVCFVCFNLMYWIIYLHVSDVVADDLVLLGE
DK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 33 | g7163.t3 | CDD | cd19008 | LGIC_ECD_GABAR_RDL-like | 75 | 304 | 5.58729E-125 |
| 34 | g7163.t3 | CDD | cd19049 | LGIC_TM_anion | 307 | 404 | 4.07625E-40 |
| 21 | g7163.t3 | Gene3D | G3DSA:2.70.170.10 | - | 45 | 238 | 7.7E-70 |
| 20 | g7163.t3 | Gene3D | G3DSA:2.70.170.10 | - | 239 | 302 | 6.3E-10 |
| 42 | g7163.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 417 | 459 | - |
| 41 | g7163.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 513 | 538 | - |
| 3 | g7163.t3 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 49 | 243 | 2.0E-177 |
| 5 | g7163.t3 | PANTHER | PTHR18945:SF856 | GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA | 49 | 243 | 2.0E-177 |
| 4 | g7163.t3 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 239 | 587 | 2.0E-177 |
| 6 | g7163.t3 | PANTHER | PTHR18945:SF856 | GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA | 239 | 587 | 2.0E-177 |
| 13 | g7163.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 97 | 113 | 1.6E-12 |
| 7 | g7163.t3 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 110 | 124 | 1.9E-8 |
| 10 | g7163.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 131 | 142 | 1.6E-12 |
| 12 | g7163.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 177 | 191 | 1.6E-12 |
| 8 | g7163.t3 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 216 | 229 | 1.9E-8 |
| 11 | g7163.t3 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 299 | 311 | 1.6E-12 |
| 15 | g7163.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 308 | 328 | 1.9E-42 |
| 17 | g7163.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 334 | 355 | 1.9E-42 |
| 16 | g7163.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 368 | 389 | 1.9E-42 |
| 9 | g7163.t3 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 552 | 566 | 1.9E-8 |
| 14 | g7163.t3 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 564 | 584 | 1.9E-42 |
| 1 | g7163.t3 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 54 | 231 | 7.7E-49 |
| 2 | g7163.t3 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 312 | 581 | 1.1E-45 |
| 22 | g7163.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 29 | g7163.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 25 | g7163.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 304 | - |
| 28 | g7163.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 329 | - |
| 23 | g7163.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 330 | 337 | - |
| 31 | g7163.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 359 | - |
| 27 | g7163.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 360 | 370 | - |
| 32 | g7163.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 393 | - |
| 24 | g7163.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 394 | 566 | - |
| 30 | g7163.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 567 | 587 | - |
| 26 | g7163.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 588 | 602 | - |
| 40 | g7163.t3 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 177 | 191 | - |
| 18 | g7163.t3 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 53 | 238 | 9.29E-53 |
| 19 | g7163.t3 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 305 | 593 | 1.31E-55 |
| 35 | g7163.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
| 38 | g7163.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 307 | 329 | - |
| 37 | g7163.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 360 | - |
| 39 | g7163.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 370 | 392 | - |
| 36 | g7163.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 567 | 584 | - |
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:0016020 | membrane | CC |
| GO:0005230 | extracellular ligand-gated ion channel activity | MF |
| GO:0034220 | ion transmembrane transport | BP |
| GO:0006811 | ion transport | BP |
| GO:0005216 | ion channel activity | MF |
| GO:0004888 | transmembrane signaling receptor activity | MF |
| GO:0004890 | GABA-A receptor activity | MF |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K05181 (gamma-aminobutyric acid receptor subunit beta)
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