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.t9 TSS g12134.t9 21225818 21225818
chr_1 g12134 g12134.t9 isoform g12134.t9 21225909 21227600
chr_1 g12134 g12134.t9 exon g12134.t9.exon1 21225909 21225965
chr_1 g12134 g12134.t9 cds g12134.t9.CDS1 21225909 21225965
chr_1 g12134 g12134.t9 exon g12134.t9.exon2 21226221 21226912
chr_1 g12134 g12134.t9 cds g12134.t9.CDS2 21226221 21226912
chr_1 g12134 g12134.t9 exon g12134.t9.exon3 21226974 21227125
chr_1 g12134 g12134.t9 cds g12134.t9.CDS3 21226974 21227125
chr_1 g12134 g12134.t9 exon g12134.t9.exon4 21227184 21227600
chr_1 g12134 g12134.t9 cds g12134.t9.CDS4 21227184 21227548
chr_1 g12134 g12134.t9 TTS g12134.t9 21227600 21227600

Sequences

>g12134.t9 Gene=g12134 Length=1318
ATGTACAGTGTAGTATTAAGAACTAGATTACTGAATGGAATCAACACGAAATCATTTAAC
TATACGCAGTCGACAACAAAACTTTATTCTTCACCCACAGTTGTACCACAAAAAAAGCTA
GATGATGAAAAATTAATTCATGATGAGGAGCGTTTGATTACAAAAATTTCAGTGAAACAA
CTTAATCCAGATATAGTGAAAGTGATAGAAAACGATGTAAAAAAACAACAGAGCAATAAT
CAAGTGGTTGCTCGAAAAGAATTAGAGCTACCATGGAGAATAACACCATCAACAGACCAA
AACAAGCTGCTCAAACATTATTTGATGTTATCGAAAATTCGACTTACATCACTTGTTGTT
ATTACATCGATGGCTGGATATGCAATGGCACCTGCACCTTTTGATCTCAGCACGTTCATT
ATGTGTTCTGTTGGTACTGGATTGTTATCATGTGCTGCAAACTCTATTAATCAATTTTTT
GAAACACCTTTTGATGCACAAATGTCGAGAACGAAAAATCGAGTGTTGGTGAAAGGCTAT
TTAACTCCTCTTCACGCTGTTGGATTTGCAGCAGTTGCTGCTTCATCAGGGCTATTAATT
CTTACATGCGGCGTAAATGAATTAACAGCTGCATTAGGCTTTTCAAATTTAATTTTGTAC
ACATGCATATACACACCAATGAAACGCTATAGCATACTTAACACATGGGTTGGCTCGATT
GTCGGAGCTATTCCACCACTTATGGGATGGGCTGGATGTGCTGGCACTCTTGATACTGGT
GCATGGATTCTAGCTGGTCTCCTTTATGCATGGCAATTTCCTCACTTTAATGCACTCTCA
TGGAATCTTAGACCAGATTATTCAAGAGCAGGGTATAGAATGATGGCTGTTACTGATCCA
GCACTATGTAGAAGAGTTGCTCTTCGATACACAGGAGTTATCAGTGCATTATCACTAAGT
GCACCAGCTTTTGATGTTACAAACATGTGGTTCGCTTTAGAAACATTGCCTTTGAATGGA
TATTTCGGATATTTAGCATGGAAATTCTATAAAGAATCCGACAGTGGAAGTTCAAGGAAA
TTGTTTAGATTTTCGTTATTACATTTGCCAGTCTTGATGGTACTATTTTTATTAAATAAG
AAAGAGTGGGTATTTAAAAAATCAAAGGATGAGAAGTTGATGTTAATGGAAAAGACAATT
TCGGATCCCCTTCAGCAATTAAAGCCTCTAACTACTACACTGATACCTAATACACAAAAG
ATGTAAATTACGAAAAATTATTTTATTTGAAAAATAAAATACAAAATTTTAAAAATTT

>g12134.t9 Gene=g12134 Length=421
MYSVVLRTRLLNGINTKSFNYTQSTTKLYSSPTVVPQKKLDDEKLIHDEERLITKISVKQ
LNPDIVKVIENDVKKQQSNNQVVARKELELPWRITPSTDQNKLLKHYLMLSKIRLTSLVV
ITSMAGYAMAPAPFDLSTFIMCSVGTGLLSCAANSINQFFETPFDAQMSRTKNRVLVKGY
LTPLHAVGFAAVAASSGLLILTCGVNELTAALGFSNLILYTCIYTPMKRYSILNTWVGSI
VGAIPPLMGWAGCAGTLDTGAWILAGLLYAWQFPHFNALSWNLRPDYSRAGYRMMAVTDP
ALCRRVALRYTGVISALSLSAPAFDVTNMWFALETLPLNGYFGYLAWKFYKESDSGSSRK
LFRFSLLHLPVLMVLFLLNKKEWVFKKSKDEKLMLMEKTISDPLQQLKPLTTTLIPNTQK
M

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g12134.t9 CDD cd13957 PT_UbiA_Cox10 108 375 9.21978E-116
5 g12134.t9 Gene3D G3DSA:1.10.357.140 - 110 262 3.4E-17
4 g12134.t9 Hamap MF_00154 Protoheme IX farnesyltransferase [cyoE]. 103 381 14.093407
2 g12134.t9 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 39 391 4.7E-148
3 g12134.t9 PANTHER PTHR43448:SF2 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 39 391 4.7E-148
19 g12134.t9 PIRSF PIRSF001773 COX10 3 406 9.3E-143
1 g12134.t9 Pfam PF01040 UbiA prenyltransferase family 120 365 3.4E-50
7 g12134.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 112 -
17 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 130 -
12 g12134.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 131 135 -
18 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 160 -
6 g12134.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 161 179 -
16 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
11 g12134.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 203 207 -
13 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 227 -
9 g12134.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 228 246 -
14 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 247 271 -
10 g12134.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 272 360 -
15 g12134.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 361 379 -
8 g12134.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 380 421 -
29 g12134.t9 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 157 179 -
30 g12134.t9 TIGRFAM TIGR01473 cyoE_ctaB: protoheme IX farnesyltransferase 105 379 2.1E-85
23 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 132 -
27 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 155 -
24 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 175 194 -
25 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 198 220 -
26 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 232 251 -
28 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 261 283 -
21 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 311 333 -
22 g12134.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 361 378 -

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:0031966 mitochondrial membrane CC
GO:0008495 protoheme IX farnesyltransferase activity MF
GO:0048034 heme O biosynthetic process BP
GO:0006783 heme 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