General information for g6338.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Gamma-aminobutyric acid type B receptor subunit 2.
Parent gene
- The parent gene g6338 is located on chr_2: 16253635..16257624 (- 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 | g6338 | g6338.t1 | isoform | g6338.t1 | 16253635 | 16257624 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon1 | 16253635 | 16253720 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS1 | 16253635 | 16253720 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon2 | 16253776 | 16254367 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS2 | 16253776 | 16254367 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon3 | 16254429 | 16255401 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS3 | 16254429 | 16255401 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon4 | 16255459 | 16255760 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS4 | 16255459 | 16255760 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon5 | 16255814 | 16256068 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS5 | 16255814 | 16256068 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon6 | 16256128 | 16256310 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS6 | 16256128 | 16256310 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon7 | 16256552 | 16256896 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS7 | 16256552 | 16256896 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon8 | 16256959 | 16257102 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS8 | 16256959 | 16257102 |
| chr_2 | g6338 | g6338.t1 | exon | g6338.t1.exon9 | 16257196 | 16257624 |
| chr_2 | g6338 | g6338.t1 | cds | g6338.t1.CDS9 | 16257196 | 16257624 |
| chr_2 | g6338 | g6338.t1 | TSS | g6338.t1 | NA | NA |
| chr_2 | g6338 | g6338.t1 | TTS | g6338.t1 | NA | NA |
Sequences
>g6338.t1 Gene=g6338 Length=3309
ATGAAGTACATCATTGTGAACTTACCGAGTGTTAAGTGGATAAACTTTGTAGTGATTCTC
ATTTTATGTGATAACATCTCTTCAACTAGTGGTGAAAATTGTCTACTATCAAATTCAAGT
ATAACAAAAAAAGATTTTAAAGTGAATGAAAATTATTTGAATTTATTTGAATGTCAAAAA
GACAAATTTAAAATTATTAATGAAGTCATGAAAAGTCAATCAAAGCGAAGTATTTTTAGG
AAAATTATTGAACCACTTTTTGGCTATGAAGAGTCAACATCGAATAAAATTACTTTGCTT
GGTCTTTTTGAATTGACGACACAAAAAGGATTAAGTGAACTTGCAGCAGCAAAATTAGCT
GTAAAACATATAAATGAAAATAATATTTTAAATGGATATGAATTGGATCTTAAAATTAAT
GACACTCAGTGTGATGCAGGAGTTTCAGTTGATAGATTTTTTCATGCCATTTATTCACAA
AATAAAACAAAAATGATGATGCTTTTAAGTTCTTCGTGCTCAGAGGTCACTGAAACTTTA
GCTAAAATTGTTCAATATTGGAGTGTTATTATGGTTTCATTTGGTACTACAGCACCAGCT
TTAAGTGATCGAGATGAATTTCCTTACTTCTTTCGCACAGTCATGCCTGACTCAGCTCAT
AATCCAGCAAGAATTTCTTTTATTCAATATTTCAAATGGGATTCAGTTGTGACATTTTCA
CAAAAAGAAGAAATTTATTCATTAGCAATTAATGACATTGTAACACAACTTGAAAGAGCA
AATATTTCATGCTCATCGATATTGACTTTTAGTGAAAATGATTATAAAGAACAATTGAAA
GTTTTGAAAGATTTAGATACGAGGATTATCATTGGAAGTTTTAGTCTTGAAAAATTTGCA
GCAAAAGTTTTTTGTGAGGCTCATAACTTAGGAATGTATGGCGATTATGTTTGGATTTTA
CCAGAATCAGAAAATGAATCTTGGTGGAATTTTGAAAAGAGCAATTGCAGTATCAAAAAT
CTTCATGACACAATAGAAAATGTCATTTTTGTCTCATCATTCAATCACATTATTGGACAT
