General information for g16960.t2
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.t2 | TSS | g16960.t2 | 11877931 | 11877931 |
| chr_4 | g16960 | g16960.t2 | isoform | g16960.t2 | 11877993 | 11879021 |
| chr_4 | g16960 | g16960.t2 | exon | g16960.t2.exon1 | 11877993 | 11878208 |
| chr_4 | g16960 | g16960.t2 | cds | g16960.t2.CDS1 | 11877993 | 11878208 |
| chr_4 | g16960 | g16960.t2 | exon | g16960.t2.exon2 | 11878264 | 11878757 |
| chr_4 | g16960 | g16960.t2 | cds | g16960.t2.CDS2 | 11878264 | 11878757 |
| chr_4 | g16960 | g16960.t2 | exon | g16960.t2.exon3 | 11878813 | 11878869 |
| chr_4 | g16960 | g16960.t2 | cds | g16960.t2.CDS3 | 11878813 | 11878869 |
| chr_4 | g16960 | g16960.t2 | exon | g16960.t2.exon4 | 11879016 | 11879021 |
| chr_4 | g16960 | g16960.t2 | cds | g16960.t2.CDS4 | 11879016 | 11879019 |
| chr_4 | g16960 | g16960.t2 | TTS | g16960.t2 | 11879923 | 11879923 |
Sequences
>g16960.t2 Gene=g16960 Length=773
ATGAGTTTAATTGCTGCATTAAGTCCAATTCGAAGAGTTTTAGGTGTCACATTTGTCAGA
CAATCAAGAAATGTTTCACATTTTACATATCAACCCGATGACAAAGCACCGATCGAGGGT
GAAAAACAAAAAATGAACATGTTCACTGCAATCAATAATGCAATGGATATGGCACTTGCA
AAAGATGACTCGACATTGCTTTTTGGCGAGGACGTTGCATTTGGTGGAGTTTTTCGTTGT
TCATTAAATCTTAAAAATAAATATGGTGGTGATCGTGTCTTTAACACTCCACTGTGTGAA
CAAGGAATTGCGGGATTTGCTATTGGTGTTGCAGCAATGAATGTCAAAGCTATTGCAGAA
ATTCAATTTGCTGATTACATTTTTCCAGCATTTGATCAAATTGTAAATGAAGCAGCAAAA
TACAGATACAGAAGTGGAAATACATTTGATTGTGGTTCATTGACAATTAGAGCGCCATGT
GGTGCTGTTGGTCATGGTGCACTTTATCATTCACAAAGTCCTGAAGCTTATTTTGCTCAT
ACACCTGGATTAAAAATTGTCGTTCCAAGAGGACCAAATAAAGCTAAAGGTTTGCTGTTG
GCTTGTATTAATGATAAAAATCCATGCTTGGTTCTGGAACCAAAAACACTTTATAGAAGT
GCAATTGAGGATGTTCCTCTGGGTTATTTTGAAAGTCCTTTAGGTCAAGCTGATATTTTA
AGAGTTGGTGGTGATGTGACATTAATTGGATGGGGAACACAAGTCCATGTTTT
>g16960.t2 Gene=g16960 Length=257
MSLIAALSPIRRVLGVTFVRQSRNVSHFTYQPDDKAPIEGEKQKMNMFTAINNAMDMALA
KDDSTLLFGEDVAFGGVFRCSLNLKNKYGGDRVFNTPLCEQGIAGFAIGVAAMNVKAIAE
IQFADYIFPAFDQIVNEAAKYRYRSGNTFDCGSLTIRAPCGAVGHGALYHSQSPEAYFAH
TPGLKIVVPRGPNKAKGLLLACINDKNPCLVLEPKTLYRSAIEDVPLGYFESPLGQADIL
RVGGDVTLIGWGTQVHV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16960.t2 | CDD | cd07036 | TPP_PYR_E1-PDHc-beta_like | 50 | 215 | 3.63922E-87 |
| 5 | g16960.t2 | Gene3D | G3DSA:3.40.50.970 | - | 41 | 237 | 4.4E-84 |
| 2 | g16960.t2 | PANTHER | PTHR42980 | 2-OXOISOVALERATE DEHYDROGENASE SUBUNIT BETA-RELATED | 18 | 257 | 1.0E-112 |
| 1 | g16960.t2 | Pfam | PF02779 | Transketolase, pyrimidine binding domain | 44 | 219 | 1.6E-41 |
| 7 | g16960.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 8 | g16960.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 9 | g16960.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 10 | - |
| 10 | g16960.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 11 | 15 | - |
| 6 | g16960.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 257 | - |
| 4 | g16960.t2 | SMART | SM00861 | Transket_pyr_3 | 45 | 220 | 3.5E-58 |
| 3 | g16960.t2 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 30 | 224 | 1.88E-64 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
