Gene loci information

Transcript annotation

  • This transcript has been annotated as Gamma-aminobutyric acid receptor subunit beta.

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 g7163 g7163.t2 isoform g7163.t2 21641630 21670596
chr_2 g7163 g7163.t2 exon g7163.t2.exon1 21641630 21641794
chr_2 g7163 g7163.t2 cds g7163.t2.CDS1 21641630 21641794
chr_2 g7163 g7163.t2 exon g7163.t2.exon2 21642140 21642630
chr_2 g7163 g7163.t2 cds g7163.t2.CDS2 21642140 21642630
chr_2 g7163 g7163.t2 exon g7163.t2.exon3 21642935 21643219
chr_2 g7163 g7163.t2 cds g7163.t2.CDS3 21642935 21643219
chr_2 g7163 g7163.t2 exon g7163.t2.exon4 21650289 21650426
chr_2 g7163 g7163.t2 cds g7163.t2.CDS4 21650289 21650426
chr_2 g7163 g7163.t2 exon g7163.t2.exon5 21656880 21656962
chr_2 g7163 g7163.t2 cds g7163.t2.CDS5 21656880 21656962
chr_2 g7163 g7163.t2 exon g7163.t2.exon6 21657053 21657279
chr_2 g7163 g7163.t2 cds g7163.t2.CDS6 21657053 21657279
chr_2 g7163 g7163.t2 exon g7163.t2.exon7 21663949 21664016
chr_2 g7163 g7163.t2 cds g7163.t2.CDS7 21663949 21664016
chr_2 g7163 g7163.t2 exon g7163.t2.exon8 21664534 21664634
chr_2 g7163 g7163.t2 cds g7163.t2.CDS8 21664534 21664634
chr_2 g7163 g7163.t2 exon g7163.t2.exon9 21670484 21670596
chr_2 g7163 g7163.t2 cds g7163.t2.CDS9 21670484 21670596
chr_2 g7163 g7163.t2 TSS g7163.t2 NA NA
chr_2 g7163 g7163.t2 TTS g7163.t2 NA NA

Sequences

>g7163.t2 Gene=g7163 Length=1671
ATGACTACACACATAGATAACATACAATTGCGAGTGCCATCTGTAGGTGCTCTTCTAGTA
GTCCTAGTATTCTTGCCACATCTTTTTAGCAAAGTACCATATGTGAATGCAGGGAGTGGT
TCTGGCGGAAGTATGCTAGGCGATGTTAATATATCAGCAATTTTAGATTCATTCAGTGTT
AGTTATGATAAAAGAGTAAGACCCAACTACGGAGGACCGCCAGTTGAAGTCGGTGTCACG
ATGTACGTCCTCAGTATCAGCTCGCTATCAGAAGTCAAAATGGACTTTACACTGGATTTT
TACTTTCGTCAATTTTGGACAGATCCTCGATTAGCTTATAGAAAGAGGCCTGGAGTCGAG
CAACTTTCAGTTGGTTCCGATTTCGTTAAGAGTATTTGGGTGCCGGATACATTCTTTGTG
AATGAAAAACAGTCTTACTTTCATATAGCCACAACTAGCAATGAGTTTATTAGAGTTCAC
CATTCAGGTTCAATCACTAGAAGTATGCGATTAACAATTACAGCCTCATGTCCTATGAAT
TTACAATACTTTCCTATGGATCGACAATTGTGTCATATCGAAATCGAAAGTTTCGGATAT
ACAATGAGAGATATCCGCTATAAATGGAATGAAGGTCCAAATTCCGTTGGAGTATCAGAA
GATGTATCTCTACCGCAATTTAAGGTATTGGGGCATCGCCAACGAGCTATGGAAATCAGT
CTCACAACAGGAAACTATTCGCGCTTAGCTTGTGAAATCCAGTTTGTTAGATCAATGGGT
TATTATTTAATTCAAATTTATATTCCATCTGGATTAATTGTAATCATATCGTGGGTATCA
TTTTGGCTTAATCGAAATGCAACTCCGGCTCGAGTTGCTCTCGGTGTAACAACTGTATTG
ACAATGACAACACTTATGTCGTCCACAAATGCTGCCTTACCCAAAATATCATACGTTAAA
TCGATTGACGTTTATTTGGGTACATGTTTCGTCATGGTGTTTGCCAGTTTGCTCGAATAT
GCTACGGTTGGTTACATGGCTAAGCGAATTCAAATGCGAAAACAGCGTTTTATGGCAATA
CAAAAAATTGCTGAGCAGAAGAAAATACAAGTGGATAATGCCCAACAGAACAATCCTCCG
AGCGGTGGTGGTAGTGTAGTTGGTGGTCCACCAAGCGAGCATTCGCATTCACATGGACAT
AGCCACTCACATCACCCGCATGTACCAAAACAACAAATGGGCATGGGAAACCGTGGTCCA
CCTGGTATGTCGTTACAAGGTAATGTTGGCTCAAGAGGATGTTCTATAGTTGGCCCCTTA
TTTCAAGAAGTTCGCTTCAAAGTTCACGATCCAAAAGCGCACTCGAAAGGTGGTACACTT
GAGAACACAATTAATGGAGGGCGTGGTGGACAACAACAACAGCAACCGCCACCACCAGCG
CCTGCAGACGAAGAATCAGGTGGTGGCGGCGGAGGACCTCCACAACATTTAATTCATCCA
GGGAAAAATATCAACACACTACTGGGAATTACTCCTTCCGATATCGATAAATATTCACGA
ATTGTGTTCCCCGTTTGTTTTGTATGTTTCAACTTAATGTATTGGATAATTTATTTACAT
GTTAGTGATGTTGTAGCCGATGATTTAGTATTACTCGGCGAAGATAAGTAG

