General information for g5494.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
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.t7 | TTS | g5494.t7 | 9853148 | 9853148 |
| chr_2 | g5494 | g5494.t7 | isoform | g5494.t7 | 9853168 | 9854164 |
| chr_2 | g5494 | g5494.t7 | exon | g5494.t7.exon1 | 9853168 | 9853508 |
| chr_2 | g5494 | g5494.t7 | exon | g5494.t7.exon2 | 9853648 | 9853839 |
| chr_2 | g5494 | g5494.t7 | cds | g5494.t7.CDS1 | 9853669 | 9853839 |
| chr_2 | g5494 | g5494.t7 | exon | g5494.t7.exon3 | 9853901 | 9854164 |
| chr_2 | g5494 | g5494.t7 | cds | g5494.t7.CDS2 | 9853901 | 9854164 |
| chr_2 | g5494 | g5494.t7 | TSS | g5494.t7 | 9854274 | 9854274 |
Sequences
>g5494.t7 Gene=g5494 Length=797
ATGAATTCAACGTGTTTACAAAAGACAACAAGAATATTAAATAAAAATGTATTTAAATGT
TTCTTAAACAGTCATATTCGAAATCAATCAAGTGCAACCAATCAGTCACTGATCCTCACT
GATGTAAATGATAAAACTGGCTTTGCAACAGTTGCTTTTAATCGTCCTCCAATGAGTAAT
TTTACGCTTGAACTTTTGCAAGACTTTTCAAAATCACTGGATGAAGTGGAGAGCAAGAAT
TACAAAGGAATGATTTTGACAAGTACATCACCAACAGTGTTTTCTGCTGGCCTTGATCTG
AAAGAATTATTGAATCCAGAACCAGCAAGATTAAAAGCATTACGTACAGCATACATTGAT
TGCTGCATAAAATTGTACAGTTCAATGTATCCAACTGTTGCTGCAATAAATGGTTACATA
TTTTACTTTTTATGATTAAAAAATGAAATCACTCAATTCATGCTACTCGTAACATAATAT
CTTCACGTGATGCTGAAATGGCTCTAACACTGGGATCAGTGTTTACCACTGACGAAGCTC
TGAAAATTGGACTCATTGATGAAGTCGCTGAAAATAAAGAAGATGCACTTGCTAAAAGTG
AAAAATTTCTCAGTTTATTCAAAAAGATTCCAAAAAGGGCTCGTGGAATCACTAAGCAGT
TCTTTAGAAAAAAAGTTATTGATTTAATGACTAATAATAGAGAAAAAGATGTAGAAGCTT
TTGTTAGTTATGTTATGAACCCAGCAAGCCAAAAATCTTTTCAAGCATTTTTAGATGAAG
CAAAAAATAAAAAGTAG
>g5494.t7 Gene=g5494 Length=144
MNSTCLQKTTRILNKNVFKCFLNSHIRNQSSATNQSLILTDVNDKTGFATVAFNRPPMSN
FTLELLQDFSKSLDEVESKNYKGMILTSTSPTVFSAGLDLKELLNPEPARLKALRTAYID
CCIKLYSSMYPTVAAINGYIFYFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5494.t7 | CDD | cd06558 | crotonase-like | 38 | 139 | 2.91732E-18 |
| 6 | g5494.t7 | Gene3D | G3DSA:3.90.226.10 | - | 35 | 142 | 5.0E-20 |
| 2 | g5494.t7 | PANTHER | PTHR11941:SF45 | ENOYL-COA DELTA ISOMERASE 1, MITOCHONDRIAL | 27 | 138 | 1.2E-26 |
| 3 | g5494.t7 | PANTHER | PTHR11941 | ENOYL-COA HYDRATASE-RELATED | 27 | 138 | 1.2E-26 |
| 1 | g5494.t7 | Pfam | PF00378 | Enoyl-CoA hydratase/isomerase | 45 | 140 | 3.7E-17 |
| 5 | g5494.t7 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 36 | 139 | 2.15E-18 |
| 4 | g5494.t7 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 143 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5494/g5494.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5494.t7.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.
