General information for g12249.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha.
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.t1 | TTS | g12249.t1 | 22000188 | 22000188 |
| chr_1 | g12249 | g12249.t1 | isoform | g12249.t1 | 22000303 | 22001517 |
| chr_1 | g12249 | g12249.t1 | exon | g12249.t1.exon1 | 22000303 | 22000882 |
| chr_1 | g12249 | g12249.t1 | cds | g12249.t1.CDS1 | 22000303 | 22000882 |
| chr_1 | g12249 | g12249.t1 | exon | g12249.t1.exon2 | 22000961 | 22001315 |
| chr_1 | g12249 | g12249.t1 | cds | g12249.t1.CDS2 | 22000961 | 22001315 |
| chr_1 | g12249 | g12249.t1 | exon | g12249.t1.exon3 | 22001382 | 22001517 |
| chr_1 | g12249 | g12249.t1 | cds | g12249.t1.CDS3 | 22001382 | 22001517 |
| chr_1 | g12249 | g12249.t1 | TSS | g12249.t1 | 22001585 | 22001585 |
Sequences
>g12249.t1 Gene=g12249 Length=1071
ATGAGTGACAGTTCAGATGAAGATTTTAATGAAAGCTATGTAATGTACAGACATCGTCGT
GAATGGAGTGACGTGCATCCAATTAAACAAAATGATGGACCAAATCCGATTGTAGCTATT
GCATACAGTGAACGATTTTTGGATGTTTACGATTATTTTAGAGCCATACTAGCAACACAA
GAAAAATCTGAAAGAGCTCTGGAACTCACAACTGATGCGCTTCGATTAAATGCAGCAAAT
TATACTGTTTGGCAATACAGAAGAGAAATCTTGCATGCACTGAAAAAGAATCTTTATGAT
GAGCTTCAATATATTGCAGAAGTGATTGAAGATAATCCTAAAAATTATCAAGTTTGGCAT
CATCGTCGTGTAATTGTTGAATGGCTAAATGATGCATCAAAAGAACTGGATCTCACTGAA
AAAATTCTCGATTTGGATGCAAAAAATTATCACGCATGGCAACATCGACAATGGGCAATT
GAGACTTTCAATCTTTTTGATAACGAGTTGGCTTTTATTGACAAACTTATTGCGGCTGAT
GTAAGAAATAATTCTGCATGGAATCAACGATTTTTCGTCTTGAAACATTTAGGCTTGACA
CCTGAGACTGTACAACGAGAAATTCATTATGCCATGAATCGTATTCGACTTATTAAAAAC
AACGAAAGCTCTTGGAATTTTTTAAAGGGTTTATTGGAGTATGGAGACTTTAGTATTAGT
CAATTTCCTGATGTTGAAACATTTACTGAGGAATTGTACAATTCTGGAAATCGATCGCCA
TATCTTTTAGCTTTTCTCGTTGATATGTACACTGAGAAGACATTACACATTTATGAAACA
AATAGCTACGATGATCCAGAAGTTTATGCTAGAAAAGTTGTTGAATTATGTGAAATGCTA
GCAAATCATTATGACACAATCAGATACAAGTATTGGAAATATGTTATTCAAAAGTTTAAC
GCAGATAAAGAACTCGCTAAAGTCGGTCCAAACGAACAAAATGAAGAAAAAGATGAAGAA
GAACATTTAGTTACAAGAGAGCCTGAGAAAGTCAATGGTGAAGCGCAATAA
>g12249.t1 Gene=g12249 Length=356
MSDSSDEDFNESYVMYRHRREWSDVHPIKQNDGPNPIVAIAYSERFLDVYDYFRAILATQ
EKSERALELTTDALRLNAANYTVWQYRREILHALKKNLYDELQYIAEVIEDNPKNYQVWH
HRRVIVEWLNDASKELDLTEKILDLDAKNYHAWQHRQWAIETFNLFDNELAFIDKLIAAD
VRNNSAWNQRFFVLKHLGLTPETVQREIHYAMNRIRLIKNNESSWNFLKGLLEYGDFSIS
QFPDVETFTEELYNSGNRSPYLLAFLVDMYTEKTLHIYETNSYDDPEVYARKVVELCEML
ANHYDTIRYKYWKYVIQKFNADKELAKVGPNEQNEEKDEEEHLVTREPEKVNGEAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12249.t1 | Gene3D | G3DSA:1.25.40.120 | Protein prenylyltransferase | 7 | 338 | 6.2E-117 |
| 8 | g12249.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 326 | 356 | - |
| 9 | g12249.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 328 | 356 | - |
| 5 | g12249.t1 | PANTHER | PTHR11129:SF5 | PROTEIN FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE TYPE-1 SUBUNIT ALPHA | 13 | 319 | 8.4E-104 |
| 6 | g12249.t1 | PANTHER | PTHR11129 | PROTEIN FARNESYLTRANSFERASE ALPHA SUBUNIT/RAB GERANYLGERANYL TRANSFERASE ALPHA SUBUNIT | 13 | 319 | 8.4E-104 |
| 3 | g12249.t1 | Pfam | PF01239 | Protein prenyltransferase alpha subunit repeat | 64 | 93 | 2.3E-7 |
| 1 | g12249.t1 | Pfam | PF01239 | Protein prenyltransferase alpha subunit repeat | 100 | 128 | 6.0E-11 |
| 2 | g12249.t1 | Pfam | PF01239 | Protein prenyltransferase alpha subunit repeat | 133 | 162 | 3.1E-10 |
| 4 | g12249.t1 | Pfam | PF01239 | Protein prenyltransferase alpha subunit repeat | 167 | 197 | 6.2E-8 |
| 13 | g12249.t1 | ProSiteProfiles | PS51147 | Protein prenyltransferases alpha subunit repeat profile. | 62 | 96 | 16.196 |
| 15 | g12249.t1 | ProSiteProfiles | PS51147 | Protein prenyltransferases alpha subunit repeat profile. | 97 | 131 | 19.825 |
| 12 | g12249.t1 | ProSiteProfiles | PS51147 | Protein prenyltransferases alpha subunit repeat profile. | 132 | 164 | 14.054 |
| 11 | g12249.t1 | ProSiteProfiles | PS51147 | Protein prenyltransferases alpha subunit repeat profile. | 165 | 199 | 16.542 |
| 14 | g12249.t1 | ProSiteProfiles | PS51147 | Protein prenyltransferases alpha subunit repeat profile. | 203 | 236 | 8.168 |
| 7 | g12249.t1 | SUPERFAMILY | SSF48439 | Protein prenylyltransferase | 8 | 319 | 8.37E-88 |
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:0018342 | protein prenylation | BP |
| GO:0008318 | protein prenyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05955 (protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha)
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.
