Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative CAAX prenyl protease 2.

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_1 g10440 g10440.t4 TTS g10440.t4 9852108 9852108
chr_1 g10440 g10440.t4 isoform g10440.t4 9852202 9852861
chr_1 g10440 g10440.t4 exon g10440.t4.exon1 9852202 9852380
chr_1 g10440 g10440.t4 cds g10440.t4.CDS1 9852202 9852380
chr_1 g10440 g10440.t4 exon g10440.t4.exon2 9852439 9852627
chr_1 g10440 g10440.t4 cds g10440.t4.CDS2 9852439 9852613
chr_1 g10440 g10440.t4 exon g10440.t4.exon3 9852690 9852861
chr_1 g10440 g10440.t4 TSS g10440.t4 9853567 9853567

Sequences

>g10440.t4 Gene=g10440 Length=540
AACCAATGTTCTGGTTTATTAATTGTCAGAATTTATTGTGGATTCGAAACCACATTGTAG
CACCGTTATCAGAAGAATTTACATTTCGAGCATGTATGCTCCCTTTACTTCTACAATGTT
TCACACCAATGACATCAATTTTCATAACTCCAATGTTTTTCGGTGTTGGTAACTCATTTA
CATCATATGATTGAAAGATTAAGAAGTGGAATGGATAAGCGGACTGCCATTATTATCTCA
TTTTTTCAATTTTTCTATACATCTGTCTTTGGAATCTATTCTGCATATCTTTTTGTGAGA
ACAGGTCATTTTGTTGCGCCTTTTATAGCTCATGCTTTTTGTAACCACATGGGATTTCCT
GATATACCAGATCTCATTGCACAACCCGAGCCGAAACGATTTGTGTTTTTAATTCTCTAT
GTTTTAGGCCTAGTCGGCTTTATTCTTCTTTTGCCAACTATGACCGAACCTACATGGTAT
CAAAATAATCAATTTTGGTACAATAATTATACCAAGTCAGCATTTAACTCGAGCATTTAA

>g10440.t4 Gene=g10440 Length=117
MIERLRSGMDKRTAIIISFFQFFYTSVFGIYSAYLFVRTGHFVAPFIAHAFCNHMGFPDI
PDLIAQPEPKRFVFLILYVLGLVGFILLLPTMTEPTWYQNNQFWYNNYTKSAFNSSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10440.t4 PANTHER PTHR13046 PROTEASE U48 CAAX PRENYL PROTEASE RCE1 3 101 4.1E-29
1 g10440.t4 Pfam PF02517 CPBP intramembrane metalloprotease 18 54 4.8E-6
6 g10440.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
9 g10440.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 36 -
7 g10440.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 41 -
11 g10440.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 42 60 -
5 g10440.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 61 71 -
10 g10440.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 92 -
8 g10440.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 117 -
4 g10440.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
3 g10440.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 89 -

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:0016020 membrane CC
GO:0004222 metalloendopeptidase activity MF
GO:0030176 integral component of endoplasmic reticulum membrane CC
GO:0071586 CAAX-box protein processing BP

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