Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t2 TTS g10440.t2 9852108 9852108
chr_1 g10440 g10440.t2 isoform g10440.t2 9852124 9853437
chr_1 g10440 g10440.t2 exon g10440.t2.exon1 9852124 9852627
chr_1 g10440 g10440.t2 cds g10440.t2.CDS1 9852419 9852627
chr_1 g10440 g10440.t2 exon g10440.t2.exon2 9852694 9852861
chr_1 g10440 g10440.t2 cds g10440.t2.CDS2 9852694 9852861
chr_1 g10440 g10440.t2 exon g10440.t2.exon3 9852929 9853437
chr_1 g10440 g10440.t2 cds g10440.t2.CDS3 9852929 9853124
chr_1 g10440 g10440.t2 TSS g10440.t2 9853567 9853567

Sequences

>g10440.t2 Gene=g10440 Length=1181
ATGGATTTGTTTCAAATTTCTATTTATGCTTCATTAGGAAGTTGCTTTTCTTTGTCATGT
TTATATGTTGCAAGGTATTTATACATTTTATTGTCCTACATACAATTAGAAATTATAATG
CATTTTAATTATTAATATTTTTTAGTCTTTATGTATGGAATGTTGAAGAAAATCGGTAAG
AAATCTGAAAAAGAAAAAAAATTCCAAAAGCATTTAGTCATCAACCTTCACGACTCTTAT
TATTCTTTAATTTTTTGCTTTTAGAGACCATCCTTCAACGATTAAAAAACGTTTTTTTAG
CGTATTCATTGTGATGCTCATTTCACCACTTTTCATCTACCTCTTCTCATCATCTGATCT
TTTAAAAACGTACACAATATGGTACGTGATGGGATTAAGGATTGAAGGATTTTTCTCCGC
TCTCATTTATCCTCTTTTACTTACTATTGTTTTATTTCTTGGACCATTGAGTGTACAGTT
GACGAATAGTATATGGAAAGTTTATTCAGAACCAATGTTCTGGTTTATTAATTGTCAGAA
TTTATTGTGGATTCGAAACCACATTGTAGCACCGTTATCAGAAGAATTTACATTTCGAGC
ATGTATGCTCCCTTTACTTCTACAATGTTTCACACCAATGACATCAATTTTCATAACTCC
AATGTTTTTCGGTGTTGCTCATTTACATCATATGATTGAAAGATTAAGAAGTGGAATGGA
TAAGCGGACTGCCATTATTATCTCATTTTTTCAATTTTTCTATACATCTGTCTTTGGAAT
CTATTCTGCATATCTTTTTGTGAGAACAGGTCATTTTGTTGCGCCTTTTATAGCTCATGC
TTTTTGTAACCACATGGGATTTCCTGGTAATTTTTTACAACAATAATCACTTGTACAAAT
GAATTTTAATTTTTAAATTCATAGATATACCAGATCTCATTGCACAACCCGAGCCGAAAC
GATTTGTGTTTTTAATTCTCTATGTTTTAGGCCTAGTCGGCTTTATTCTTCTTTTGCCAA
CTATGACCGAACCTACATGGTATCAAAATAATCAATTTTGGTACAATAATTATACCAAGT
CAGCATTTAACTCGAGCATTTAATTAACCTTCAAGTATTTTTGAATGTATGCATTGAAAA
TAGGACAAATTTTTGCATAATAAATTCTGTTAATAAAAAAA

>g10440.t2 Gene=g10440 Length=190
MLISPLFIYLFSSSDLLKTYTIWYVMGLRIEGFFSALIYPLLLTIVLFLGPLSVQLTNSI
WKVYSEPMFWFINCQNLLWIRNHIVAPLSEEFTFRACMLPLLLQCFTPMTSIFITPMFFG
VAHLHHMIERLRSGMDKRTAIIISFFQFFYTSVFGIYSAYLFVRTGHFVAPFIAHAFCNH
MGFPGNFLQQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10440.t2 PANTHER PTHR13046 PROTEASE U48 CAAX PRENYL PROTEASE RCE1 2 185 3.8E-59
1 g10440.t2 Pfam PF02517 CPBP intramembrane metalloprotease 77 180 2.3E-18
11 g10440.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
15 g10440.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 26 -
9 g10440.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 27 32 -
14 g10440.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 33 54 -
10 g10440.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 97 -
13 g10440.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 98 119 -
8 g10440.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 139 -
17 g10440.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 162 -
12 g10440.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 163 167 -
16 g10440.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 188 -
7 g10440.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 189 190 -
6 g10440.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
3 g10440.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 32 54 -
5 g10440.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
4 g10440.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -

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

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