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.t4 isoform g7163.t4 21641630 21670596
chr_2 g7163 g7163.t4 exon g7163.t4.exon1 21641630 21641794
chr_2 g7163 g7163.t4 cds g7163.t4.CDS1 21641630 21641794
chr_2 g7163 g7163.t4 exon g7163.t4.exon2 21642140 21642630
chr_2 g7163 g7163.t4 cds g7163.t4.CDS2 21642140 21642630
chr_2 g7163 g7163.t4 exon g7163.t4.exon3 21642935 21643219
chr_2 g7163 g7163.t4 cds g7163.t4.CDS3 21642935 21643219
chr_2 g7163 g7163.t4 exon g7163.t4.exon4 21650289 21650426
chr_2 g7163 g7163.t4 cds g7163.t4.CDS4 21650289 21650426
chr_2 g7163 g7163.t4 exon g7163.t4.exon5 21656880 21656962
chr_2 g7163 g7163.t4 cds g7163.t4.CDS5 21656880 21656962
chr_2 g7163 g7163.t4 exon g7163.t4.exon6 21657053 21657279
chr_2 g7163 g7163.t4 cds g7163.t4.CDS6 21657053 21657279
chr_2 g7163 g7163.t4 exon g7163.t4.exon7 21661268 21661483
chr_2 g7163 g7163.t4 cds g7163.t4.CDS7 21661268 21661483
chr_2 g7163 g7163.t4 exon g7163.t4.exon8 21663949 21664016
chr_2 g7163 g7163.t4 cds g7163.t4.CDS8 21663949 21664016
chr_2 g7163 g7163.t4 exon g7163.t4.exon9 21664534 21664634
chr_2 g7163 g7163.t4 cds g7163.t4.CDS9 21664534 21664634
chr_2 g7163 g7163.t4 exon g7163.t4.exon10 21670484 21670596
chr_2 g7163 g7163.t4 cds g7163.t4.CDS10 21670484 21670596
chr_2 g7163 g7163.t4 TSS g7163.t4 NA NA
chr_2 g7163 g7163.t4 TTS g7163.t4 NA NA

Sequences

>g7163.t4 Gene=g7163 Length=1887
ATGACTACACACATAGATAACATACAATTGCGAGTGCCATCTGTAGGTGCTCTTCTAGTA
GTCCTAGTATTCTTGCCACATCTTTTTAGCAAAGTACCATATGTGAATGCAGGGAGTGGT
TCTGGCGGAAGTATGCTAGGCGATGTTAATATATCAGCAATTTTAGATTCATTCAGTGTT
AGTTATGATAAAAGAGTAAGACCCAACTACGGAGGACCGCCAGTTGAAGTCGGTGTCACG
ATGTACGTCCTCAGTATCAGCTCGCTATCAGAAGTCAAAATGAAAAAATGTTGGAGAAAA
AGTACTGTCCGAGAGGAATTGCGAATGAAAAAGGACGTTAATAAGACGCTCTTTCATCTG
CAATTCCAATTCGCACGACACAAAGTAAAACTTTTAACAGGATTTAGTTTCAAATTTAAT
AACTTTTCAGGACCGCCTGTAACTGTCGGTGTCACCATGTACGTCCTCAGTATAAGTTCC
GTGTCTGAAGTTCTCATGGACTTTACACTGGATTTTTACTTTCGTCAATTTTGGACAGAT
CCTCGATTAGCTTATAGAAAGAGGCCTGGAGTCGAGCAACTTTCAGTTGGTTCCGATTTC
GTTAAGAGTATTTGGGTGCCGGATACATTCTTTGTGAATGAAAAACAGTCTTACTTTCAT
ATAGCCACAACTAGCAATGAGTTTATTAGAGTTCACCATTCAGGTTCAATCACTAGAAGT
ATGCGATTAACAATTACAGCCTCATGTCCTATGAATTTACAATACTTTCCTATGGATCGA
CAATTGTGTCATATCGAAATCGAAAGTTTCGGATATACAATGAGAGATATCCGCTATAAA
TGGAATGAAGGTCCAAATTCCGTTGGAGTATCAGAAGATGTATCTCTACCGCAATTTAAG
GTATTGGGGCATCGCCAACGAGCTATGGAAATCAGTCTCACAACAGGAAACTATTCGCGC
TTAGCTTGTGAAATCCAGTTTGTTAGATCAATGGGTTATTATTTAATTCAAATTTATATT
CCATCTGGATTAATTGTAATCATATCGTGGGTATCATTTTGGCTTAATCGAAATGCAACT
CCGGCTCGAGTTGCTCTCGGTGTAACAACTGTATTGACAATGACAACACTTATGTCGTCC
ACAAATGCTGCCTTACCCAAAATATCATACGTTAAATCGATTGACGTTTATTTGGGTACA
TGTTTCGTCATGGTGTTTGCCAGTTTGCTCGAATATGCTACGGTTGGTTACATGGCTAAG
CGAATTCAAATGCGAAAACAGCGTTTTATGGCAATACAAAAAATTGCTGAGCAGAAGAAA
ATACAAGTGGATAATGCCCAACAGAACAATCCTCCGAGCGGTGGTGGTAGTGTAGTTGGT
GGTCCACCAAGCGAGCATTCGCATTCACATGGACATAGCCACTCACATCACCCGCATGTA
CCAAAACAACAAATGGGCATGGGAAACCGTGGTCCACCTGGTATGTCGTTACAAGGTAAT
GTTGGCTCAAGAGGATGTTCTATAGTTGGCCCCTTATTTCAAGAAGTTCGCTTCAAAGTT
CACGATCCAAAAGCGCACTCGAAAGGTGGTACACTTGAGAACACAATTAATGGAGGGCGT
GGTGGACAACAACAACAGCAACCGCCACCACCAGCGCCTGCAGACGAAGAATCAGGTGGT
GGCGGCGGAGGACCTCCACAACATTTAATTCATCCAGGGAAAAATATCAACACACTACTG
GGAATTACTCCTTCCGATATCGATAAATATTCACGAATTGTGTTCCCCGTTTGTTTTGTA
TGTTTCAACTTAATGTATTGGATAATTTATTTACATGTTAGTGATGTTGTAGCCGATGAT
TTAGTATTACTCGGCGAAGATAAGTAG