GAAAAATCCATTAATGATCTTACAAAAACTCGCTTTGAAGAAGAATTGTCGGCAATGAAC
ATAACAAAGCCATATTCGCGCAATATACTCACTACTTATGATGCTATTTGGAGCATAGCA
TTAGTACTTAAAAATGCTGAAGAATTATGGAAAAATCAATCAGAAGTTCATGCTTTGCAA
GAACTAAAGAAATTGAATCAATTTGATTACAACAGAATTGATTTTGCAAATGAATTCGTG
AAACAATTTGCAAAATTAAAATTTCAAGGAATTTCTGGACCCGTGTCATTCGATGGTAAT
GATCGGATTGGCATTACAATTTTTAAACAAATTCAAAACTCTCAACGTCAACCTATTGCT
CTTTTTCACCCTGAGATTGATCACTTGAATTTTAATTGTCCATTTTGTACAACAATAAAA
TGGAAAAATAATAATGTGCCAATTGCCAAAAGATTCTTTAAATTGCGTTATGTAACAATT
TCAAATATTGCATTTTTCACAATCTCTTCGTGTGCTGTCATAGGAATTATTTCGTCGATC
ATGTTTCTCGCCTTTAATTTACATTTTCGAAAGCTCAAGTCAATCAAATTGTCCAGCTAT
AAACTTTCAAATATCACAGCTGTCGGCTGCATATTCATCTATAGTGCAGTAATTTTATTA
GGTCTCGATCATTCATCTTTACCATTTTTCTCATCATTTCCAACAATTTGCATGGCAAGA
GTTTATTTATTATCATCAGGATTTTCATTGACTTTTGGTTCAATGTTTGCCAAAACATAT
CGAGTTCATCGAATTTTTATTCACAATTATGGAGGCATTTTTTGCCGTGACAAAATGCTA
AAAGATAGAAAATTAATTTCTTTAATTTGTTGCTTGCTACTTGTTGATACATTATTTATA
ACATGTTGGACCTTGATAGATCCAATGCAAAGAAATTTAAGAAATTTGACTCTTGAAATT
AGTCACACTGATCGTTCAGTGGTGTATCAACCTCAAGTTGAAGTTTGTGAAAGTTTAAAT
ACAAAAAGTTGGCTACTATTTCTCTATGCTTACAAAGGTTTATTGTTAGCTGTTGGTGTA
TATATGGCGTGGGAGACAAGAAATGTAAAGATTCCAGCATTAAACGATTCAAAATACATT
GGAATTTCTGTATATGGAGCTGTGATAACTAGTGTTTCTGTCGTTGTATTTGCTAATATT
CTAGCAGATAAAGTCACAACTTCGTTCATCATTATTGCTGTTATAATTTTAATATCAACA
ACAGCAACATTATGTCTTGTATTTGTGCCAAAAATGAGTGCAATATTGAATAAAGAAGTT
CAAGAAGATGCAGTCATTCATAGTATGGGATTAAAAATGGAATATAATACAAGAAGATTT
GCAATTGATGACAAAAAAGAGCTGCAATATCGAGTTGAAGTTCAAAATCGAGTTTATCTA
AAAGAATTGGAAGCATTGGATGCAGAAATAAAAACTTTAGAAAAAATGTTGGGTGATCGC
TCATCATCATCAAGAACTTCATCATCTCATTCGATTGTTGCTTATGTCAAGCCAGAAATT
GTCATCAATGATTCTTCATCAATTGATCAATTTAAATCACCAAGAACAAGTATCACTAAC
ACTTTGCCGCTCTTACTTTTATCAGTTTTACCACCAGTAATTCCACGAGCTTCTTGGCCA
AATGCTGAACAAATTCCATCACCAATTAAACAATCACATTGCTTTAGTTCACACCCACAA
ATTCCAAGCAATCACGGAAGCGATTTTAACATTCCAGCAATCGATTTGCTCAATCTTCGT
CTCAATCAACAGCAGCAAGAAGAACATGAAAATGTTGGTCTTTTTAAGAAAATTAAAAAT
CTTTTTGGTTCACGTGGTCCAAGTAGAAAAGAGTCAACAACTTCGCTTGCTACGAGTCAC
ATAACAAATGCAATTAGATCTCACGTTAATATGCTATCAGATTTATTTCCACATGGTAGC
TCAAACAATAGCATTGACAAAGACAATTGGAATGTTGAGAAATTCAAGAAAGCTTCAGTG
TTCACAATTAATATTGTTGAAGATGATATGAACATTTTACCGGTCAGAAAGCACAGAATT
ATTCTTACAAATAGTTTAAGTAACATTGAAGAGTCATTGAAAGATACAACAACAAAAGAA
ATGAATTTAGCATCAAAATGGAAGTCTTTGGAAGAAGAAGCACTTTATGTTAGCAGTAAT
AAATTTTAA
>g6338.t1 Gene=g6338 Length=1102
MKYIIVNLPSVKWINFVVILILCDNISSTSGENCLLSNSSITKKDFKVNENYLNLFECQK
DKFKIINEVMKSQSKRSIFRKIIEPLFGYEESTSNKITLLGLFELTTQKGLSELAAAKLA
VKHINENNILNGYELDLKINDTQCDAGVSVDRFFHAIYSQNKTKMMMLLSSSCSEVTETL
AKIVQYWSVIMVSFGTTAPALSDRDEFPYFFRTVMPDSAHNPARISFIQYFKWDSVVTFS
QKEEIYSLAINDIVTQLERANISCSSILTFSENDYKEQLKVLKDLDTRIIIGSFSLEKFA
AKVFCEAHNLGMYGDYVWILPESENESWWNFEKSNCSIKNLHDTIENVIFVSSFNHIIGH
EKSINDLTKTRFEEELSAMNITKPYSRNILTTYDAIWSIALVLKNAEELWKNQSEVHALQ
ELKKLNQFDYNRIDFANEFVKQFAKLKFQGISGPVSFDGNDRIGITIFKQIQNSQRQPIA
LFHPEIDHLNFNCPFCTTIKWKNNNVPIAKRFFKLRYVTISNIAFFTISSCAVIGIISSI
MFLAFNLHFRKLKSIKLSSYKLSNITAVGCIFIYSAVILLGLDHSSLPFFSSFPTICMAR
VYLLSSGFSLTFGSMFAKTYRVHRIFIHNYGGIFCRDKMLKDRKLISLICCLLLVDTLFI
TCWTLIDPMQRNLRNLTLEISHTDRSVVYQPQVEVCESLNTKSWLLFLYAYKGLLLAVGV
