General information for g5661.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Frataxin homolog, mitochondrial.
Parent gene
- The parent gene g5661 is located on chr_2: 11111466..11112054 (- strand)
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.t3 | TTS | g5661.t3 | 11111432 | 11111432 |
| chr_2 | g5661 | g5661.t3 | isoform | g5661.t3 | 11111466 | 11112054 |
| chr_2 | g5661 | g5661.t3 | exon | g5661.t3.exon1 | 11111466 | 11111699 |
| chr_2 | g5661 | g5661.t3 | cds | g5661.t3.CDS1 | 11111466 | 11111699 |
| chr_2 | g5661 | g5661.t3 | exon | g5661.t3.exon2 | 11111785 | 11112054 |
| chr_2 | g5661 | g5661.t3 | cds | g5661.t3.CDS2 | 11111785 | 11112054 |
| chr_2 | g5661 | g5661.t3 | TSS | g5661.t3 | 11112120 | 11112120 |
Sequences
>g5661.t3 Gene=g5661 Length=504
ATGAATATAACAAGACATTCTCGTGTGCTTATAAGAAATTTAAGATATTTAACTTCATGT
AAAATCTCAAGAACATCATCCACAATTCTTAAATATTATAAAAATGAAGAATTTGTTTTT
GTGAGGAATTTTTCTTCAGTTTTTTCAAAATCACCGGAATATACGGAAGTTCCTTTAGTT
GATTTAGCTACATTTGAACCAATTTGTGCAGAAACATTGGAAACATTGACTGAATATTTT
GAGGAAATTGTTGAAGCCGATGAAAAGTTAGATGGAGTGCTTACAGTCAAATTAGGTAAT
GGCTATGGAACATATGTGATAAATCGGCAAACACCTAATCGTCAAATATGGTTGAGTTCA
CCAAAGAGCGGCCCAAAAAGGTATGACTTAATTGATGGAAAATGGATTTACAAACATGAT
GGAGTCTCAATGTATCAGCTTTTGCAAGAAGAACTTGAACAAATAATGTCTAAACCAGTT
GACTTTTTACAATTTGCGAAATAA
>g5661.t3 Gene=g5661 Length=167
MNITRHSRVLIRNLRYLTSCKISRTSSTILKYYKNEEFVFVRNFSSVFSKSPEYTEVPLV
DLATFEPICAETLETLTEYFEEIVEADEKLDGVLTVKLGNGYGTYVINRQTPNRQIWLSS
PKSGPKRYDLIDGKWIYKHDGVSMYQLLQEELEQIMSKPVDFLQFAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5661.t3 | CDD | cd00503 | Frataxin | 63 | 162 | 2.02739E-36 |
| 4 | g5661.t3 | Gene3D | G3DSA:3.30.920.10 | Metal Transport | 55 | 167 | 1.9E-37 |
| 2 | g5661.t3 | PANTHER | PTHR16821 | FRATAXIN | 17 | 163 | 3.4E-38 |
| 1 | g5661.t3 | Pfam | PF01491 | Frataxin-like domain | 63 | 159 | 1.8E-29 |
| 6 | g5661.t3 | ProSitePatterns | PS01344 | Frataxin family signature. | 106 | 120 | - |
| 10 | g5661.t3 | ProSiteProfiles | PS50810 | Frataxin family profile. | 59 | 160 | 23.924 |
| 7 | g5661.t3 | SMART | SM01219 | Frataxin_Cyay_2 | 60 | 163 | 3.8E-40 |
| 3 | g5661.t3 | SUPERFAMILY | SSF55387 | Frataxin/Nqo15-like | 62 | 164 | 7.15E-31 |
| 8 | g5661.t3 | TIGRFAM | TIGR03421 | FeS_CyaY: iron donor protein CyaY | 64 | 162 | 1.3E-19 |
| 9 | g5661.t3 | TIGRFAM | TIGR03422 | mito_frataxin: frataxin | 65 | 153 | 3.5E-31 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5661/g5661.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5661.t3.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
- This transcript has been annotated with K19054 (frataxin)
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