General information for g2508.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t17 | isoform | g2508.t17 | 18335460 | 18337750 |
| chr_3 | g2508 | g2508.t17 | exon | g2508.t17.exon1 | 18335460 | 18335816 |
| chr_3 | g2508 | g2508.t17 | cds | g2508.t17.CDS1 | 18335613 | 18335816 |
| chr_3 | g2508 | g2508.t17 | exon | g2508.t17.exon2 | 18335881 | 18336327 |
| chr_3 | g2508 | g2508.t17 | cds | g2508.t17.CDS2 | 18335881 | 18336327 |
| chr_3 | g2508 | g2508.t17 | exon | g2508.t17.exon3 | 18336707 | 18336739 |
| chr_3 | g2508 | g2508.t17 | cds | g2508.t17.CDS3 | 18336707 | 18336739 |
| chr_3 | g2508 | g2508.t17 | exon | g2508.t17.exon4 | 18336828 | 18337750 |
| chr_3 | g2508 | g2508.t17 | cds | g2508.t17.CDS4 | 18336828 | 18337010 |
| chr_3 | g2508 | g2508.t17 | TSS | g2508.t17 | NA | NA |
| chr_3 | g2508 | g2508.t17 | TTS | g2508.t17 | NA | NA |
Sequences
>g2508.t17 Gene=g2508 Length=1760
AGTAAATTTGAATAAAAGAAAAGTTAGAAAATAATAGAATTTTTTTACTGAGTTTGTCTC
CCTCTGATTAAAATTTACAAGTGAAATAATTCTATCGGCGTATCAAATTTTTTAAATAAA
GAATACTAAAAGTAAAGGGTTTCATTTATTACTATGATATGCCATGAAGGAAAAGTTAGT
GTCATAGCATTCATTACAAGCTTGCTAGTGCAATTGTTTGGTGTATCAGAATTCGGAGAA
AAACTTGCTCTATTCATTAGTGAATCATTTTTTTCATCAATTTACACTCTTTTTGTTCTG
TATTTTATCGTGCTGATATTATTCTTATCAATATGTTTCAAATCAACAGACTTTCAGATT
GCTATTCGAGCTGGAATTTTAGGGTATTTTTTTGGCATTGCTCTTTTTATTTCAATTACA
ATGGAGGATAAATACAAGTCTTTTGGAATTTATTTGGCTTTTTTAACATTCTTTCATTAC
TCGGAGTATTTTGTAATTTCGTTAAGTCATCCAGAATCATTGACACTTGATTCTTTTATG
CTTAATCATTCAATTCAATATGAATTTGCGGCTATAATTAGTTGGATAGAATATTTCGTT
GAAGTTTATTATTATCCTGAAATGAAAAAGTGCAAAACAATTTGGATAATAGGTTCTACT
ATTTGCTTAAGTGGTGAAATTTTGAGAAAGGTTGCAATGTTAACAGCCAAAAAAAGTTTC
CATCATTTAGTGCAATTTCAGCAAGCCGATGATCATAAATTAATAACGATAGGAGTTTAT
AGTTGGTTTCGACATCCTGCTTATGTGGGATGGTTTTATTGGTCTATAGCTACTCAGCTA
ATAATGGCAAACCCAATTTGTTTTGTTCTCTATCTCATTGCAAGCTGGCTTTTTTTCAAA
GAGAGAATCCATACTGAAGAGATCACTTTACTCAATTTCTTTGGACAAGAATATGTTCAA
TATCAGCAAAGAACAAAGACTGGTTTACCATTCATAAATGGATATATTACAACAAACTAA
TGCGAAATATTTTAATCTGTGATAAAGAAATCCAAATATGTTAAATTTAATTTCAGCACA
ATGCTTAGTACTTATTACACAACCACCACCGCAAATGCAAATTTAGGATCGAAATTGAAA
CCAGAATTTGAAATCGTTACGTTTAAGTAAATTTAGTTGCTTTTAGTTACTCATGAAACG
ATTTCGGACTCTGAATGAAACATTAATGTTATTATAGGTTTCAAAAATTTAATTTTATTA
TTTTCTCGATATACCTTTCATAATAAGATTTTAAATAACATTAATATGTGAGAAAAAATT
AAGGAAAAGAACTTATTCATTTTCATTTTTATACTTTTCTAATCGCTCTTTAATCCAAGC
ATCGATTTGAGCTTTTAATTTAGTATCGGGAATAAGTTGATCCATTGAAAGTGGAGAACG
ATTAAATGGATCACTTTGATCACTAAGAAGATGCCTTGAAATTGTTGACTTATCACAAGT
TACACGTGATGATGGTAAAATTACAGGATCGCGCATTAAAATCGATAATATTGGATCTAA
AAAGTTATCTGGTGGATTGACAAGCGCTTCTTCATTTTCTTTTTGTCGTTGTTCAACTTG
TCTTACTTTTTCAGCAAATTCTGTTATGTCAGTAATAAGTTGTCCGCCGCCAATCTTAAC
TACATAGATGATATTTAAAGAAAAATTTAATAAATATTTTATACTTGCTAAATGAATAAA
AGAATGAATTTCAACTTACT
>g2508.t17 Gene=g2508 Length=288
MICHEGKVSVIAFITSLLVQLFGVSEFGEKLALFISESFFSSIYTLFVLYFIVLILFLSI
