General information for g9942.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 4-aminobutyrate aminotransferase, mitochondrial.
Parent gene
- The parent gene g9942 is located on chr_1: 6124353..6126013 (- 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_1 | g9942 | g9942.t1 | TTS | g9942.t1 | 6123024 | 6123024 |
| chr_1 | g9942 | g9942.t1 | isoform | g9942.t1 | 6123325 | 6125593 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon1 | 6123325 | 6123417 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS1 | 6123325 | 6123417 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon2 | 6123480 | 6123744 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS2 | 6123480 | 6123744 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon3 | 6123804 | 6124278 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS3 | 6123804 | 6124278 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon4 | 6124354 | 6124740 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS4 | 6124354 | 6124740 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon5 | 6124806 | 6124890 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS5 | 6124806 | 6124890 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon6 | 6125366 | 6125487 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS6 | 6125366 | 6125487 |
| chr_1 | g9942 | g9942.t1 | exon | g9942.t1.exon7 | 6125557 | 6125593 |
| chr_1 | g9942 | g9942.t1 | cds | g9942.t1.CDS7 | 6125557 | 6125593 |
| chr_1 | g9942 | g9942.t1 | TSS | g9942.t1 | 6125686 | 6125686 |
Sequences
>g9942.t1 Gene=g9942 Length=1464
ATGCTTCGTAGTGTCATACGAAATCCCAAGGCGTTTGCTTCTGAAGCGAGATGTCTTTAT
AGCACATATGTAAAAAATGAACCATCAGCACCAAAAGTTTGCACCGAGATCCCTGGACCA
AAGTCAAAAAGTCTGCTCAAAAATTTAAATCAACTTCAACAAGCTGGCTCAGTTCAATTA
TTTGCTGACTACGATGCGAGCATTGGAAATTATTTGATTGATGTTGATGGAAATCAGTTA
TTGGATATTTTCACGCAAATTTCAAGCGTTCCATTAGGCTACAATCATCCCGAGTTGCTA
AAAGTTTTTGAAAATGAGCATAATATAAAAACATTAGTGAATAGGCCTGCATTAGGCGTT
TTCCCAGGCGCTGATTGGCCTGATAAACTGCAAAATGTTCTTATGTCAGTTGCACCAAAA
GGACTAAAAAACATAACTACAATGATGTGTGGATCATGCAGCAATGAAAATGCATTTAAG
AACATGTTCTTGTGGTATTGTAAAAATCGTCGTGGTGAAAATGTTGATTTCACTGATGCT
GAAAAGGAAACTTGTATGATCAATCAACAACCAGGTTCACCAAACCTTTCGATTTTATCT
TTTATGGGCAGCTTTCATGGACGTACAATAGGAGCATTATCGACTACTCACTCAAAGTAT
ATTCACAAAATTGATGTACCGGCTCTTGATTGGCCAATTGCACCATTTCCTCGTTATAAA
TATCCATTAGAGGAAAATGTTCGTGAGAATAAAGCTGAAGACGAACGTTGCTTGGCAGAA
GTTGAGTCGTTGATTGAAAAGTGGAATAAGAAAGGACAGGATGTTGCTGGCATTATTGTG
GAACCAATTCAGGCTGAAGGAGGCGATAATGAAGGCTCGCCAGAGTTCTTCCAGGGATTG
CAAAAAATTACAAAACGAAATGGTGTTGCATTGCTCATTGATGAGGTTCAAACCGGAGGT
GGACCAACAGGGAAATTCTGGTGTCATGAATGGTTCAATTTAGAATCTTCACCAGACATT
GTAACATTCTCGAAGAAAATGCAACTCGGTGGTTATTATCATTCTGAAGATTTTAAGCCT
CAACAAGAATATCGCATCTTTAATACATGGTGTGGAGATCCTGGAAAATTGTTAATTCTT
GAGAAAGTTTTGGAAGTTATAAAACGCGAGAATCTTCTTGATAACGTTAATAAAACTGGT
GCTGTTTTAAAACAAGGACTTTTGGATGCACAAAAAGAATTTCCATCAATATTGAACTCA
GCACGAGGTCGTGGAACATTCTTAGCTATAAATGCAAAAGATGGAAAGATCCGTGATACA
ATTGTTGGAAATTTAAAGAAGAAAGGCATTCAATCTGGAGGATGTGGAGAAGTATCAATT
CGGTTCCGACCAGCATTGATTTTTGAACCAAAACATGCAAATATTTTCTTAGATAAATTT
CGTCAAGTATTAAAGGAGCTTTAA
>g9942.t1 Gene=g9942 Length=487
MLRSVIRNPKAFASEARCLYSTYVKNEPSAPKVCTEIPGPKSKSLLKNLNQLQQAGSVQL
FADYDASIGNYLIDVDGNQLLDIFTQISSVPLGYNHPELLKVFENEHNIKTLVNRPALGV
FPGADWPDKLQNVLMSVAPKGLKNITTMMCGSCSNENAFKNMFLWYCKNRRGENVDFTDA
EKETCMINQQPGSPNLSILSFMGSFHGRTIGALSTTHSKYIHKIDVPALDWPIAPFPRYK
YPLEENVRENKAEDERCLAEVESLIEKWNKKGQDVAGIIVEPIQAEGGDNEGSPEFFQGL
QKITKRNGVALLIDEVQTGGGPTGKFWCHEWFNLESSPDIVTFSKKMQLGGYYHSEDFKP
QQEYRIFNTWCGDPGKLLILEKVLEVIKRENLLDNVNKTGAVLKQGLLDAQKEFPSILNS
ARGRGTFLAINAKDGKIRDTIVGNLKKKGIQSGGCGEVSIRFRPALIFEPKHANIFLDKF
RQVLKEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9942.t1 | CDD | cd00610 | OAT_like | 65 | 484 | 0 |
| 5 | g9942.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 34 | 480 | 0 |
| 6 | g9942.t1 | Gene3D | G3DSA:3.40.640.10 | - | 96 | 391 | 0 |
| 2 | g9942.t1 | PANTHER | PTHR43206 | AMINOTRANSFERASE | 21 | 487 | 0 |
| 3 | g9942.t1 | PANTHER | PTHR43206:SF1 | 4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL | 21 | 487 | 0 |
| 8 | g9942.t1 | PIRSF | PIRSF000521 | Transaminase_4ab_Lys_Orn | 5 | 487 | 0 |
| 1 | g9942.t1 | Pfam | PF00202 | Aminotransferase class-III | 55 | 484 | 0 |
| 4 | g9942.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 66 | 487 | 0 |
| 7 | g9942.t1 | TIGRFAM | TIGR00699 | GABAtrns_euk: 4-aminobutyrate aminotransferase | 22 | 483 | 0 |
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:0009448 | gamma-aminobutyric acid metabolic process | BP |
| GO:0008483 | transaminase activity | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0030170 | pyridoxal phosphate binding | MF |
| GO:0003867 | 4-aminobutyrate transaminase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13524 (4-aminobutyrate aminotransferase / (S)-3-amino-2-methylpropionate transaminase)
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.