>g7163.t4 Gene=g7163 Length=628
MTTHIDNIQLRVPSVGALLVVLVFLPHLFSKVPYVNAGSGSGGSMLGDVNISAILDSFSV
SYDKRVRPNYGGPPVEVGVTMYVLSISSLSEVKMKKCWRKSTVREELRMKKDVNKTLFHL
QFQFARHKVKLLTGFSFKFNNFSGPPVTVGVTMYVLSISSVSEVLMDFTLDFYFRQFWTD
PRLAYRKRPGVEQLSVGSDFVKSIWVPDTFFVNEKQSYFHIATTSNEFIRVHHSGSITRS
MRLTITASCPMNLQYFPMDRQLCHIEIESFGYTMRDIRYKWNEGPNSVGVSEDVSLPQFK
VLGHRQRAMEISLTTGNYSRLACEIQFVRSMGYYLIQIYIPSGLIVIISWVSFWLNRNAT
PARVALGVTTVLTMTTLMSSTNAALPKISYVKSIDVYLGTCFVMVFASLLEYATVGYMAK
RIQMRKQRFMAIQKIAEQKKIQVDNAQQNNPPSGGGSVVGGPPSEHSHSHGHSHSHHPHV
PKQQMGMGNRGPPGMSLQGNVGSRGCSIVGPLFQEVRFKVHDPKAHSKGGTLENTINGGR
GGQQQQQPPPPAPADEESGGGGGGPPQHLIHPGKNINTLLGITPSDIDKYSRIVFPVCFV
CFNLMYWIIYLHVSDVVADDLVLLGEDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
35 g7163.t4 CDD cd19008 LGIC_ECD_GABAR_RDL-like 147 330 7.45573E-132
36 g7163.t4 CDD cd19049 LGIC_TM_anion 333 430 8.02769E-40
22 g7163.t4 Gene3D G3DSA:2.70.170.10 - 45 104 3.9E-8
23 g7163.t4 Gene3D G3DSA:2.70.170.10 - 130 328 3.4E-69
44 g7163.t4 MobiDBLite mobidb-lite consensus disorder prediction 443 485 -
43 g7163.t4 MobiDBLite mobidb-lite consensus disorder prediction 539 564 -
4 g7163.t4 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 49 95 1.2E-173
6 g7163.t4 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 49 95 1.2E-173
3 g7163.t4 PANTHER PTHR18945 NEUROTRANSMITTER GATED ION CHANNEL 141 613 1.2E-173
5 g7163.t4 PANTHER PTHR18945:SF856 GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA 141 613 1.2E-173
11 g7163.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 169 185 1.9E-12
9 g7163.t4 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 182 196 5.7E-14
14 g7163.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 203 214 1.9E-12
13 g7163.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 249 263 1.9E-12
10 g7163.t4 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 288 301 5.7E-14
12 g7163.t4 PRINTS PR00252 Neurotransmitter-gated ion channel family signature 325 337 1.9E-12
16 g7163.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 334 354 2.3E-42
18 g7163.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 360 381 2.3E-42
8 g7163.t4 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 388 400 5.7E-14
15 g7163.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 394 415 2.3E-42
7 g7163.t4 PRINTS PR01160 Gamma-aminobutyric-acid A receptor beta subunit signature 578 592 5.7E-14
17 g7163.t4 PRINTS PR00253 Gamma-aminobutyric acid A (GABAA) receptor signature 590 610 2.3E-42
1 g7163.t4 Pfam PF02931 Neurotransmitter-gated ion-channel ligand binding domain 132 321 6.7E-46
2 g7163.t4 Pfam PF02932 Neurotransmitter-gated ion-channel transmembrane region 338 607 1.2E-45
24 g7163.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
30 g7163.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
27 g7163.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 330 -
34 g7163.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 331 355 -
26 g7163.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 356 363 -
33 g7163.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 364 385 -
28 g7163.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 386 396 -
32 g7163.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 397 419 -
25 g7163.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 420 592 -
31 g7163.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 593 613 -
29 g7163.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 614 628 -
42 g7163.t4 ProSitePatterns PS00236 Neurotransmitter-gated ion-channels signature. 249 263 -
19 g7163.t4 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 53 95 6.54E-7
20 g7163.t4 SUPERFAMILY SSF63712 Nicotinic receptor ligand binding domain-like 142 330 2.22E-50
21 g7163.t4 SUPERFAMILY SSF90112 Neurotransmitter-gated ion-channel transmembrane pore 331 619 1.57E-55
45 g7163.t4 TIGRFAM TIGR00860 LIC: cation transporter family protein 140 451 3.6E-111
37 g7163.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
41 g7163.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -
40 g7163.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 364 386 -
39 g7163.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 396 418 -
38 g7163.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 593 610 -

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 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