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.t13 TSS g12134.t13 21225818 21225818
chr_1 g12134 g12134.t13 isoform g12134.t13 21225909 21236138
chr_1 g12134 g12134.t13 exon g12134.t13.exon1 21225909 21225974
chr_1 g12134 g12134.t13 cds g12134.t13.CDS1 21225909 21225974
chr_1 g12134 g12134.t13 exon g12134.t13.exon2 21226221 21226912
chr_1 g12134 g12134.t13 cds g12134.t13.CDS2 21226221 21226912
chr_1 g12134 g12134.t13 exon g12134.t13.exon3 21226974 21227125
chr_1 g12134 g12134.t13 cds g12134.t13.CDS3 21226974 21227125
chr_1 g12134 g12134.t13 exon g12134.t13.exon4 21227184 21227596
chr_1 g12134 g12134.t13 cds g12134.t13.CDS4 21227184 21227548
chr_1 g12134 g12134.t13 exon g12134.t13.exon5 21236122 21236138
chr_1 g12134 g12134.t13 TTS g12134.t13 NA NA

Sequences

>g12134.t13 Gene=g12134 Length=1340
ATGTACAGTGTAGTATTAAGAACTAGATTACTGAATGGAATCAACACGAAATCATTTGTA
TTTAAGAACTATACGCAGTCGACAACAAAACTTTATTCTTCACCCACAGTTGTACCACAA
AAAAAGCTAGATGATGAAAAATTAATTCATGATGAGGAGCGTTTGATTACAAAAATTTCA
GTGAAACAACTTAATCCAGATATAGTGAAAGTGATAGAAAACGATGTAAAAAAACAACAG
AGCAATAATCAAGTGGTTGCTCGAAAAGAATTAGAGCTACCATGGAGAATAACACCATCA
ACAGACCAAAACAAGCTGCTCAAACATTATTTGATGTTATCGAAAATTCGACTTACATCA
CTTGTTGTTATTACATCGATGGCTGGATATGCAATGGCACCTGCACCTTTTGATCTCAGC
ACGTTCATTATGTGTTCTGTTGGTACTGGATTGTTATCATGTGCTGCAAACTCTATTAAT
CAATTTTTTGAAACACCTTTTGATGCACAAATGTCGAGAACGAAAAATCGAGTGTTGGTG
AAAGGCTATTTAACTCCTCTTCACGCTGTTGGATTTGCAGCAGTTGCTGCTTCATCAGGG
CTATTAATTCTTACATGCGGCGTAAATGAATTAACAGCTGCATTAGGCTTTTCAAATTTA
ATTTTGTACACATGCATATACACACCAATGAAACGCTATAGCATACTTAACACATGGGTT
GGCTCGATTGTCGGAGCTATTCCACCACTTATGGGATGGGCTGGATGTGCTGGCACTCTT
GATACTGGTGCATGGATTCTAGCTGGTCTCCTTTATGCATGGCAATTTCCTCACTTTAAT
GCACTCTCATGGAATCTTAGACCAGATTATTCAAGAGCAGGGTATAGAATGATGGCTGTT
ACTGATCCAGCACTATGTAGAAGAGTTGCTCTTCGATACACAGGAGTTATCAGTGCATTA
TCACTAAGTGCACCAGCTTTTGATGTTACAAACATGTGGTTCGCTTTAGAAACATTGCCT
TTGAATGGATATTTCGGATATTTAGCATGGAAATTCTATAAAGAATCCGACAGTGGAAGT
TCAAGGAAATTGTTTAGATTTTCGTTATTACATTTGCCAGTCTTGATGGTACTATTTTTA
TTAAATAAGAAAGAGTGGGTATTTAAAAAATCAAAGGATGAGAAGTTGATGTTAATGGAA
AAGACAATTTCGGATCCCCTTCAGCAATTAAAGCCTCTAACTACTACACTGATACCTAAT
ACACAAAAGATGTAAATTACGAAAAATTATTTTATTTGAAAAATAAAATACAAAATTTTA
AAATTTAAAAAAAAAAAAAA

>g12134.t13 Gene=g12134 Length=424
MYSVVLRTRLLNGINTKSFVFKNYTQSTTKLYSSPTVVPQKKLDDEKLIHDEERLITKIS
VKQLNPDIVKVIENDVKKQQSNNQVVARKELELPWRITPSTDQNKLLKHYLMLSKIRLTS
LVVITSMAGYAMAPAPFDLSTFIMCSVGTGLLSCAANSINQFFETPFDAQMSRTKNRVLV
KGYLTPLHAVGFAAVAASSGLLILTCGVNELTAALGFSNLILYTCIYTPMKRYSILNTWV
GSIVGAIPPLMGWAGCAGTLDTGAWILAGLLYAWQFPHFNALSWNLRPDYSRAGYRMMAV
TDPALCRRVALRYTGVISALSLSAPAFDVTNMWFALETLPLNGYFGYLAWKFYKESDSGS
SRKLFRFSLLHLPVLMVLFLLNKKEWVFKKSKDEKLMLMEKTISDPLQQLKPLTTTLIPN
TQKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g12134.t13 CDD cd13957 PT_UbiA_Cox10 111 378 1.05508E-115
5 g12134.t13 Gene3D G3DSA:1.10.357.140 - 113 265 3.5E-17
4 g12134.t13 Hamap MF_00154 Protoheme IX farnesyltransferase [cyoE]. 106 384 14.093407
2 g12134.t13 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 394 4.8E-148
3 g12134.t13 PANTHER PTHR43448:SF2 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL 46 394 4.8E-148
19 g12134.t13 PIRSF PIRSF001773 COX10 3 409 8.2E-143
1 g12134.t13 Pfam PF01040 UbiA prenyltransferase family 123 368 3.5E-50
7 g12134.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
15 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 133 -
10 g12134.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 134 138 -
16 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 163 -
9 g12134.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 164 182 -
14 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -
11 g12134.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 210 -
17 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 230 -
6 g12134.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 249 -
18 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 250 274 -
12 g12134.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 275 363 -
13 g12134.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 364 382 -
8 g12134.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 383 424 -
29 g12134.t13 ProSitePatterns PS00943 UbiA prenyltransferase family signature. 160 182 -
30 g12134.t13 TIGRFAM TIGR01473 cyoE_ctaB: protoheme IX farnesyltransferase 108 382 2.1E-85
23 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
21 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 139 158 -
22 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
26 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
27 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 254 -
25 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 264 286 -
24 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 314 336 -
28 g12134.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 364 381 -

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. There were no conditions that were differentially expressed