Gene loci information

Transcript annotation

  • This transcript has been annotated as 4-hydroxybenzoate polyprenyltransferase, mitochondrial.

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_2 g8115 g8115.t4 TSS g8115.t4 28647153 28647153
chr_2 g8115 g8115.t4 isoform g8115.t4 28647396 28648422
chr_2 g8115 g8115.t4 exon g8115.t4.exon1 28647396 28647660
chr_2 g8115 g8115.t4 cds g8115.t4.CDS1 28647396 28647660
chr_2 g8115 g8115.t4 exon g8115.t4.exon2 28647729 28648422
chr_2 g8115 g8115.t4 cds g8115.t4.CDS2 28647729 28648420
chr_2 g8115 g8115.t4 TTS g8115.t4 28648726 28648726

Sequences

>g8115.t4 Gene=g8115 Length=959
ATGCTTTTGAGACTTAAAAGTTCTCGCTTAATTGATACCAGGACTTGGAAAAAAGTGTTA
AACTATAATTTAAACTATACGACGCTTGAAATACCAAAAATTACCTTTATTAGCTCATCT
TCATTTAGCACATGCAAAAACATCAACTATAGTCCTATTAAGCAGAATGAAGCTAATACA
GTTACAAAGAACATTGTGAAAGACTATTTTGAAAAATTTCGAAGTTCACCGTATGTGAGA
ATCATGAGATTGGATCGACCCATTGGTTCATTATTGCTTTATTGGCCATGTAGTTGGTCA
ATAGCAGTGGCTGCACAACCTGGATGTATACCTGATCTTTATATGCTTGCTTTATTTGCA
TCGGGGGCAATAATAATGAGAGGAGCAGGATGCACTATAAATGATATGTGGGATAAAAAT
ATTGATGCAAAAGTGCAGAGAACAAGTACACGACCGTTAGTAACAGGAGAGATGACTCAC
TTAGATGCATGGTTTTTCCTTGGTGCACAACTTGGTTTAGGGCTTTTAATTCTCCTAGAA
CTTAATTGGAATGCGATTCTTCTCGGTGCCAGTTCATTAGGTTTAGTAATCGTCTATCCA
CTTATGAAACGTATTACTAATTGGCCTCAGTTTGTGCTCGGTATGACATTTAATTGGGGT
GCACTTCTTGGATTCTGTGCAATACATGGCGATGTCAATTGGGCTGCATGCTTGCCACTT
TATACCGCCGGCATTTGTTGGACAATTATTTATGATACAATTTATGCTCATCAAGATAGA
GTTGATGACTTAATAGTTGGTGTAAAATCTACTGCTCTTCGTTTTGGAAGAGACACTAAA
AAGTGGCTTACATGTTTTGCAGTTTTAATGAACTCAAGTTTGATAACTACTGGATTAGTT
TGTGATTTGACATGGCCATATTACGCTTCAATCTCTGTTATCGCTGCGCATATAGGACA

>g8115.t4 Gene=g8115 Length=319
MLLRLKSSRLIDTRTWKKVLNYNLNYTTLEIPKITFISSSSFSTCKNINYSPIKQNEANT
VTKNIVKDYFEKFRSSPYVRIMRLDRPIGSLLLYWPCSWSIAVAAQPGCIPDLYMLALFA
SGAIIMRGAGCTINDMWDKNIDAKVQRTSTRPLVTGEMTHLDAWFFLGAQLGLGLLILLE
LNWNAILLGASSLGLVIVYPLMKRITNWPQFVLGMTFNWGALLGFCAIHGDVNWAACLPL
YTAGICWTIIYDTIYAHQDRVDDLIVGVKSTALRFGRDTKKWLTCFAVLMNSSLITTGLV
CDLTWPYYASISVIAAHIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g8115.t4 CDD cd13959 PT_UbiA_COQ2 82 318 2.51139E-98
6 g8115.t4 Gene3D G3DSA:1.10.357.140 - 89 238 2.9E-42
5 g8115.t4 Gene3D G3DSA:1.20.120.1780 - 239 319 1.1E-6
4 g8115.t4 Hamap MF_01635 4-hydroxybenzoate octaprenyltransferase [ubiA]. 71 318 22.690058
2 g8115.t4 PANTHER PTHR11048 PRENYLTRANSFERASES 46 318 1.6E-116
3 g8115.t4 PANTHER PTHR11048:SF28 4-HYDROXYBENZOATE POLYPRENYLTRANSFERASE, MITOCHONDRIAL 46 318 1.6E-116
1 g8115.t4 Pfam PF01040 UbiA prenyltransferase family 93 318 2.9E-62
8 g8115.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 87 -
13 g8115.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 107 -
11 g8115.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 108 112 -
14 g8115.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 137 -
9 g8115.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 138 157 -
12 g8115.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 158 179 -
10 g8115.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 180 184 -
15 g8115.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 185 202 -
7 g8115.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 203 319 -
20 g8115.t4 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 134 156 -
21 g8115.t4 TIGRFAM TIGR01474 ubiA_proteo: 4-hydroxybenzoate polyprenyl transferase 77 318 1.0E-96
19 g8115.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -
17 g8115.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 211 228 -
18 g8115.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 232 251 -

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:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups MF
GO:0004659 prenyltransferase activity MF
GO:0016021 integral component of membrane CC

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