General information for g5490.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Enoyl-CoA delta isomerase 1, mitochondrial.
Parent gene
- The parent gene g5490 is located on chr_2: 9848696..9849125 (- 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 | g5490 | g5490.t1 | TTS | g5490.t1 | 9848057 | 9848057 |
| chr_2 | g5490 | g5490.t1 | isoform | g5490.t1 | 9848136 | 9849125 |
| chr_2 | g5490 | g5490.t1 | exon | g5490.t1.exon1 | 9848136 | 9848599 |
| chr_2 | g5490 | g5490.t1 | cds | g5490.t1.CDS1 | 9848136 | 9848599 |
| chr_2 | g5490 | g5490.t1 | exon | g5490.t1.exon2 | 9848663 | 9848813 |
| chr_2 | g5490 | g5490.t1 | cds | g5490.t1.CDS2 | 9848663 | 9848813 |
| chr_2 | g5490 | g5490.t1 | exon | g5490.t1.exon3 | 9848874 | 9849125 |
| chr_2 | g5490 | g5490.t1 | cds | g5490.t1.CDS3 | 9848874 | 9849125 |
| chr_2 | g5490 | g5490.t1 | TSS | g5490.t1 | 9849168 | 9849168 |
Sequences
>g5490.t1 Gene=g5490 Length=867
ATGAATTTTTCGCGTTTACTTAAAACTACCTCAGCACTTACATCTCGATGGCTATGCAGT
GGAAGATTTCAATCAACAAGTGCTGCAGCACAAAAGCTAGTTGATGTTAGTGTGGATTCT
AAGACCGGTGTTTCGATTGTTTCGTTGAATCGTAAGCCAGTGAATAGTTTATCCTTGGAA
TTATTTAAAGAATTTTGTGGAGTGATGGATGATTTGGAGAGTGAAAAAGTTCGAGGGATG
ATTTTGAAAAGTTCATGTGATAATGTGTTCTCGAGTGGGCTTGATATAACTGAATTATAC
CCTCATCCAGATGAAGATCGTTTTCATGCGTTTTGGTTGTGGTTTCAAGAAACTTGGATT
AAATTATATGGCTCTTCATTTCCAACAGTTGCATTTATTAATGGACACGCTCCAGCTGGA
GGATGCGTCTTGGCAATTTCATGCGAGTACAGAATAATGCTTCCATACTATAAAATAGGT
TTGAATGAAGCACCAGTTGGAATTGTTGCACCTGATTGGGTTGTTAATTCATTGAAAAGT
GTATTAGCATCAAGAAAAGCTGAACAATTATTAACCTCAGGAAGACTTCTCGATACTCAG
GAAGCATTTGACATTGGTCTTATTGACAAAATTGTCAATAATGAAGAAGAGGCACTTGCT
CGAAGTGAAGAGTTTTTCTCTACATTTGATAATGTTCCAAAATTAGCTCGTGCACTGACC
AAACAGCAAGTCCGCAAAAATGAAATTTCTAAATTGATTAAAAATCGTTCTAATGACGCA
AAACTGTTTCTTAATCACATCCTTCGTCCTGAAACACAAAAAATCATTGGATCATATTTT
AAAAGTCTTAAAGATCGTAAAAAATAA
>g5490.t1 Gene=g5490 Length=288
MNFSRLLKTTSALTSRWLCSGRFQSTSAAAQKLVDVSVDSKTGVSIVSLNRKPVNSLSLE
LFKEFCGVMDDLESEKVRGMILKSSCDNVFSSGLDITELYPHPDEDRFHAFWLWFQETWI
KLYGSSFPTVAFINGHAPAGGCVLAISCEYRIMLPYYKIGLNEAPVGIVAPDWVVNSLKS
VLASRKAEQLLTSGRLLDTQEAFDIGLIDKIVNNEEEALARSEEFFSTFDNVPKLARALT
KQQVRKNEISKLIKNRSNDAKLFLNHILRPETQKIIGSYFKSLKDRKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5490.t1 | CDD | cd06558 | crotonase-like | 36 | 225 | 2.71316E-46 |
| 6 | g5490.t1 | Gene3D | G3DSA:3.90.226.10 | - | 31 | 262 | 3.6E-52 |
| 2 | g5490.t1 | PANTHER | PTHR11941:SF45 | ENOYL-COA DELTA ISOMERASE 1, MITOCHONDRIAL | 23 | 287 | 2.5E-85 |
| 3 | g5490.t1 | PANTHER | PTHR11941 | ENOYL-COA HYDRATASE-RELATED | 23 | 287 | 2.5E-85 |
| 1 | g5490.t1 | Pfam | PF00378 | Enoyl-CoA hydratase/isomerase | 41 | 279 | 2.8E-42 |
| 4 | g5490.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 36 | 280 | 7.23E-46 |
| 5 | g5490.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5490/g5490.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5490.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003824 | catalytic activity | 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.
