Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Frataxin homolog, 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_2 g5661 g5661.t1 TTS g5661.t1 11111432 11111432
chr_2 g5661 g5661.t1 isoform g5661.t1 11111466 11112054
chr_2 g5661 g5661.t1 exon g5661.t1.exon1 11111466 11111699
chr_2 g5661 g5661.t1 cds g5661.t1.CDS1 11111466 11111699
chr_2 g5661 g5661.t1 exon g5661.t1.exon2 11111761 11112054
chr_2 g5661 g5661.t1 cds g5661.t1.CDS2 11111761 11112054
chr_2 g5661 g5661.t1 TSS g5661.t1 11112120 11112120

Sequences

>g5661.t1 Gene=g5661 Length=528
ATGAATATAACAAGACATTCTCGTGTGCTTATAAGAAATTTAAGATATTTAACTTCATGT
AAAATCTCAAGAACATCATCCACAATTCTTAAATATTATAAAAATGAAGAATTTGTTTTT
GTGAGGAATTTTTCTTCAGTTTTTTCAAAATCACCGGAATATACGGAAGTTCCTTTAGTT
GATTTAGCTACATTTGAACCAATTTGTGCAGAAACATTGGAAACATTGACTGAATATTTT
GAGGAAATTGTTGAAGCCGATGAAAAGTTAGTAAATGCTGATATTAGTTATTCGGATGGA
GTGCTTACAGTCAAATTAGGTAATGGCTATGGAACATATGTGATAAATCGGCAAACACCT
AATCGTCAAATATGGTTGAGTTCACCAAAGAGCGGCCCAAAAAGGTATGACTTAATTGAT
GGAAAATGGATTTACAAACATGATGGAGTCTCAATGTATCAGCTTTTGCAAGAAGAACTT
GAACAAATAATGTCTAAACCAGTTGACTTTTTACAATTTGCGAAATAA

>g5661.t1 Gene=g5661 Length=175
MNITRHSRVLIRNLRYLTSCKISRTSSTILKYYKNEEFVFVRNFSSVFSKSPEYTEVPLV
DLATFEPICAETLETLTEYFEEIVEADEKLVNADISYSDGVLTVKLGNGYGTYVINRQTP
NRQIWLSSPKSGPKRYDLIDGKWIYKHDGVSMYQLLQEELEQIMSKPVDFLQFAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5661.t1 CDD cd00503 Frataxin 63 170 3.48933E-39
8 g5661.t1 Gene3D G3DSA:3.30.920.10 Metal Transport 55 175 1.6E-43
2 g5661.t1 PANTHER PTHR16821 FRATAXIN 17 171 1.3E-43
5 g5661.t1 PRINTS PR00904 Frataxin signature 60 78 5.0E-20
4 g5661.t1 PRINTS PR00904 Frataxin signature 78 97 5.0E-20
3 g5661.t1 PRINTS PR00904 Frataxin signature 100 115 5.0E-20
6 g5661.t1 PRINTS PR00904 Frataxin signature 115 130 5.0E-20
1 g5661.t1 Pfam PF01491 Frataxin-like domain 63 167 1.0E-33
10 g5661.t1 ProSitePatterns PS01344 Frataxin family signature. 114 128 -
14 g5661.t1 ProSiteProfiles PS50810 Frataxin family profile. 59 168 27.538
11 g5661.t1 SMART SM01219 Frataxin_Cyay_2 60 171 7.3E-47
7 g5661.t1 SUPERFAMILY SSF55387 Frataxin/Nqo15-like 62 172 2.27E-34
12 g5661.t1 TIGRFAM TIGR03421 FeS_CyaY: iron donor protein CyaY 64 170 2.6E-22
13 g5661.t1 TIGRFAM TIGR03422 mito_frataxin: frataxin 65 161 2.9E-36

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5661/g5661.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5661.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016226 iron-sulfur cluster assembly BP
GO:0004322 ferroxidase activity MF
GO:0008199 ferric iron binding MF
GO:0005739 mitochondrion CC
GO:0055114 NA NA

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