>g7163.t2 Gene=g7163 Length=556
MTTHIDNIQLRVPSVGALLVVLVFLPHLFSKVPYVNAGSGSGGSMLGDVNISAILDSFSV
SYDKRVRPNYGGPPVEVGVTMYVLSISSLSEVKMDFTLDFYFRQFWTDPRLAYRKRPGVE
QLSVGSDFVKSIWVPDTFFVNEKQSYFHIATTSNEFIRVHHSGSITRSMRLTITASCPMN
LQYFPMDRQLCHIEIESFGYTMRDIRYKWNEGPNSVGVSEDVSLPQFKVLGHRQRAMEIS
LTTGNYSRLACEIQFVRSMGYYLIQIYIPSGLIVIISWVSFWLNRNATPARVALGVTTVL
TMTTLMSSTNAALPKISYVKSIDVYLGTCFVMVFASLLEYATVGYMAKRIQMRKQRFMAI
QKIAEQKKIQVDNAQQNNPPSGGGSVVGGPPSEHSHSHGHSHSHHPHVPKQQMGMGNRGP
PGMSLQGNVGSRGCSIVGPLFQEVRFKVHDPKAHSKGGTLENTINGGRGGQQQQQPPPPA
PADEESGGGGGGPPQHLIHPGKNINTLLGITPSDIDKYSRIVFPVCFVCFNLMYWIIYLH
VSDVVADDLVLLGEDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
31 g7163.t2 CDD cd19008 LGIC_ECD_GABAR_RDL-like 75 258 1.24366E-134
32 g7163.t2 CDD cd19049 LGIC_TM_anion 261 358 3.47344E-40
19 g7163.t2 Gene3D G3DSA:2.70.170.10 - 45 256 1.6E-76
40 g7163.t2 MobiDBLite mobidb-lite consensus disorder prediction 371 413 -
39 g7163.t2 MobiDBLite mobidb-lite consensus disorder prediction 467 492 -
3 g7163.t2 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 49 541 1.4E-170
4 g7163.t2 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 49 541 1.4E-170
12 g7163.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 97 113 1.2E-12
7 g7163.t2 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 110 124 3.7E-14
10 g7163.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 131 142 1.2E-12
11 g7163.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 177 191 1.2E-12
8 g7163.t2 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 216 229 3.7E-14
9 g7163.t2 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 253 265 1.2E-12
15 g7163.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 262 282 1.5E-42
14 g7163.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 288 309 1.5E-42
6 g7163.t2 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 316 328 3.7E-14
13 g7163.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 322 343 1.5E-42
5 g7163.t2 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 506 520 3.7E-14
16 g7163.t2 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 518 538 1.5E-42
1 g7163.t2 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 54 249 3.4E-50
2 g7163.t2 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 266 535 8.8E-46
20 g7163.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
27 g7163.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
25 g7163.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 258 -
30 g7163.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 283 -
21 g7163.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 284 291 -
29 g7163.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 292 313 -
24 g7163.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 314 324 -
26 g7163.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 325 347 -
22 g7163.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 348 520 -
28 g7163.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 521 541 -
23 g7163.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 542 556 -
38 g7163.t2 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 177 191 -
17 g7163.t2 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 53 258 3.01E-56
18 g7163.t2 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 259 547 1.14E-55
41 g7163.t2 TIGRFAM TIGR00860 LIC: cation transporter family protein 53 379 2.7E-116
34 g7163.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
37 g7163.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 261 283 -
36 g7163.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 292 314 -
33 g7163.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 324 346 -
35 g7163.t2 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

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