General information for g5143.t2
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 g5143 is located on chr_2: 7260309..7268647 (- 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 | g5143 | g5143.t2 | isoform | g5143.t2 | 7259942 | 7260706 |
| chr_2 | g5143 | g5143.t2 | exon | g5143.t2.exon1 | 7259942 | 7260706 |
| chr_2 | g5143 | g5143.t2 | TTS | g5143.t2 | 7259954 | 7259954 |
| chr_2 | g5143 | g5143.t2 | cds | g5143.t2.CDS1 | 7260309 | 7260695 |
| chr_2 | g5143 | g5143.t2 | TSS | g5143.t2 | NA | NA |
Sequences
>g5143.t2 Gene=g5143 Length=765
ATACTTACTACATGTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTCTGGTGGAAAA
AGTATTTGACAATGTTCCAAATGATTCAATTTATTGGAATTTTCACACATGCATTCCAAT
TGTTCTTCCACAATCCATGCAACTATCCAATTGTGTTGGCTTACTGGATCGGCGGTCATG
GCGTTTTGTTCTTGTTCCTCTTTGCAAATTTCTATAAGCAAGCTTATACAAAGAAGGAAG
TCAAGGTAAAAGTTGATCGAGATATCAACGAAAATGCACTGAACGGAGGCAATGGACTTT
ATGAAGCAAAACAGAAAGCAGCAACTGCATTTGATCAAAATGGAAATCATGCATACAGTA
ATGGAGTGCGAAATAGAATCACTGCAGTGGCGGAATAATATTTCTTGTTGGGCAAAGCCA
TCCCTTTCTTACAAGTCACGTCGTTTTCATTTAAACCCTTGGTGCTGATTGGGTTTAATT
TTGAATTTTACTTCTTTATTTTTAATGTTTAAAAACAGCCACACAACAATACACAGATTT
TTTTAAGATTGTACTTAATGACAAAAAAAACTATATAAAATAAGTGATAAATGTATAACT
AGGAGTTAATTAGAATGAGATGCTGCAATGAACATGATGATTAAGGAAAGTTTTATGATC
TAAATACAAATTTTTATACATACTGAGAAGAGAAAAAAGAAAGAAATGTAAAAAAACTAT
TTAATAAAGACAACTTAAACTTAATTTATAGCTAAAATAATATAT
>g5143.t2 Gene=g5143 Length=128
MLAAMGPEMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVLAYWIGGHGVLF
LFLFANFYKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQKAATAFDQNGNHAYSNGVR
NRITAVAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5143.t2 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 1 | 92 | 3.7E-36 |
| 3 | g5143.t2 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 1 | 92 | 3.7E-36 |
| 1 | g5143.t2 | Pfam | PF01151 | GNS1/SUR4 family | 2 | 78 | 2.6E-13 |
| 6 | g5143.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 10 | g5143.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 39 | - |
| 8 | g5143.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 40 | 44 | - |
| 9 | g5143.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 68 | - |
| 7 | g5143.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 69 | 128 | - |
| 5 | g5143.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 4 | g5143.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 67 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5143/g5143.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.t2.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.
