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.t8 TSS g12134.t8 21225818 21225818
chr_1 g12134 g12134.t8 isoform g12134.t8 21225909 21227596
chr_1 g12134 g12134.t8 exon g12134.t8.exon1 21225909 21226912
chr_1 g12134 g12134.t8 cds g12134.t8.CDS1 21226488 21226912
chr_1 g12134 g12134.t8 exon g12134.t8.exon2 21226974 21227125
chr_1 g12134 g12134.t8 cds g12134.t8.CDS2 21226974 21227125
chr_1 g12134 g12134.t8 exon g12134.t8.exon3 21227184 21227596
chr_1 g12134 g12134.t8 cds g12134.t8.CDS3 21227184 21227548
chr_1 g12134 g12134.t8 TTS g12134.t8 21227600 21227600

Sequences

>g12134.t8 Gene=g12134 Length=1569
ATGTACAGTGTAGTATTAAGAACTAGATTACTGAATGGAATCAACACGAAATCATTTGTA
TTTAAGGTGAAAACAAAAGGTTTTAGAAAAGCCCTTAAAAATGATTAAATAACAAGTGAT
CCTTGTTATTTCGGTCGCTAATAAAGATAAAATACTAAAAATCAATAGATAACAAACTGA
TTAGTGACATTTAACTCATATTATCAAGAAATTTTAGTGTTTTATGCAAATTTTCAAATT
TTATTTATTTGCGTGTGCAGGTTAAAATATGCCCTTCAATTATTGACTTGTATTTCTTAT
AATTTTTCATAGAACTATACGCAGTCGACAACAAAACTTTATTCTTCACCCACAGTTGTA
CCACAAAAAAAGCTAGATGATGAAAAATTAATTCATGATGAGGAGCGTTTGATTACAAAA
ATTTCAGTGAAACAACTTAATCCAGATATAGTGAAAGTGATAGAAAACGATGTAAAAAAA
CAACAGAGCAATAATCAAGTGGTTGCTCGAAAAGAATTAGAGCTACCATGGAGAATAACA
CCATCAACAGACCAAAACAAGCTGCTCAAACATTATTTGATGTTATCGAAAATTCGACTT
ACATCACTTGTTGTTATTACATCGATGGCTGGATATGCAATGGCACCTGCACCTTTTGAT
CTCAGCACGTTCATTATGTGTTCTGTTGGTACTGGATTGTTATCATGTGCTGCAAACTCT
ATTAATCAATTTTTTGAAACACCTTTTGATGCACAAATGTCGAGAACGAAAAATCGAGTG
TTGGTGAAAGGCTATTTAACTCCTCTTCACGCTGTTGGATTTGCAGCAGTTGCTGCTTCA
TCAGGGCTATTAATTCTTACATGCGGCGTAAATGAATTAACAGCTGCATTAGGCTTTTCA
AATTTAATTTTGTACACATGCATATACACACCAATGAAACGCTATAGCATACTTAACACA
TGGGTTGGCTCGATTGTCGGAGCTATTCCACCACTTATGGGATGGGCTGGATGTGCTGGC
ACTCTTGATACTGGTGCATGGATTCTAGCTGGTCTCCTTTATGCATGGCAATTTCCTCAC
TTTAATGCACTCTCATGGAATCTTAGACCAGATTATTCAAGAGCAGGGTATAGAATGATG
GCTGTTACTGATCCAGCACTATGTAGAAGAGTTGCTCTTCGATACACAGGAGTTATCAGT
GCATTATCACTAAGTGCACCAGCTTTTGATGTTACAAACATGTGGTTCGCTTTAGAAACA
TTGCCTTTGAATGGATATTTCGGATATTTAGCATGGAAATTCTATAAAGAATCCGACAGT
GGAAGTTCAAGGAAATTGTTTAGATTTTCGTTATTACATTTGCCAGTCTTGATGGTACTA
TTTTTATTAAATAAGAAAGAGTGGGTATTTAAAAAATCAAAGGATGAGAAGTTGATGTTA
ATGGAAAAGACAATTTCGGATCCCCTTCAGCAATTAAAGCCTCTAACTACTACACTGATA
CCTAATACACAAAAGATGTAAATTACGAAAAATTATTTTATTTGAAAAATAAAATACAAA
ATTTTAAAA

>g12134.t8 Gene=g12134 Length=313
MLSKIRLTSLVVITSMAGYAMAPAPFDLSTFIMCSVGTGLLSCAANSINQFFETPFDAQM
SRTKNRVLVKGYLTPLHAVGFAAVAASSGLLILTCGVNELTAALGFSNLILYTCIYTPMK
RYSILNTWVGSIVGAIPPLMGWAGCAGTLDTGAWILAGLLYAWQFPHFNALSWNLRPDYS
RAGYRMMAVTDPALCRRVALRYTGVISALSLSAPAFDVTNMWFALETLPLNGYFGYLAWK
FYKESDSGSSRKLFRFSLLHLPVLMVLFLLNKKEWVFKKSKDEKLMLMEKTISDPLQQLK
PLTTTLIPNTQKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g12134.t8 CDD cd13957 PT_UbiA_Cox10 2 267 2.24205E-109
6 g12134.t8 Gene3D G3DSA:1.10.357.140 - 2 155 2.0E-17
2 g12134.t8 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 2 283 1.6E-140
3 g12134.t8 PANTHER PTHR43448:SF2 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 2 283 1.6E-140
22 g12134.t8 PIRSF PIRSF001773 COX10 1 298 3.7E-136
1 g12134.t8 Pfam PF01040 UbiA prenyltransferase family 12 257 1.4E-50
13 g12134.t8 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
14 g12134.t8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
15 g12134.t8 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 15 -
21 g12134.t8 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
11 g12134.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 29 -
20 g12134.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
8 g12134.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 53 71 -
18 g12134.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 94 -
12 g12134.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 95 99 -
16 g12134.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
7 g12134.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 138 -
19 g12134.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 163 -
10 g12134.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 164 252 -
17 g12134.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 253 271 -
9 g12134.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 272 313 -
33 g12134.t8 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 49 71 -
5 g12134.t8 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
24 g12134.t8 SignalP_GRAM_NEGATIVE SignalP-TM SignalP-TM 1 22 -
4 g12134.t8 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 22 -
34 g12134.t8 TIGRFAM TIGR01473 cyoE_ctaB: protoheme IX farnesyltransferase 2 271 4.0E-84
30 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 24 -
29 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
26 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
25 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
27 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -
31 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 153 175 -
32 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 203 225 -
28 g12134.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 253 270 -

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