General information for g5625.t2
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.t2 | TSS | g5625.t2 | 10715512 | 10715512 |
| chr_2 | g5625 | g5625.t2 | isoform | g5625.t2 | 10715579 | 10716385 |
| chr_2 | g5625 | g5625.t2 | exon | g5625.t2.exon1 | 10715579 | 10716385 |
| chr_2 | g5625 | g5625.t2 | cds | g5625.t2.CDS1 | 10715773 | 10716243 |
| chr_2 | g5625 | g5625.t2 | TTS | g5625.t2 | 10716331 | 10716331 |
Sequences
>g5625.t2 Gene=g5625 Length=807
ATGAGCGATGATTATTTGAATAAACCATTATCATTCGGTAGTGGAAGTGATTTAGGATTA
GCACCAGGTAAATTAAGAATCAAAATTTAACGTGTGAAATAAAATTTTTGTAATGCGAAA
TATTTTATTTTTCAGCACCTTCAAAATCAACTCCTAGTTTCACATCGCCTTATCTCAATT
ATGATCAACGTTATATGAGACAAGCACAGCCTGAATTTATATTTCCTGAAGGTGCGTCGA
AACAACGAGGTCGATTTGAATTAGCTTTCTCACAAATTGGTTCGTCAGTTATGGTCGGAG
CCGCTGTTGGTGGCGTAGGAGGACTTTATAATGGAGTTAAAGCAACTGCATTAGCACAAC
AAACAGGAAAACTTAGACGGACACAAATATTGAATCATGTTATGAAGCAAGGAGCAGGAA
CTGCAAATACTTTGGGTACAATTGCAGTCTTATACTCAGCATTCGGTGTACTTTTATCTT
GGGCAAGAGGAGAAGACGATGAGATTAATACGATAGCAGCTGGTACAGCTACCGGTCTCA
TGTATAAATCAACAGCTGGTCTAAGAAGATGTGCGATTGGAGGTGGAATAGGTCTCGCTT
TGAGTTCAGCATGGGTTCTTTATAATATGTCAAGTTCAAAATTCAACAAAAATCAATATA
TTTAAGTATAACAGTCGTGATTAATTAGATATAGACAAAAAAGATCAATGAATGATTCAA
TAAAATATTTTATTTCTGCTCTTTATTGAATTGAAAATTATTTTGTTAAATTGTTATTAA
GTTATAGTGAATAAGTTGTGTATGCGT
>g5625.t2 Gene=g5625 Length=156
MRQAQPEFIFPEGASKQRGRFELAFSQIGSSVMVGAAVGGVGGLYNGVKATALAQQTGKL
RRTQILNHVMKQGAGTANTLGTIAVLYSAFGVLLSWARGEDDEINTIAAGTATGLMYKST
AGLRRCAIGGGIGLALSSAWVLYNMSSSKFNKNQYI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5625.t2 | PANTHER | PTHR15371 | TIM23 | 3 | 145 | 4.6E-41 |
| 3 | g5625.t2 | PANTHER | PTHR15371:SF27 | MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM23 | 3 | 145 | 4.6E-41 |
| 1 | g5625.t2 | Pfam | PF02466 | Tim17/Tim22/Tim23/Pmp24 family | 25 | 137 | 2.7E-18 |
| 7 | g5625.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 125 | - |
| 9 | g5625.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 143 | - |
| 8 | g5625.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 144 | 156 | - |
| 4 | g5625.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 53 | - |
| 5 | g5625.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 96 | - |
| 6 | g5625.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 143 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5625/g5625.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5625.t2.fa.iupred3.txt does not exist
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.
