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.t6 TSS g12134.t6 21225818 21225818
chr_1 g12134 g12134.t6 isoform g12134.t6 21225909 21227548
chr_1 g12134 g12134.t6 exon g12134.t6.exon1 21225909 21225974
chr_1 g12134 g12134.t6 cds g12134.t6.CDS1 21225909 21225974
chr_1 g12134 g12134.t6 exon g12134.t6.exon2 21226221 21226912
chr_1 g12134 g12134.t6 cds g12134.t6.CDS2 21226221 21226912
chr_1 g12134 g12134.t6 exon g12134.t6.exon3 21226974 21227125
chr_1 g12134 g12134.t6 cds g12134.t6.CDS3 21226974 21227125
chr_1 g12134 g12134.t6 exon g12134.t6.exon4 21227194 21227548
chr_1 g12134 g12134.t6 cds g12134.t6.CDS4 21227194 21227240
chr_1 g12134 g12134.t6 TTS g12134.t6 21227600 21227600

Sequences

>g12134.t6 Gene=g12134 Length=1265
ATGTACAGTGTAGTATTAAGAACTAGATTACTGAATGGAATCAACACGAAATCATTTGTA
TTTAAGAACTATACGCAGTCGACAACAAAACTTTATTCTTCACCCACAGTTGTACCACAA
AAAAAGCTAGATGATGAAAAATTAATTCATGATGAGGAGCGTTTGATTACAAAAATTTCA
GTGAAACAACTTAATCCAGATATAGTGAAAGTGATAGAAAACGATGTAAAAAAACAACAG
AGCAATAATCAAGTGGTTGCTCGAAAAGAATTAGAGCTACCATGGAGAATAACACCATCA
ACAGACCAAAACAAGCTGCTCAAACATTATTTGATGTTATCGAAAATTCGACTTACATCA
CTTGTTGTTATTACATCGATGGCTGGATATGCAATGGCACCTGCACCTTTTGATCTCAGC
ACGTTCATTATGTGTTCTGTTGGTACTGGATTGTTATCATGTGCTGCAAACTCTATTAAT
CAATTTTTTGAAACACCTTTTGATGCACAAATGTCGAGAACGAAAAATCGAGTGTTGGTG
AAAGGCTATTTAACTCCTCTTCACGCTGTTGGATTTGCAGCAGTTGCTGCTTCATCAGGG
CTATTAATTCTTACATGCGGCGTAAATGAATTAACAGCTGCATTAGGCTTTTCAAATTTA
ATTTTGTACACATGCATATACACACCAATGAAACGCTATAGCATACTTAACACATGGGTT
GGCTCGATTGTCGGAGCTATTCCACCACTTATGGGATGGGCTGGATGTGCTGGCACTCTT
GATACTGGTGCATGGATTCTAGCTGGTCTCCTTTATGCATGGCAATTTCCTCACTTTAAT
GCACTCTCATGGAATCTTAGACCAGATTATTCAAGAGCAGGGTATAGAATGATGGCTGTT
ACTGATCCAGAAGAGTTGCTCTTCGATACACAGGAGTTATCAGTGCATTATCACTAAGTG
CACCAGCTTTTGATGTTACAAACATGTGGTTCGCTTTAGAAACATTGCCTTTGAATGGAT
ATTTCGGATATTTAGCATGGAAATTCTATAAAGAATCCGACAGTGGAAGTTCAAGGAAAT
TGTTTAGATTTTCGTTATTACATTTGCCAGTCTTGATGGTACTATTTTTATTAAATAAGA
AAGAGTGGGTATTTAAAAAATCAAAGGATGAGAAGTTGATGTTAATGGAAAAGACAATTT
CGGATCCCCTTCAGCAATTAAAGCCTCTAACTACTACACTGATACCTAATACACAAAAGA
TGTAA

>g12134.t6 Gene=g12134 Length=318
MYSVVLRTRLLNGINTKSFVFKNYTQSTTKLYSSPTVVPQKKLDDEKLIHDEERLITKIS
VKQLNPDIVKVIENDVKKQQSNNQVVARKELELPWRITPSTDQNKLLKHYLMLSKIRLTS
LVVITSMAGYAMAPAPFDLSTFIMCSVGTGLLSCAANSINQFFETPFDAQMSRTKNRVLV
KGYLTPLHAVGFAAVAASSGLLILTCGVNELTAALGFSNLILYTCIYTPMKRYSILNTWV
GSIVGAIPPLMGWAGCAGTLDTGAWILAGLLYAWQFPHFNALSWNLRPDYSRAGYRMMAV
TDPEELLFDTQELSVHYH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12134.t6 CDD cd13957 PT_UbiA_Cox10 111 305 1.39979E-92
4 g12134.t6 Gene3D G3DSA:1.10.357.140 - 113 266 2.1E-17
2 g12134.t6 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 304 2.8E-111
3 g12134.t6 PANTHER PTHR43448:SF2 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 304 2.8E-111
1 g12134.t6 Pfam PF01040 UbiA prenyltransferase family 123 302 2.6E-46
6 g12134.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
12 g12134.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 133 -
8 g12134.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 134 138 -
13 g12134.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 163 -
7 g12134.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 164 182 -
11 g12134.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -
9 g12134.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 210 -
14 g12134.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 230 -
5 g12134.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 249 -
15 g12134.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 250 274 -
10 g12134.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 275 318 -
23 g12134.t6 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 160 182 -
24 g12134.t6 TIGRFAM TIGR01473 cyoE_ctaB: protoheme IX farnesyltransferase 108 306 2.3E-71
20 g12134.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
17 g12134.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 139 158 -
19 g12134.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
22 g12134.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
18 g12134.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 254 -
21 g12134.t6 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. There were no conditions that were differentially expressed