General information for g2508.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein-S-isoprenylcysteine O-methyltransferase.
Parent gene
- The parent gene g2508 is located on chr_3: 18335879..18337750 (+ 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_3 | g2508 | g2508.t18 | TSS | g2508.t18 | 18335520 | 18335520 |
| chr_3 | g2508 | g2508.t18 | isoform | g2508.t18 | 18335804 | 18337750 |
| chr_3 | g2508 | g2508.t18 | exon | g2508.t18.exon1 | 18335804 | 18335816 |
| chr_3 | g2508 | g2508.t18 | exon | g2508.t18.exon2 | 18335881 | 18336327 |
| chr_3 | g2508 | g2508.t18 | cds | g2508.t18.CDS1 | 18335944 | 18336327 |
| chr_3 | g2508 | g2508.t18 | exon | g2508.t18.exon3 | 18336805 | 18337750 |
| chr_3 | g2508 | g2508.t18 | cds | g2508.t18.CDS2 | 18336805 | 18336831 |
| chr_3 | g2508 | g2508.t18 | TTS | g2508.t18 | NA | NA |
Sequences
>g2508.t18 Gene=g2508 Length=1406
AACAGACTTTCAGATTGCTATTCGAGCTGGAATTTTAGGGTATTTTTTTGGCATTGCTCT
TTTTATTTCAATTACAATGGAGGATAAATACAAGTCTTTTGGAATTTATTTGGCTTTTTT
AACATTCTTTCATTACTCGGAGTATTTTGTAATTTCGTTAAGTCATCCAGAATCATTGAC
ACTTGATTCTTTTATGCTTAATCATTCAATTCAATATGAATTTGCGGCTATAATTAGTTG
GATAGAATATTTCGTTGAAGTTTATTATTATCCTGAAATGAAAAAGTGCAAAACAATTTG
GATAATAGGTTCTACTATTTGCTTAAGTGGTGAAATTTTGAGAAAGGTTGCAATGTTAAC
AGCCAAAAAAAGTTTCCATCATTTAGTGCAATTTCAGCAAGCCGATGATCATAAATTAAT
AACGATAGGAGTTTATAGTTGGTTTCGACATCCTGCTTATATTAATCTTTCTTTTTTTTT
CAGCTAATAATGGCAAACCCAATTTGTTTTGTTCTCTATCTCATTGCAAGCTGGCTTTTT
TTCAAAGAGAGAATCCATACTGAAGAGATCACTTTACTCAATTTCTTTGGACAAGAATAT
GTTCAATATCAGCAAAGAACAAAGACTGGTTTACCATTCATAAATGGATATATTACAACA
AACTAATGCGAAATATTTTAATCTGTGATAAAGAAATCCAAATATGTTAAATTTAATTTC
AGCACAATGCTTAGTACTTATTACACAACCACCACCGCAAATGCAAATTTAGGATCGAAA
TTGAAACCAGAATTTGAAATCGTTACGTTTAAGTAAATTTAGTTGCTTTTAGTTACTCAT
GAAACGATTTCGGACTCTGAATGAAACATTAATGTTATTATAGGTTTCAAAAATTTAATT
TTATTATTTTCTCGATATACCTTTCATAATAAGATTTTAAATAACATTAATATGTGAGAA
AAAATTAAGGAAAAGAACTTATTCATTTTCATTTTTATACTTTTCTAATCGCTCTTTAAT
CCAAGCATCGATTTGAGCTTTTAATTTAGTATCGGGAATAAGTTGATCCATTGAAAGTGG
AGAACGATTAAATGGATCACTTTGATCACTAAGAAGATGCCTTGAAATTGTTGACTTATC
ACAAGTTACACGTGATGATGGTAAAATTACAGGATCGCGCATTAAAATCGATAATATTGG
ATCTAAAAAGTTATCTGGTGGATTGACAAGCGCTTCTTCATTTTCTTTTTGTCGTTGTTC
AACTTGTCTTACTTTTTCAGCAAATTCTGTTATGTCAGTAATAAGTTGTCCGCCGCCAAT
CTTAACTACATAGATGATATTTAAAGAAAAATTTAATAAATATTTTATACTTGCTAAATG
AATAAAAGAATGAATTTCAACTTACT
>g2508.t18 Gene=g2508 Length=136
MEDKYKSFGIYLAFLTFFHYSEYFVISLSHPESLTLDSFMLNHSIQYEFAAIISWIEYFV
EVYYYPEMKKCKTIWIIGSTICLSGEILRKVAMLTAKKSFHHLVQFQQADDHKLITIGVY
SWFRHPAYINLSFFFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2508.t18 | Gene3D | G3DSA:1.20.120.1630 | - | 6 | 136 | 1.9E-11 |
| 2 | g2508.t18 | PANTHER | PTHR12714:SF9 | PROTEIN-S-ISOPRENYLCYSTEINE O-METHYLTRANSFERASE | 7 | 130 | 2.0E-31 |
| 3 | g2508.t18 | PANTHER | PTHR12714 | PROTEIN-S ISOPRENYLCYSTEINE O-METHYLTRANSFERASE | 7 | 130 | 2.0E-31 |
| 1 | g2508.t18 | Pfam | PF04140 | Isoprenylcysteine carboxyl methyltransferase (ICMT) family | 81 | 130 | 3.4E-12 |
| 7 | g2508.t18 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 10 | g2508.t18 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
| 9 | g2508.t18 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 45 | - |
| 11 | g2508.t18 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 65 | - |
| 8 | g2508.t18 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 66 | 136 | - |
| 4 | g2508.t18 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
| 5 | g2508.t18 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 66 | - |
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:0016021 | integral component of membrane | CC |
| GO:0006481 | C-terminal protein methylation | BP |
| GO:0004671 | protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity | MF |
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.
