General information for g16960.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial.
Parent gene
- The parent gene g16960 is located on chr_4: 11879110..11880536 (+ 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_4 | g16960 | g16960.t3 | TSS | g16960.t3 | 11877931 | 11877931 |
| chr_4 | g16960 | g16960.t3 | isoform | g16960.t3 | 11877993 | 11880536 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon1 | 11877993 | 11878208 |
| chr_4 | g16960 | g16960.t3 | cds | g16960.t3.CDS1 | 11877993 | 11878208 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon2 | 11878264 | 11878757 |
| chr_4 | g16960 | g16960.t3 | cds | g16960.t3.CDS2 | 11878264 | 11878757 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon3 | 11878813 | 11878869 |
| chr_4 | g16960 | g16960.t3 | cds | g16960.t3.CDS3 | 11878813 | 11878869 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon4 | 11879016 | 11879121 |
| chr_4 | g16960 | g16960.t3 | cds | g16960.t3.CDS4 | 11879016 | 11879121 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon5 | 11879331 | 11879479 |
| chr_4 | g16960 | g16960.t3 | cds | g16960.t3.CDS5 | 11879331 | 11879333 |
| chr_4 | g16960 | g16960.t3 | exon | g16960.t3.exon6 | 11879833 | 11880536 |
| chr_4 | g16960 | g16960.t3 | TTS | g16960.t3 | NA | NA |
Sequences
>g16960.t3 Gene=g16960 Length=1726
ATGAGTTTAATTGCTGCATTAAGTCCAATTCGAAGAGTTTTAGGTGTCACATTTGTCAGA
CAATCAAGAAATGTTTCACATTTTACATATCAACCCGATGACAAAGCACCGATCGAGGGT
GAAAAACAAAAAATGAACATGTTCACTGCAATCAATAATGCAATGGATATGGCACTTGCA
AAAGATGACTCGACATTGCTTTTTGGCGAGGACGTTGCATTTGGTGGAGTTTTTCGTTGT
TCATTAAATCTTAAAAATAAATATGGTGGTGATCGTGTCTTTAACACTCCACTGTGTGAA
CAAGGAATTGCGGGATTTGCTATTGGTGTTGCAGCAATGAATGTCAAAGCTATTGCAGAA
ATTCAATTTGCTGATTACATTTTTCCAGCATTTGATCAAATTGTAAATGAAGCAGCAAAA
TACAGATACAGAAGTGGAAATACATTTGATTGTGGTTCATTGACAATTAGAGCGCCATGT
GGTGCTGTTGGTCATGGTGCACTTTATCATTCACAAAGTCCTGAAGCTTATTTTGCTCAT
ACACCTGGATTAAAAATTGTCGTTCCAAGAGGACCAAATAAAGCTAAAGGTTTGCTGTTG
GCTTGTATTAATGATAAAAATCCATGCTTGGTTCTGGAACCAAAAACACTTTATAGAAGT
GCAATTGAGGATGTTCCTCTGGGTTATTTTGAAAGTCCTTTAGGTCAAGCTGATATTTTA
AGAGTTGGTGGTGATGTGACATTAATTGGATGGGGAACACAAGTCCATGTTTTAAGAGAA
ACTGCCGAATATGCAAAAAGAAAACTCAATGTTAATTGTGAAGTTATTGATTTAGTTTCT
ATTTTGCCATGGGATGTTGAGACTGTTTGCAATTAAAGAAGACTGGTCGTTGTATTATTG
CACATGAGGCTCCAGTAACAAATGGCTTTGGTGCAGAAATTGCAGCTACAGTTCAAGAAG
AATGTTTCTTGCATTTAGAAGCACCGATTCAAAGAGTTTGCGGATGGGATACTCCGTTTC
CGCATGTTTTTGAACCATTTTATCTTCCTGATAAATATCGATGCTTAGAAGCAATTAAAA
AAGTAATTGACTATTAAAACTTTGGTGCAAGATAAAAATTAATTTGAACCCAACGTACAA
AAATAATTTTTAAAACACTTAAAATTCTTTGGTTTAAATTTTTTGTACATAATTTTACAT
TCAAACAGTGTCCGAAATTATTTTAAATTTATTTACAAGTAAATAAAAATTAAGTCAATT
TTTTCGAGTAAAAAAATAAATTTTACTTAATTTTTAGTAACTCTTAAATAAAATTTAAAA
CGATTTCGGACTTTGCTTTCAAAAATGAAATTTTACAAAAAATTTTGATGGAAGAATTTT
AAGTTTTGCATTTATTGAAATTTACTGGGAAATTATGAAAAAATAAATTTTTGTGTAAAA
AATTCATGAAATATAACTGAAATATTGAAACTTGTTGCATTTATTAATTTTAAAATGAGA
AAATTATAAATTTTGAGAATTTTCAAAAGATTTGTTAAAAAAAATGTTGATGTATTTTAT
TGTAACAATAAAAACCGTTTAAAAAAAGGAAAAAAAATCAAGAATTTTTTTTATTTTTCA
AGGAAATAAAAACAAAAAATTGAATTTTTGATAAAAAGACTAAATTTTATTCAAATTTTA
CTTTTTTAATCATTTTTGGAACAAAAATATTTTAAAATCTGTATTT
>g16960.t3 Gene=g16960 Length=291
MSLIAALSPIRRVLGVTFVRQSRNVSHFTYQPDDKAPIEGEKQKMNMFTAINNAMDMALA
KDDSTLLFGEDVAFGGVFRCSLNLKNKYGGDRVFNTPLCEQGIAGFAIGVAAMNVKAIAE
IQFADYIFPAFDQIVNEAAKYRYRSGNTFDCGSLTIRAPCGAVGHGALYHSQSPEAYFAH
TPGLKIVVPRGPNKAKGLLLACINDKNPCLVLEPKTLYRSAIEDVPLGYFESPLGQADIL
RVGGDVTLIGWGTQVHVLRETAEYAKRKLNVNCEVIDLVSILPWDVETVCN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16960.t3 | CDD | cd07036 | TPP_PYR_E1-PDHc-beta_like | 50 | 215 | 7.70899E-88 |
| 7 | g16960.t3 | Gene3D | G3DSA:3.40.50.970 | - | 41 | 233 | 6.6E-84 |
| 8 | g16960.t3 | Gene3D | G3DSA:3.40.50.920 | - | 234 | 291 | 2.7E-16 |
| 3 | g16960.t3 | PANTHER | PTHR42980 | 2-OXOISOVALERATE DEHYDROGENASE SUBUNIT BETA-RELATED | 18 | 291 | 2.1E-126 |
| 2 | g16960.t3 | Pfam | PF02779 | Transketolase, pyrimidine binding domain | 44 | 219 | 2.3E-41 |
| 1 | g16960.t3 | Pfam | PF02780 | Transketolase, C-terminal domain | 235 | 290 | 4.4E-11 |
| 10 | g16960.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 11 | g16960.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 12 | g16960.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 10 | - |
| 13 | g16960.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 11 | 15 | - |
| 9 | g16960.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 291 | - |
| 6 | g16960.t3 | SMART | SM00861 | Transket_pyr_3 | 45 | 220 | 3.5E-58 |
| 4 | g16960.t3 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 30 | 224 | 2.77E-64 |
| 5 | g16960.t3 | SUPERFAMILY | SSF52922 | TK C-terminal domain-like | 230 | 290 | 1.44E-15 |
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:0003824 | catalytic activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
