General information for g10336.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative YrdC domain-containing protein, mitochondrial.
Parent gene
- The parent gene g10336 is located on chr_1: 8936960..8937610 (- 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_1 | g10336 | g10336.t1 | TTS | g10336.t1 | 8936814 | 8936814 |
| chr_1 | g10336 | g10336.t1 | isoform | g10336.t1 | 8936960 | 8937610 |
| chr_1 | g10336 | g10336.t1 | exon | g10336.t1.exon1 | 8936960 | 8937610 |
| chr_1 | g10336 | g10336.t1 | cds | g10336.t1.CDS1 | 8936960 | 8937610 |
| chr_1 | g10336 | g10336.t1 | TSS | g10336.t1 | 8938224 | 8938224 |
Sequences
>g10336.t1 Gene=g10336 Length=651
ATGAACATTATTAAAACGTGTGATACACAAAGTATAAAAATAGCTTCCAATTTACTGAAA
AATGGCAATGTTATTGGGATTCCAACTGATACAATTTATGGATTAGCATGTAGTGCAAAT
GACAGTGAGGCTATTAAAAATCTTTATGACATAAAAGGACGAAATGAAGAGAAACCAGTA
GCGATATGTGTTAGTGATTTTAATGACTTAAAACATTGGGGACAAGCTTCACATTTGAAA
GATGAATTATTAAGACAATTACTACCTGGTCCTGTCACAATAGTTCTTAATAAAAGTATA
CATCTAAATAATCCATACTTAAATCCAGGTACAGAAAAAATTGGTATTCGAATTCCAGAT
TTTAATTTTATCAGAGATGTCTGTCGTGAATTTTCTATGCCTGTTGCATTAACATCTGCC
AACAAAAGTAGCGAAAAGAGCTCATTGAGTATAGAAGAATTTCAAGCACTTTGGTGTAAA
TTGGGTGCTGTTTTTGACGGAGGTCGTTTAAGTGATGCCGAAGAAAATAGAAAAGGATCA
ACAGTCATTGACCTCTCAGTACCAAATGAATATAAAGTTATACGACAAGGAATTGCATTC
GAAAATACCATAAGTTTAGTTGAAGAATACGATTTTAGAGAAGCTATTTAG
>g10336.t1 Gene=g10336 Length=216
MNIIKTCDTQSIKIASNLLKNGNVIGIPTDTIYGLACSANDSEAIKNLYDIKGRNEEKPV
AICVSDFNDLKHWGQASHLKDELLRQLLPGPVTIVLNKSIHLNNPYLNPGTEKIGIRIPD
FNFIRDVCREFSMPVALTSANKSSEKSSLSIEEFQALWCKLGAVFDGGRLSDAEENRKGS
TVIDLSVPNEYKVIRQGIAFENTISLVEEYDFREAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10336.t1 | Gene3D | G3DSA:3.90.870.10 | DHBP synthase | 3 | 207 | 0.000 |
| 2 | g10336.t1 | PANTHER | PTHR17490:SF10 | YRDC DOMAIN-CONTAINING PROTEIN, MITOCHONDRIAL | 7 | 215 | 0.000 |
| 3 | g10336.t1 | PANTHER | PTHR17490 | SUA5 | 7 | 215 | 0.000 |
| 1 | g10336.t1 | Pfam | PF01300 | Telomere recombination | 18 | 197 | 0.000 |
| 7 | g10336.t1 | ProSiteProfiles | PS51163 | YrdC-like domain profile. | 9 | 199 | 24.181 |
| 4 | g10336.t1 | SUPERFAMILY | SSF55821 | YrdC/RibB | 8 | 201 | 0.000 |
| 6 | g10336.t1 | TIGRFAM | TIGR00057 | TIGR00057: tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family | 7 | 202 | 0.000 |
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:0003725 | double-stranded RNA binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
