Gene loci information

Transcript annotation

  • This transcript has been annotated as Protoheme IX farnesyltransferase, 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_1 g12134 g12134.t5 TSS g12134.t5 21225818 21225818
chr_1 g12134 g12134.t5 isoform g12134.t5 21225909 21227115
chr_1 g12134 g12134.t5 exon g12134.t5.exon1 21225909 21225974
chr_1 g12134 g12134.t5 cds g12134.t5.CDS1 21225909 21225974
chr_1 g12134 g12134.t5 exon g12134.t5.exon2 21226221 21226912
chr_1 g12134 g12134.t5 cds g12134.t5.CDS2 21226221 21226912
chr_1 g12134 g12134.t5 exon g12134.t5.exon3 21226974 21227115
chr_1 g12134 g12134.t5 cds g12134.t5.CDS3 21226974 21227115
chr_1 g12134 g12134.t5 TTS g12134.t5 21227600 21227600

Sequences

>g12134.t5 Gene=g12134 Length=900
ATGTACAGTGTAGTATTAAGAACTAGATTACTGAATGGAATCAACACGAAATCATTTGTA
TTTAAGAACTATACGCAGTCGACAACAAAACTTTATTCTTCACCCACAGTTGTACCACAA
AAAAAGCTAGATGATGAAAAATTAATTCATGATGAGGAGCGTTTGATTACAAAAATTTCA
GTGAAACAACTTAATCCAGATATAGTGAAAGTGATAGAAAACGATGTAAAAAAACAACAG
AGCAATAATCAAGTGGTTGCTCGAAAAGAATTAGAGCTACCATGGAGAATAACACCATCA
ACAGACCAAAACAAGCTGCTCAAACATTATTTGATGTTATCGAAAATTCGACTTACATCA
CTTGTTGTTATTACATCGATGGCTGGATATGCAATGGCACCTGCACCTTTTGATCTCAGC
ACGTTCATTATGTGTTCTGTTGGTACTGGATTGTTATCATGTGCTGCAAACTCTATTAAT
CAATTTTTTGAAACACCTTTTGATGCACAAATGTCGAGAACGAAAAATCGAGTGTTGGTG
AAAGGCTATTTAACTCCTCTTCACGCTGTTGGATTTGCAGCAGTTGCTGCTTCATCAGGG
CTATTAATTCTTACATGCGGCGTAAATGAATTAACAGCTGCATTAGGCTTTTCAAATTTA
ATTTTGTACACATGCATATACACACCAATGAAACGCTATAGCATACTTAACACATGGGTT
GGCTCGATTGTCGGAGCTATTCCACCACTTATGGGATGGGCTGGATGTGCTGGCACTCTT
GATACTGGTGCATGGATTCTAGCTGGTCTCCTTTATGCATGGCAATTTCCTCACTTTAAT
GCACTCTCATGGAATCTTAGACCAGATTATTCAAGAGCAGGGTATAGAATGATGGCTGTT

>g12134.t5 Gene=g12134 Length=300
MYSVVLRTRLLNGINTKSFVFKNYTQSTTKLYSSPTVVPQKKLDDEKLIHDEERLITKIS
VKQLNPDIVKVIENDVKKQQSNNQVVARKELELPWRITPSTDQNKLLKHYLMLSKIRLTS
LVVITSMAGYAMAPAPFDLSTFIMCSVGTGLLSCAANSINQFFETPFDAQMSRTKNRVLV
KGYLTPLHAVGFAAVAASSGLLILTCGVNELTAALGFSNLILYTCIYTPMKRYSILNTWV
GSIVGAIPPLMGWAGCAGTLDTGAWILAGLLYAWQFPHFNALSWNLRPDYSRAGYRMMAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12134.t5 CDD cd13957 PT_UbiA_Cox10 111 300 1.56825E-89
4 g12134.t5 Gene3D G3DSA:1.10.357.140 - 113 266 1.8E-17
2 g12134.t5 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 300 7.7E-109
3 g12134.t5 PANTHER PTHR43448:SF2 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 300 7.7E-109
1 g12134.t5 Pfam PF01040 UbiA prenyltransferase family 123 300 6.4E-45
6 g12134.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
12 g12134.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 133 -
9 g12134.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 134 138 -
13 g12134.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 163 -
7 g12134.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 164 182 -
11 g12134.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -
10 g12134.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 210 -
14 g12134.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 230 -
5 g12134.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 249 -
15 g12134.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 250 274 -
8 g12134.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 275 300 -
23 g12134.t5 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 160 182 -
24 g12134.t5 TIGRFAM TIGR01473 cyoE_ctaB: protoheme IX farnesyltransferase 108 300 1.2E-68
20 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
17 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 139 158 -
19 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
22 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
18 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 254 -
21 g12134.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 264 286 -

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:0016021 integral component of membrane CC
GO:0008495 protoheme IX farnesyltransferase activity MF
GO:0048034 heme O biosynthetic process 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