General information for g5625.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Mitochondrial import inner membrane translocase subunit Tim23.
Parent gene
- The parent gene g5625 is located on chr_2: 10716243..10717439 (+ 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 | g5625 | g5625.t1 | TSS | g5625.t1 | 10715512 | 10715512 |
| chr_2 | g5625 | g5625.t1 | isoform | g5625.t1 | 10715579 | 10716243 |
| chr_2 | g5625 | g5625.t1 | exon | g5625.t1.exon1 | 10715579 | 10715645 |
| chr_2 | g5625 | g5625.t1 | cds | g5625.t1.CDS1 | 10715579 | 10715645 |
| chr_2 | g5625 | g5625.t1 | exon | g5625.t1.exon2 | 10715714 | 10716243 |
| chr_2 | g5625 | g5625.t1 | cds | g5625.t1.CDS2 | 10715714 | 10716243 |
| chr_2 | g5625 | g5625.t1 | TTS | g5625.t1 | 10716331 | 10716331 |
Sequences
>g5625.t1 Gene=g5625 Length=597
ATGAGCGATGATTATTTGAATAAACCATTATCATTCGGTAGTGGAAGTGATTTAGGATTA
GCACCAGCACCTTCAAAATCAACTCCTAGTTTCACATCGCCTTATCTCAATTATGATCAA
CGTTATATGAGACAAGCACAGCCTGAATTTATATTTCCTGAAGGTGCGTCGAAACAACGA
GGTCGATTTGAATTAGCTTTCTCACAAATTGGTTCGTCAGTTATGGTCGGAGCCGCTGTT
GGTGGCGTAGGAGGACTTTATAATGGAGTTAAAGCAACTGCATTAGCACAACAAACAGGA
AAACTTAGACGGACACAAATATTGAATCATGTTATGAAGCAAGGAGCAGGAACTGCAAAT
ACTTTGGGTACAATTGCAGTCTTATACTCAGCATTCGGTGTACTTTTATCTTGGGCAAGA
GGAGAAGACGATGAGATTAATACGATAGCAGCTGGTACAGCTACCGGTCTCATGTATAAA
TCAACAGCTGGTCTAAGAAGATGTGCGATTGGAGGTGGAATAGGTCTCGCTTTGAGTTCA
GCATGGGTTCTTTATAATATGTCAAGTTCAAAATTCAACAAAAATCAATATATTTAA
>g5625.t1 Gene=g5625 Length=198
MSDDYLNKPLSFGSGSDLGLAPAPSKSTPSFTSPYLNYDQRYMRQAQPEFIFPEGASKQR
GRFELAFSQIGSSVMVGAAVGGVGGLYNGVKATALAQQTGKLRRTQILNHVMKQGAGTAN
TLGTIAVLYSAFGVLLSWARGEDDEINTIAAGTATGLMYKSTAGLRRCAIGGGIGLALSS
AWVLYNMSSSKFNKNQYI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5625.t1 | PANTHER | PTHR15371 | TIM23 | 30 | 187 | 5.1E-48 |
| 3 | g5625.t1 | PANTHER | PTHR15371:SF27 | MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM23 | 30 | 187 | 5.1E-48 |
| 1 | g5625.t1 | Pfam | PF02466 | Tim17/Tim22/Tim23/Pmp24 family | 67 | 179 | 5.5E-18 |
| 7 | g5625.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 167 | - |
| 9 | g5625.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 185 | - |
| 8 | g5625.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 198 | - |
| 6 | g5625.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 4 | g5625.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 138 | - |
| 5 | g5625.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 163 | 185 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5625/g5625.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5625.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K17794 (mitochondrial import inner membrane translocase subunit TIM23)
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.
