Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein-S-isoprenylcysteine O-methyltransferase.

Parent gene

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.t11 isoform g2508.t11 18335460 18337010
chr_3 g2508 g2508.t11 exon g2508.t11.exon1 18335460 18335816
chr_3 g2508 g2508.t11 cds g2508.t11.CDS1 18335613 18335816
chr_3 g2508 g2508.t11 exon g2508.t11.exon2 18335881 18336739
chr_3 g2508 g2508.t11 cds g2508.t11.CDS2 18335881 18336363
chr_3 g2508 g2508.t11 exon g2508.t11.exon3 18336828 18337010
chr_3 g2508 g2508.t11 TSS g2508.t11 NA NA
chr_3 g2508 g2508.t11 TTS g2508.t11 NA NA

Sequences

>g2508.t11 Gene=g2508 Length=1399
AGTAAATTTGAATAAAAGAAAAGTTAGAAAATAATAGAATTTTTTTACTGAGTTTGTCTC
CCTCTGATTAAAATTTACAAGTGAAATAATTCTATCGGCGTATCAAATTTTTTAAATAAA
GAATACTAAAAGTAAAGGGTTTCATTTATTACTATGATATGCCATGAAGGAAAAGTTAGT
GTCATAGCATTCATTACAAGCTTGCTAGTGCAATTGTTTGGTGTATCAGAATTCGGAGAA
AAACTTGCTCTATTCATTAGTGAATCATTTTTTTCATCAATTTACACTCTTTTTGTTCTG
TATTTTATCGTGCTGATATTATTCTTATCAATATGTTTCAAATCAACAGACTTTCAGATT
GCTATTCGAGCTGGAATTTTAGGGTATTTTTTTGGCATTGCTCTTTTTATTTCAATTACA
ATGGAGGATAAATACAAGTCTTTTGGAATTTATTTGGCTTTTTTAACATTCTTTCATTAC
TCGGAGTATTTTGTAATTTCGTTAAGTCATCCAGAATCATTGACACTTGATTCTTTTATG
CTTAATCATTCAATTCAATATGAATTTGCGGCTATAATTAGTTGGATAGAATATTTCGTT
GAAGTTTATTATTATCCTGAAATGAAAAAGTGCAAAACAATTTGGATAATAGGTTCTACT
ATTTGCTTAAGTGGTGAAATTTTGAGAAAGGTTGCAATGTTAACAGCCAAAAAAAGTTTC
CATCATTTAGTGCAATTTCAGCAAGCCGATGATCATAAATTAATAACGATAGGAGTTTAT
AGTTGGTTTCGACATCCTGCTTATGTGAGTGATAACATAAAAGAAAAAAGCAAGAAATAA
TAGAATATTTCAATCAAGTCAAAAAAGTGGCCGTTTGAAAACCGTTAAAATAACTGATAT
AAAATTAATATTGTGATTATTCTCAAATCCAATATACTTTTTAAATTTTACTTGTACATA
TTTTAATATGTTAAGAGCATGAAAAAATTTTAAATTACAATTAAATGCCAATTTACATCT
TTTTTAATCTAAAAATAATATTTTCTTGTTTTAAAAATCTAAAAAATAGCGCCACCTACA
ATTAATTGTAACAGCCAAATTGTCAATTGAAATATTCTATTACCATAGGTATTTCCTGAA
AAAATATTTTCTTATAATTTATTTAAAATTATAATCATCATAGGTGGGATGGTTTTATTG
GTCTATAGCTACTCAGCTAATAATGGCAAACCCAATTTGTTTTGTTCTCTATCTCATTGC
AAGCTGGCTTTTTTTCAAAGAGAGAATCCATACTGAAGAGATCACTTTACTCAATTTCTT
TGGACAAGAATATGTTCAATATCAGCAAAGAACAAAGACTGGTTTACCATTCATAAATGG
ATATATTACAACAAACTAA

>g2508.t11 Gene=g2508 Length=228
MICHEGKVSVIAFITSLLVQLFGVSEFGEKLALFISESFFSSIYTLFVLYFIVLILFLSI
CFKSTDFQIAIRAGILGYFFGIALFISITMEDKYKSFGIYLAFLTFFHYSEYFVISLSHP
ESLTLDSFMLNHSIQYEFAAIISWIEYFVEVYYYPEMKKCKTIWIIGSTICLSGEILRKV
AMLTAKKSFHHLVQFQQADDHKLITIGVYSWFRHPAYVSDNIKEKSKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2508.t11 Gene3D G3DSA:1.20.120.1630 - 96 221 1.9E-10
2 g2508.t11 PANTHER PTHR12714:SF9 PROTEIN-S-ISOPRENYLCYSTEINE O-METHYLTRANSFERASE 75 218 2.0E-30
3 g2508.t11 PANTHER PTHR12714 PROTEIN-S ISOPRENYLCYSTEINE O-METHYLTRANSFERASE 75 218 2.0E-30
1 g2508.t11 Pfam PF04140 Isoprenylcysteine carboxyl methyltransferase (ICMT) family 170 219 6.4E-12
17 g2508.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 23 -
18 g2508.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
19 g2508.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 19 -
25 g2508.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 20 23 -
14 g2508.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 24 38 -
24 g2508.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 39 62 -
13 g2508.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 63 68 -
23 g2508.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 69 90 -
15 g2508.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 91 95 -
21 g2508.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 115 -
11 g2508.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 135 -
22 g2508.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 155 -
16 g2508.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 160 -
20 g2508.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 161 177 -
12 g2508.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 178 228 -
10 g2508.t11 ProSiteProfiles PS51564 Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) family profile. 9 218 15.833
7 g2508.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 27 -
6 g2508.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 62 -
4 g2508.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 89 -
5 g2508.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 118 -
8 g2508.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -

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 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.

Raw TPM values