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.t8 TTS g10440.t8 9852108 9852108
chr_1 g10440 g10440.t8 isoform g10440.t8 9852202 9853437
chr_1 g10440 g10440.t8 exon g10440.t8.exon1 9852202 9852314
chr_1 g10440 g10440.t8 cds g10440.t8.CDS1 9852202 9852314
chr_1 g10440 g10440.t8 exon g10440.t8.exon2 9852439 9852627
chr_1 g10440 g10440.t8 cds g10440.t8.CDS2 9852439 9852627
chr_1 g10440 g10440.t8 exon g10440.t8.exon3 9852694 9852861
chr_1 g10440 g10440.t8 cds g10440.t8.CDS3 9852694 9852861
chr_1 g10440 g10440.t8 exon g10440.t8.exon4 9852929 9853173
chr_1 g10440 g10440.t8 cds g10440.t8.CDS4 9852929 9853173
chr_1 g10440 g10440.t8 exon g10440.t8.exon5 9853263 9853292
chr_1 g10440 g10440.t8 cds g10440.t8.CDS5 9853263 9853292
chr_1 g10440 g10440.t8 exon g10440.t8.exon6 9853364 9853437
chr_1 g10440 g10440.t8 cds g10440.t8.CDS6 9853364 9853437
chr_1 g10440 g10440.t8 TSS g10440.t8 9853567 9853567

Sequences

>g10440.t8 Gene=g10440 Length=819
ATGGATTTGTTTCAAATTTCTATTTATGCTTCATTAGGAAGTTGCTTTTCTTTGTCATGT
TTATATGTTGCAAGTCTTTATGTATGGAATGTTGAAGAAAATCGAGACCATCCTTCAACG
ATTAAAAAACGTTTTTTTAGCGTATTCATTGTGATGCTCATTTCACCACTTTTCATCTAC
CTCTTCTCATCATCTGATCTTTTAAAAACGTACACAATATGGTACGTGATGGGATTAAGG
ATTGAAGGATTTTTCTCCGCTCTCATTTATCCTCTTTTACTTACTATTGTTTTATTTCTT
GGACCATTGAGTGTACAGTTGACGAATAGTATATGGAAAGTTTATTCAGAACCAATGTTC
TGGTTTATTAATTGTCAGAATTTATTGTGGATTCGAAACCACATTGTAGCACCGTTATCA
GAAGAATTTACATTTCGAGCATGTATGCTCCCTTTACTTCTACAATGTTTCACACCAATG
ACATCAATTTTCATAACTCCAATGTTTTTCGGTGTTGCTCATTTACATCATATGATTGAA
AGATTAAGAAGTGGAATGGATAAGCGGACTGCCATTATTATCTCATTTTTTCAATTTTTC
TATACATCTGTCTTTGGAATCTATTCTGCATATCTTTTTGTGAGAACAGGTCATTTTGTT
GCGCCTTTTATAGCTCATGCTTTTTGTAACCACATGGGATTTCCTGGCCTAGTCGGCTTT
ATTCTTCTTTTGCCAACTATGACCGAACCTACATGGTATCAAAATAATCAATTTTGGTAC
AATAATTATACCAAGTCAGCATTTAACTCGAGCATTTAA

>g10440.t8 Gene=g10440 Length=272
MDLFQISIYASLGSCFSLSCLYVASLYVWNVEENRDHPSTIKKRFFSVFIVMLISPLFIY
LFSSSDLLKTYTIWYVMGLRIEGFFSALIYPLLLTIVLFLGPLSVQLTNSIWKVYSEPMF
WFINCQNLLWIRNHIVAPLSEEFTFRACMLPLLLQCFTPMTSIFITPMFFGVAHLHHMIE
RLRSGMDKRTAIIISFFQFFYTSVFGIYSAYLFVRTGHFVAPFIAHAFCNHMGFPGLVGF
ILLLPTMTEPTWYQNNQFWYNNYTKSAFNSSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10440.t8 PANTHER PTHR13046 PROTEASE U48 CAAX PRENYL PROTEASE RCE1 5 240 6.6E-77
1 g10440.t8 Pfam PF02517 CPBP intramembrane metalloprotease 127 231 9.4E-18
15 g10440.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
22 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 29 -
12 g10440.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 30 44 -
21 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 63 -
16 g10440.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 64 82 -
23 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 83 107 -
9 g10440.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 108 118 -
19 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 137 -
13 g10440.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 148 -
20 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 149 170 -
10 g10440.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 171 190 -
18 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 211 -
14 g10440.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 212 222 -
17 g10440.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 223 244 -
11 g10440.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 245 272 -
3 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
8 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 63 -
7 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 83 105 -
5 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 179 -
6 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 191 213 -
4 g10440.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 223 245 -

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