General information for g12249.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12249 is located on chr_1: 22000303..22001517 (- 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 | g12249 | g12249.t2 | isoform | g12249.t2 | 22000150 | 22000882 |
| chr_1 | g12249 | g12249.t2 | exon | g12249.t2.exon1 | 22000150 | 22000882 |
| chr_1 | g12249 | g12249.t2 | TTS | g12249.t2 | 22000188 | 22000188 |
| chr_1 | g12249 | g12249.t2 | cds | g12249.t2.CDS1 | 22000303 | 22000740 |
| chr_1 | g12249 | g12249.t2 | TSS | g12249.t2 | 22001585 | 22001585 |
Sequences
>g12249.t2 Gene=g12249 Length=733
TCTTTTTGATAACGAGTTGGCTTTTATTGACAAACTTATTGCGGCTGATGTAAGAAATAA
TTCTGCATGGAATCAACGATTTTTCGTCTTGAAACATTTAGGCTTGACACCTGAGACTGT
ACAACGAGAAATTCATTATGCCATGAATCGTATTCGACTTATTAAAAACAACGAAAGCTC
TTGGAATTTTTTAAAGGGTTTATTGGAGTATGGAGACTTTAGTATTAGTCAATTTCCTGA
TGTTGAAACATTTACTGAGGAATTGTACAATTCTGGAAATCGATCGCCATATCTTTTAGC
TTTTCTCGTTGATATGTACACTGAGAAGACATTACACATTTATGAAACAAATAGCTACGA
TGATCCAGAAGTTTATGCTAGAAAAGTTGTTGAATTATGTGAAATGCTAGCAAATCATTA
TGACACAATCAGATACAAGTATTGGAAATATGTTATTCAAAAGTTTAACGCAGATAAAGA
ACTCGCTAAAGTCGGTCCAAACGAACAAAATGAAGAAAAAGATGAAGAAGAACATTTAGT
TACAAGAGAGCCTGAGAAAGTCAATGGTGAAGCGCAATAATAGATGGATTTTATTTGAAG
CATTTTTTTGCATCTCGTATGATGAGATTTTAAAATTAGATTTGAATTTTTGTTGTTTTA
TAATAATTTTAAAATAAAATTTAGTATGGATCGGGAAAAAATTTTATTCAAAAATTTCTT
TTCTACAAAAAAT
>g12249.t2 Gene=g12249 Length=145
MNRIRLIKNNESSWNFLKGLLEYGDFSISQFPDVETFTEELYNSGNRSPYLLAFLVDMYT
EKTLHIYETNSYDDPEVYARKVVELCEMLANHYDTIRYKYWKYVIQKFNADKELAKVGPN
EQNEEKDEEEHLVTREPEKVNGEAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12249.t2 | Gene3D | G3DSA:1.25.40.120 | Protein prenylyltransferase | 1 | 128 | 1.7E-19 |
| 5 | g12249.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 115 | 145 | - |
| 4 | g12249.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 117 | 145 | - |
| 1 | g12249.t2 | PANTHER | PTHR11129:SF5 | PROTEIN FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE TYPE-1 SUBUNIT ALPHA | 3 | 108 | 3.8E-14 |
| 2 | g12249.t2 | PANTHER | PTHR11129 | PROTEIN FARNESYLTRANSFERASE ALPHA SUBUNIT/RAB GERANYLGERANYL TRANSFERASE ALPHA SUBUNIT | 3 | 108 | 3.8E-14 |
| 3 | g12249.t2 | SUPERFAMILY | SSF48439 | Protein prenylyltransferase | 2 | 107 | 1.1E-10 |
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.
