General information for g7163.t1
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.t1 | isoform | g7163.t1 | 21641630 | 21670596 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon1 | 21641630 | 21641794 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS1 | 21641630 | 21641794 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon2 | 21642140 | 21642630 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS2 | 21642140 | 21642630 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon3 | 21642935 | 21643219 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS3 | 21642935 | 21643219 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon4 | 21651387 | 21651524 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS4 | 21651387 | 21651524 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon5 | 21656880 | 21656962 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS5 | 21656880 | 21656962 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon6 | 21657053 | 21657279 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS6 | 21657053 | 21657279 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon7 | 21663949 | 21664016 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS7 | 21663949 | 21664016 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon8 | 21664534 | 21664634 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS8 | 21664534 | 21664634 |
| chr_2 | g7163 | g7163.t1 | exon | g7163.t1.exon9 | 21670484 | 21670596 |
| chr_2 | g7163 | g7163.t1 | cds | g7163.t1.CDS9 | 21670484 | 21670596 |
| chr_2 | g7163 | g7163.t1 | TSS | g7163.t1 | NA | NA |
| chr_2 | g7163 | g7163.t1 | TTS | g7163.t1 | NA | NA |
Sequences
>g7163.t1 Gene=g7163 Length=1671
ATGACTACACACATAGATAACATACAATTGCGAGTGCCATCTGTAGGTGCTCTTCTAGTA
GTCCTAGTATTCTTGCCACATCTTTTTAGCAAAGTACCATATGTGAATGCAGGGAGTGGT
TCTGGCGGAAGTATGCTAGGCGATGTTAATATATCAGCAATTTTAGATTCATTCAGTGTT
AGTTATGATAAAAGAGTAAGACCCAACTACGGAGGACCGCCAGTTGAAGTCGGTGTCACG
ATGTACGTCCTCAGTATCAGCTCGCTATCAGAAGTCAAAATGGACTTTACACTGGATTTT
TACTTTCGTCAATTTTGGACAGATCCTCGATTAGCTTATAGAAAGAGGCCTGGAGTCGAG
CAACTTTCAGTTGGTTCCGATTTCGTTAAGAGTATTTGGGTGCCGGATACATTCTTTGTG
AATGAAAAACAGTCTTACTTTCATATAGCCACAACTAGCAATGAGTTTATTAGAGTTCAC
CATTCAGGTTCAATCACTAGAAGTATGCGATTAACAATTACAGCCTCATGTCCTATGAAT
TTACAATACTTTCCTATGGATCGACAATTGTGTCATATCGAAATCGAAAGTTTTGGCTAC
ACAATGCGAGATATTCGATACTTCTGGAGAGATGGACTGAACTCTGTAGGAATGAGCAGC
GAAGTAGAGCTTCCACAATTTAGAGTACTGGGACACAGGCAGAGGGCGACCGAAATTAAC
CTAACTACAGGAAACTATTCGCGCTTAGCTTGTGAAATCCAGTTTGTTAGATCAATGGGT
TATTATTTAATTCAAATTTATATTCCATCTGGATTAATTGTAATCATATCGTGGGTATCA
TTTTGGCTTAATCGAAATGCAACTCCGGCTCGAGTTGCTCTCGGTGTAACAACTGTATTG
ACAATGACAACACTTATGTCGTCCACAAATGCTGCCTTACCCAAAATATCATACGTTAAA
TCGATTGACGTTTATTTGGGTACATGTTTCGTCATGGTGTTTGCCAGTTTGCTCGAATAT
GCTACGGTTGGTTACATGGCTAAGCGAATTCAAATGCGAAAACAGCGTTTTATGGCAATA
CAAAAAATTGCTGAGCAGAAGAAAATACAAGTGGATAATGCCCAACAGAACAATCCTCCG
AGCGGTGGTGGTAGTGTAGTTGGTGGTCCACCAAGCGAGCATTCGCATTCACATGGACAT
AGCCACTCACATCACCCGCATGTACCAAAACAACAAATGGGCATGGGAAACCGTGGTCCA
CCTGGTATGTCGTTACAAGGTAATGTTGGCTCAAGAGGATGTTCTATAGTTGGCCCCTTA
TTTCAAGAAGTTCGCTTCAAAGTTCACGATCCAAAAGCGCACTCGAAAGGTGGTACACTT
GAGAACACAATTAATGGAGGGCGTGGTGGACAACAACAACAGCAACCGCCACCACCAGCG
CCTGCAGACGAAGAATCAGGTGGTGGCGGCGGAGGACCTCCACAACATTTAATTCATCCA
GGGAAAAATATCAACACACTACTGGGAATTACTCCTTCCGATATCGATAAATATTCACGA
ATTGTGTTCCCCGTTTGTTTTGTATGTTTCAACTTAATGTATTGGATAATTTATTTACAT
GTTAGTGATGTTGTAGCCGATGATTTAGTATTACTCGGCGAAGATAAGTAG
>g7163.t1 Gene=g7163 Length=556
MTTHIDNIQLRVPSVGALLVVLVFLPHLFSKVPYVNAGSGSGGSMLGDVNISAILDSFSV
SYDKRVRPNYGGPPVEVGVTMYVLSISSLSEVKMDFTLDFYFRQFWTDPRLAYRKRPGVE
QLSVGSDFVKSIWVPDTFFVNEKQSYFHIATTSNEFIRVHHSGSITRSMRLTITASCPMN
LQYFPMDRQLCHIEIESFGYTMRDIRYFWRDGLNSVGMSSEVELPQFRVLGHRQRATEIN
LTTGNYSRLACEIQFVRSMGYYLIQIYIPSGLIVIISWVSFWLNRNATPARVALGVTTVL
TMTTLMSSTNAALPKISYVKSIDVYLGTCFVMVFASLLEYATVGYMAKRIQMRKQRFMAI
QKIAEQKKIQVDNAQQNNPPSGGGSVVGGPPSEHSHSHGHSHSHHPHVPKQQMGMGNRGP
PGMSLQGNVGSRGCSIVGPLFQEVRFKVHDPKAHSKGGTLENTINGGRGGQQQQQPPPPA
