Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t19 TSS g2508.t19 18335520 18335520
chr_3 g2508 g2508.t19 isoform g2508.t19 18335879 18337323
chr_3 g2508 g2508.t19 exon g2508.t19.exon1 18335879 18336327
chr_3 g2508 g2508.t19 cds g2508.t19.CDS1 18335944 18336327
chr_3 g2508 g2508.t19 exon g2508.t19.exon2 18336707 18336739
chr_3 g2508 g2508.t19 cds g2508.t19.CDS2 18336707 18336739
chr_3 g2508 g2508.t19 exon g2508.t19.exon3 18336828 18337323
chr_3 g2508 g2508.t19 cds g2508.t19.CDS3 18336828 18337010
chr_3 g2508 g2508.t19 TTS g2508.t19 NA NA

Sequences

>g2508.t19 Gene=g2508 Length=978
AGATTGCTATTCGAGCTGGAATTTTAGGGTATTTTTTTGGCATTGCTCTTTTTATTTCAA
TTACAATGGAGGATAAATACAAGTCTTTTGGAATTTATTTGGCTTTTTTAACATTCTTTC
ATTACTCGGAGTATTTTGTAATTTCGTTAAGTCATCCAGAATCATTGACACTTGATTCTT
TTATGCTTAATCATTCAATTCAATATGAATTTGCGGCTATAATTAGTTGGATAGAATATT
TCGTTGAAGTTTATTATTATCCTGAAATGAAAAAGTGCAAAACAATTTGGATAATAGGTT
CTACTATTTGCTTAAGTGGTGAAATTTTGAGAAAGGTTGCAATGTTAACAGCCAAAAAAA
GTTTCCATCATTTAGTGCAATTTCAGCAAGCCGATGATCATAAATTAATAACGATAGGAG
TTTATAGTTGGTTTCGACATCCTGCTTATGTGGGATGGTTTTATTGGTCTATAGCTACTC
AGCTAATAATGGCAAACCCAATTTGTTTTGTTCTCTATCTCATTGCAAGCTGGCTTTTTT
TCAAAGAGAGAATCCATACTGAAGAGATCACTTTACTCAATTTCTTTGGACAAGAATATG
TTCAATATCAGCAAAGAACAAAGACTGGTTTACCATTCATAAATGGATATATTACAACAA
ACTAATGCGAAATATTTTAATCTGTGATAAAGAAATCCAAATATGTTAAATTTAATTTCA
GCACAATGCTTAGTACTTATTACACAACCACCACCGCAAATGCAAATTTAGGATCGAAAT
TGAAACCAGAATTTGAAATCGTTACGTTTAAGTAAATTTAGTTGCTTTTAGTTACTCATG
AAACGATTTCGGACTCTGAATGAAACATTAATGTTATTATAGGTTTCAAAAATTTAATTT
TATTATTTTCTCGATATACCTTTCATAATAAGATTTTAAATAACATTAATATGTGAGAAA
AAATTAAGGAAAAGAACT

>g2508.t19 Gene=g2508 Length=199
MEDKYKSFGIYLAFLTFFHYSEYFVISLSHPESLTLDSFMLNHSIQYEFAAIISWIEYFV
EVYYYPEMKKCKTIWIIGSTICLSGEILRKVAMLTAKKSFHHLVQFQQADDHKLITIGVY
SWFRHPAYVGWFYWSIATQLIMANPICFVLYLIASWLFFKERIHTEEITLLNFFGQEYVQ
YQQRTKTGLPFINGYITTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2508.t19 Gene3D G3DSA:1.20.120.1630 - 4 192 1.3E-30
2 g2508.t19 PANTHER PTHR12714:SF9 PROTEIN-S-ISOPRENYLCYSTEINE O-METHYLTRANSFERASE 7 192 5.2E-64
3 g2508.t19 PANTHER PTHR12714 PROTEIN-S ISOPRENYLCYSTEINE O-METHYLTRANSFERASE 7 192 5.2E-64
1 g2508.t19 Pfam PF04140 Isoprenylcysteine carboxyl methyltransferase (ICMT) family 81 170 2.9E-28
12 g2508.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
18 g2508.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 26 -
13 g2508.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 45 -
15 g2508.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 46 66 -
11 g2508.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 67 72 -
16 g2508.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 73 92 -
14 g2508.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 130 -
17 g2508.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 159 -
10 g2508.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 160 199 -
9 g2508.t19 ProSiteProfiles PS51564 Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) family profile. 5 199 27.921
4 g2508.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
6 g2508.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
7 g2508.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
5 g2508.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 153 -

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

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.

Raw TPM values