General information for g5142.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Elongation of very long chain fatty acids protein.
Parent gene
- The parent gene g5142 is located on chr_2: 7252456..7256378 (- 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 | g5142 | g5142.t10 | TTS | g5142.t10 | 7252080 | 7252080 |
| chr_2 | g5142 | g5142.t10 | isoform | g5142.t10 | 7252456 | 7253056 |
| chr_2 | g5142 | g5142.t10 | exon | g5142.t10.exon1 | 7252456 | 7252859 |
| chr_2 | g5142 | g5142.t10 | cds | g5142.t10.CDS1 | 7252456 | 7252755 |
| chr_2 | g5142 | g5142.t10 | exon | g5142.t10.exon2 | 7252924 | 7253056 |
| chr_2 | g5142 | g5142.t10 | TSS | g5142.t10 | NA | NA |
Sequences
>g5142.t10 Gene=g5142 Length=537
GAGTTTGTTGGCTATATTTTATTAGTAAATTCACAGAATTTTTCGACACATTCTTCTTTG
TTTTGAGAAAAAGATACGACCAAGTTTCAACACTTCATATCATTCATCACAGAATTATGC
CATTTAGTGGTAATTTGGTGGGGTTTAAAGTTTATGCCTGGAGGTCATAGCACGTTTTTT
TTCTTTCTTAATACATTCGTTCATATTGTGATGTATACTTACTACATGTTAGCAGCAATG
GGACCAGAAATGCAAAAATATCTCTGGTGGAAACGATATTTGACAATGTTCCAAATGATT
CAATTTATTGGAATTTTCACACATGCATTCCAATTGTTCTTCCACAATCCATGCAACTAT
CCGATTGTTTTCTCTTACTGGATTGGTGGTCATGGTGTTTTGTTCTTGTTCCTTTTCGCT
AATTTCTATGTACAAACTTATACAAAGAAAAAGAGCAAGAAAACTTTAGAAAATGGAAAA
GTTAATGGTTTAATTAAGAAAGAAATTGAAACAAATGGATTGAAAAAGGAACTGTAA
>g5142.t10 Gene=g5142 Length=99
MGPEMQKYLWWKRYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVFSYWIGGHGVLFLFLF
ANFYVQTYTKKKSKKTLENGKVNGLIKKEIETNGLKKEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5142.t10 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 1 | 79 | 1.1E-31 |
| 3 | g5142.t10 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 1 | 79 | 1.1E-31 |
| 1 | g5142.t10 | Pfam | PF01151 | GNS1/SUR4 family | 7 | 75 | 5.7E-14 |
| 7 | g5142.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 13 | - |
| 9 | g5142.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 14 | 35 | - |
| 8 | g5142.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 46 | - |
| 10 | g5142.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 47 | 65 | - |
| 6 | g5142.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 66 | 99 | - |
| 4 | g5142.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 33 | - |
| 5 | g5142.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 65 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5142/g5142.t10; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5142.t10.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016021 | integral component of membrane | CC |
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. There were no conditions that were differentially expressed