PADEESGGGGGGPPQHLIHPGKNINTLLGITPSDIDKYSRIVFPVCFVCFNLMYWIIYLH
VSDVVADDLVLLGEDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 31 | g7163.t1 | CDD | cd19008 | LGIC_ECD_GABAR_RDL-like | 75 | 258 | 2.3313E-132 |
| 32 | g7163.t1 | CDD | cd19049 | LGIC_TM_anion | 261 | 358 | 4.72245E-40 |
| 19 | g7163.t1 | Gene3D | G3DSA:2.70.170.10 | - | 45 | 256 | 2.2E-75 |
| 40 | g7163.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 371 | 413 | - |
| 39 | g7163.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 467 | 492 | - |
| 3 | g7163.t1 | PANTHER | PTHR18945 | NEUROTRANSMITTER GATED ION CHANNEL | 49 | 541 | 8.6E-169 |
| 4 | g7163.t1 | PANTHER | PTHR18945:SF856 | GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA | 49 | 541 | 8.6E-169 |
| 12 | g7163.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 97 | 113 | 1.2E-12 |
| 7 | g7163.t1 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 110 | 124 | 5.0E-15 |
| 10 | g7163.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 131 | 142 | 1.2E-12 |
| 11 | g7163.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 177 | 191 | 1.2E-12 |
| 8 | g7163.t1 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 216 | 229 | 5.0E-15 |
| 9 | g7163.t1 | PRINTS | PR00252 | Neurotransmitter-gated ion channel family signature | 253 | 265 | 1.2E-12 |
| 15 | g7163.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 262 | 282 | 1.5E-42 |
| 14 | g7163.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 288 | 309 | 1.5E-42 |
| 6 | g7163.t1 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 316 | 328 | 5.0E-15 |
| 13 | g7163.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 322 | 343 | 1.5E-42 |
| 5 | g7163.t1 | PRINTS | PR01160 | Gamma-aminobutyric-acid A receptor beta subunit signature | 506 | 520 | 5.0E-15 |
| 16 | g7163.t1 | PRINTS | PR00253 | Gamma-aminobutyric acid A (GABAA) receptor signature | 518 | 538 | 1.5E-42 |
| 1 | g7163.t1 | Pfam | PF02931 | Neurotransmitter-gated ion-channel ligand binding domain | 54 | 250 | 1.3E-49 |
| 2 | g7163.t1 | Pfam | PF02932 | Neurotransmitter-gated ion-channel transmembrane region | 266 | 535 | 8.8E-46 |
| 20 | g7163.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 27 | g7163.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 25 | g7163.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 258 | - |
| 30 | g7163.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 259 | 283 | - |
| 21 | g7163.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 284 | 291 | - |
| 29 | g7163.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 313 | - |
| 24 | g7163.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 314 | 324 | - |
| 26 | g7163.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 325 | 347 | - |
| 22 | g7163.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 348 | 520 | - |
| 28 | g7163.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 521 | 541 | - |
| 23 | g7163.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 542 | 556 | - |
| 38 | g7163.t1 | ProSitePatterns | PS00236 | Neurotransmitter-gated ion-channels signature. | 177 | 191 | - |
| 17 | g7163.t1 | SUPERFAMILY | SSF63712 | Nicotinic receptor ligand binding domain-like | 53 | 258 | 4.71E-56 |
| 18 | g7163.t1 | SUPERFAMILY | SSF90112 | Neurotransmitter-gated ion-channel transmembrane pore | 259 | 547 | 1.14E-55 |
| 41 | g7163.t1 | TIGRFAM | TIGR00860 | LIC: cation transporter family protein | 53 | 379 | 1.7E-114 |
| 34 | g7163.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
| 37 | g7163.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 283 | - |
| 36 | g7163.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 314 | - |
| 33 | g7163.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 324 | 346 | - |
| 35 | g7163.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 521 | 538 | - |
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