General information for g9560.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g9560 is located on chr_1: 4060822..4066169 (- 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 | g9560 | g9560.t2 | isoform | g9560.t2 | 4054738 | 4061060 |
| chr_1 | g9560 | g9560.t2 | exon | g9560.t2.exon1 | 4054738 | 4054767 |
| chr_1 | g9560 | g9560.t2 | exon | g9560.t2.exon2 | 4060473 | 4060741 |
| chr_1 | g9560 | g9560.t2 | cds | g9560.t2.CDS1 | 4060525 | 4060741 |
| chr_1 | g9560 | g9560.t2 | exon | g9560.t2.exon3 | 4060813 | 4061060 |
| chr_1 | g9560 | g9560.t2 | cds | g9560.t2.CDS2 | 4060813 | 4061060 |
| chr_1 | g9560 | g9560.t2 | TSS | g9560.t2 | 4061074 | 4061074 |
| chr_1 | g9560 | g9560.t2 | TTS | g9560.t2 | NA | NA |
Sequences
>g9560.t2 Gene=g9560 Length=547
ATGGCACGAGAAGGAAGGCCTTTGATTAGAATAATAATTCAAAATTTCCTCAATTCTTTT
CGTCCTCGACAAATCAGAGGAGATTTAAAAGGTGAAGATTATTTTGGAAATAAGTATTAT
GAAATACCTGCAGACCCTTCAAGAGGGAAAAGAAAGCCAAGTAGGTGGTTTGAACCACCT
GGAAAACCTAAAGACGATCATGGACATGAATTAACAGCAGAATGGGAGAGTTGGTTGAGA
GGACGAAGAAATGATCCACCGACTCAAGAGGAACTTATTAAAAATTTATCTATAATGGAG
ATGAAAAAGAGAAATGCTGCACTCTTAGAAGAGAAGCATAAACAACCTCAAGATCACGCT
GCAATAAAGCATGATCAAGCGACTGGTAGAGCTCATTTCCCTAGATATGATGATGAATAC
GAAATAATGCCTGGTTCAAAGCCGATTAATAAGAAAGATGAATAATAATGATCTTTAGTG
TGTAATAAAATTGTAGATTTTCCCAATAATCAATTCTGTGAAATCGTTAAGACAAAATAA
ATTCATG
>g9560.t2 Gene=g9560 Length=154
MAREGRPLIRIIIQNFLNSFRPRQIRGDLKGEDYFGNKYYEIPADPSRGKRKPSRWFEPP
GKPKDDHGHELTAEWESWLRGRRNDPPTQEELIKNLSIMEMKKRNAALLEEKHKQPQDHA
AIKHDQATGRAHFPRYDDEYEIMPGSKPINKKDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g9560.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 71 | - |
| 3 | g9560.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 154 | - |
| 2 | g9560.t2 | PANTHER | PTHR32470 | ADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX ASSEMBLY FACTOR 2 | 9 | 139 | 4.4E-28 |
| 1 | g9560.t2 | Pfam | PF05071 | NADH ubiquinone oxidoreductase subunit NDUFA12 | 27 | 118 | 6.2E-11 |
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:0032981 | mitochondrial respiratory chain complex I assembly | BP |
| GO:0016020 | membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K18160 (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 2)
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.