YMAWETRNVKIPALNDSKYIGISVYGAVITSVSVVVFANILADKVTTSFIIIAVIILIST
TATLCLVFVPKMSAILNKEVQEDAVIHSMGLKMEYNTRRFAIDDKKELQYRVEVQNRVYL
KELEALDAEIKTLEKMLGDRSSSSRTSSSHSIVAYVKPEIVINDSSSIDQFKSPRTSITN
TLPLLLLSVLPPVIPRASWPNAEQIPSPIKQSHCFSSHPQIPSNHGSDFNIPAIDLLNLR
LNQQQQEEHENVGLFKKIKNLFGSRGPSRKESTTSLATSHITNAIRSHVNMLSDLFPHGS
SNNSIDKDNWNVEKFKKASVFTINIVEDDMNILPVRKHRIILTNSLSNIEESLKDTTTKE
MNLASKWKSLEEEALYVSSNKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 51 | g6338.t1 | CDD | cd06366 | PBP1_GABAb_receptor | 98 | 503 | 1.31491E-130 |
| 50 | g6338.t1 | CDD | cd15047 | 7tmC_GABA-B-like | 524 | 797 | 6.45728E-77 |
| 30 | g6338.t1 | Coils | Coil | Coil | 836 | 856 | - |
| 29 | g6338.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 107 | 466 | 5.7E-111 |
| 28 | g6338.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 218 | 485 | 5.7E-111 |
| 3 | g6338.t1 | PANTHER | PTHR10519:SF46 | METABOTROPIC GABA-B RECEPTOR SUBTYPE 3, ISOFORM A | 142 | 1016 | 7.9E-297 |
| 4 | g6338.t1 | PANTHER | PTHR10519 | GABA-B RECEPTOR | 142 | 1016 | 7.9E-297 |
| 13 | g6338.t1 | PRINTS | PR00248 | Metabotropic glutamate GPCR signature | 110 | 125 | 3.3E-6 |
| 17 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 110 | 126 | 1.5E-61 |
| 23 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 173 | 201 | 1.5E-61 |
| 8 | g6338.t1 | PRINTS | PR01177 | Metabotropic gamma-aminobutyric acid type B1 receptor signature | 178 | 195 | 6.4E-13 |
| 11 | g6338.t1 | PRINTS | PR00248 | Metabotropic glutamate GPCR signature | 201 | 220 | 3.3E-6 |
| 19 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 208 | 227 | 1.5E-61 |
| 10 | g6338.t1 | PRINTS | PR00248 | Metabotropic glutamate GPCR signature | 220 | 236 | 3.3E-6 |
| 18 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 271 | 294 | 1.5E-61 |
| 15 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 392 | 404 | 1.5E-61 |
| 7 | g6338.t1 | PRINTS | PR01177 | Metabotropic gamma-aminobutyric acid type B1 receptor signature | 523 | 548 | 6.4E-13 |
| 25 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 524 | 547 | 1.5E-61 |
| 20 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 563 | 584 | 1.5E-61 |
| 9 | g6338.t1 | PRINTS | PR01177 | Metabotropic gamma-aminobutyric acid type B1 receptor signature | 565 | 586 | 6.4E-13 |
| 22 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 597 | 616 | 1.5E-61 |
| 14 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 649 | 674 | 1.5E-61 |
| 21 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 686 | 706 | 1.5E-61 |
| 12 | g6338.t1 | PRINTS | PR00248 | Metabotropic glutamate GPCR signature | 735 | 756 | 3.3E-6 |
| 24 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 735 | 758 | 1.5E-61 |
| 6 | g6338.t1 | PRINTS | PR01177 | Metabotropic gamma-aminobutyric acid type B1 receptor signature | 739 | 761 | 6.4E-13 |
| 5 | g6338.t1 | PRINTS | PR01177 | Metabotropic gamma-aminobutyric acid type B1 receptor signature | 766 | 789 | 6.4E-13 |
| 16 | g6338.t1 | PRINTS | PR01176 | Metabotropic gamma-aminobutyric acid type B receptor signature | 769 | 791 | 1.5E-61 |