CFKSTDFQIAIRAGILGYFFGIALFISITMEDKYKSFGIYLAFLTFFHYSEYFVISLSHP
ESLTLDSFMLNHSIQYEFAAIISWIEYFVEVYYYPEMKKCKTIWIIGSTICLSGEILRKV
AMLTAKKSFHHLVQFQQADDHKLITIGVYSWFRHPAYVGWFYWSIATQLIMANPICFVLY
LIASWLFFKERIHTEEITLLNFFGQEYVQYQQRTKTGLPFINGYITTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2508.t17 | Gene3D | G3DSA:1.20.120.1630 | - | 97 | 281 | 3.1E-30 |
| 2 | g2508.t17 | PANTHER | PTHR12714:SF9 | PROTEIN-S-ISOPRENYLCYSTEINE O-METHYLTRANSFERASE | 75 | 281 | 1.0E-62 |
| 3 | g2508.t17 | PANTHER | PTHR12714 | PROTEIN-S ISOPRENYLCYSTEINE O-METHYLTRANSFERASE | 75 | 281 | 1.0E-62 |
| 1 | g2508.t17 | Pfam | PF04140 | Isoprenylcysteine carboxyl methyltransferase (ICMT) family | 170 | 259 | 6.6E-28 |
| 19 | g2508.t17 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 20 | g2508.t17 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 21 | g2508.t17 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 19 | - |
| 27 | g2508.t17 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 20 | 23 | - |
| 17 | g2508.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 38 | - |
| 26 | g2508.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 62 | - |
| 15 | g2508.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 63 | 68 | - |
| 25 | g2508.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 90 | - |
| 18 | g2508.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 91 | 95 | - |
| 23 | g2508.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 115 | - |
| 14 | g2508.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 116 | 135 | - |
| 24 | g2508.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 154 | - |
| 16 | g2508.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 155 | 219 | - |
| 22 | g2508.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 248 | - |
| 13 | g2508.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 249 | 288 | - |
| 12 | g2508.t17 | ProSiteProfiles | PS51564 | Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) family profile. | 9 | 288 | 32.972 |
| 7 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 27 | - |
| 6 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 40 | 62 | - |
| 4 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 89 | - |
| 5 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 118 | - |
| 9 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 155 | - |
| 10 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 184 | - |
| 8 | g2508.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 242 | - |
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:0005783 | endoplasmic reticulum | CC |
| 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 transcript has been annotated with K00587 (protein-S-isoprenylcysteine O-methyltransferase)
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.
