General information for g5494.t12
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 g5494 is located on chr_2: 9853168..9861920 (- 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 | g5494 | g5494.t12 | TTS | g5494.t12 | 9853148 | 9853148 |
| chr_2 | g5494 | g5494.t12 | isoform | g5494.t12 | 9853168 | 9861920 |
| chr_2 | g5494 | g5494.t12 | exon | g5494.t12.exon1 | 9853168 | 9853628 |
| chr_2 | g5494 | g5494.t12 | cds | g5494.t12.CDS1 | 9853168 | 9853628 |
| chr_2 | g5494 | g5494.t12 | exon | g5494.t12.exon2 | 9853692 | 9853839 |
| chr_2 | g5494 | g5494.t12 | cds | g5494.t12.CDS2 | 9853692 | 9853719 |
| chr_2 | g5494 | g5494.t12 | exon | g5494.t12.exon3 | 9853903 | 9854182 |
| chr_2 | g5494 | g5494.t12 | TSS | g5494.t12 | 9854274 | 9854274 |
| chr_2 | g5494 | g5494.t12 | exon | g5494.t12.exon4 | 9861904 | 9861920 |
Sequences
>g5494.t12 Gene=g5494 Length=906
TTTTAAAATTATTAGAAAGTACAAAGTTCATAATCATGAATTCAACGTGTTTACAAAAGA
CAACAAGAATATTAAATAAAAATGTATTTAAATGTTTCTTAAACAGTCATATTCGAAATC
AATCAAGTGCAACCAATCAGTCACTGATCCTCACTGATGTAAATGATAAAACTGGCTTTG
CAACAGTTGCTTTTAATCGTCCTCCAATGAGTAATTTTACGCTTGAACTTTTGCAAGACT
TTTCAAAATCACTGGATGAAGTGGAGAGCAAGAATTACAAAGGAATGATTTTGACAAACA
TCACCAACAGTGTTTTCTGCTGGCCTTGATCTGAAAGAATTATTGAATCCAGAACCAGCA
AGATTAAAAGCATTACGTACAGCATACATTGATTGCTGCATAAAATTGTACAGTTCAATG
TATCCAACTGTTGCTGCAATAAATGGTCATGCAATTGGAGGAGGCTGTTTCATTGCTATG
GCTTGTGAATATCGAATAATGTTGCCAAATTCCAAAATAGGACTCAATGAAACTCAACTG
GGGATTGCAATTCCTGAAGTTGCAGTTCATGCTACTCGTAACATAATATCTTCACGTGAT
GCTGAAATGGCTCTAACACTGGGATCAGTGTTTACCACTGACGAAGCTCTGAAAATTGGA
CTCATTGATGAAGTCGCTGAAAATAAAGAAGATGCACTTGCTAAAAGTGAAAAATTTCTC
AGTTTATTCAAAAAGATTCCAAAAAGGGCTCGTGGAATCACTAAGCAGTTCTTTAGAAAA
AAAGTTATTGATTTAATGACTAATAATAGAGAAAAAGATGTAGAAGCTTTTGTTAGTTAT
GTTATGAACCCAGCAAGCCAAAAATCTTTTCAAGCATTTTTAGATGAAGCAAAAAATAAA
AAGTAG
>g5494.t12 Gene=g5494 Length=162
MYPTVAAINGHAIGGGCFIAMACEYRIMLPNSKIGLNETQLGIAIPEVAVHATRNIISSR
DAEMALTLGSVFTTDEALKIGLIDEVAENKEDALAKSEKFLSLFKKIPKRARGITKQFFR
KKVIDLMTNNREKDVEAFVSYVMNPASQKSFQAFLDEAKNKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5494.t12 | CDD | cd06558 | crotonase-like | 3 | 101 | 0 |
| 5 | g5494.t12 | Gene3D | G3DSA:3.90.226.10 | - | 1 | 139 | 0 |
| 2 | g5494.t12 | PANTHER | PTHR11941:SF45 | ENOYL-COA DELTA ISOMERASE 1, MITOCHONDRIAL | 3 | 162 | 0 |
| 3 | g5494.t12 | PANTHER | PTHR11941 | ENOYL-COA HYDRATASE-RELATED | 3 | 162 | 0 |
| 1 | g5494.t12 | Pfam | PF00378 | Enoyl-CoA hydratase/isomerase | 2 | 159 | 0 |
| 4 | g5494.t12 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 3 | 159 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5494/g5494.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5494.t12.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.