| 1 | g6338.t1 | Pfam | PF01094 | Receptor family ligand binding region | 114 | 460 | 2.7E-47 |
| 2 | g6338.t1 | Pfam | PF00003 | 7 transmembrane sweet-taste receptor of 3 GCPR | 536 | 792 | 1.0E-47 |
| 39 | g6338.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 31 | - |
| 40 | g6338.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 15 | - |
| 41 | g6338.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 16 | 23 | - |
| 49 | g6338.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 24 | 31 | - |
| 37 | g6338.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 32 | 522 | - |
| 48 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 523 | 545 | - |
| 33 | g6338.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 546 | 564 | - |
| 42 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 565 | 582 | - |
| 36 | g6338.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 583 | 601 | - |
| 44 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 602 | 620 | - |
| 32 | g6338.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 621 | 644 | - |
| 43 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 645 | 666 | - |
| 35 | g6338.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 667 | 703 | - |
| 45 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 704 | 724 | - |
| 34 | g6338.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 725 | 743 | - |
| 47 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 744 | 762 | - |
| 38 | g6338.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 763 | 767 | - |
| 46 | g6338.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 768 | 789 | - |
| 31 | g6338.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 790 | 1102 | - |
| 59 | g6338.t1 | ProSiteProfiles | PS50259 | G-protein coupled receptors family 3 profile. | 594 | 798 | 24.495 |
| 26 | g6338.t1 | SUPERFAMILY | SSF53822 | Periplasmic binding protein-like I | 93 | 508 | 6.73E-64 |
| 27 | g6338.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 31 | - |
| 58 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 523 | 545 | - |
| 56 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 558 | 580 | - |
| 57 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 595 | 617 | - |
| 55 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 645 | 667 | - |
| 53 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 704 | 726 | - |
| 54 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 739 | 761 | - |
| 52 | g6338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 766 | 788 | - |
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:0007186 | G protein-coupled receptor signaling pathway | BP |
| GO:0004965 | G protein-coupled GABA receptor activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0004930 | G protein-coupled receptor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04615 (gamma-aminobutyric acid type B receptor)
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