General information for g5142.t6
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.t6 | TTS | g5142.t6 | 7252080 | 7252080 |
| chr_2 | g5142 | g5142.t6 | isoform | g5142.t6 | 7252084 | 7256277 |
| chr_2 | g5142 | g5142.t6 | exon | g5142.t6.exon1 | 7252084 | 7252859 |
| chr_2 | g5142 | g5142.t6 | cds | g5142.t6.CDS1 | 7252456 | 7252859 |
| chr_2 | g5142 | g5142.t6 | exon | g5142.t6.exon2 | 7252928 | 7253031 |
| chr_2 | g5142 | g5142.t6 | cds | g5142.t6.CDS2 | 7252928 | 7252940 |
| chr_2 | g5142 | g5142.t6 | exon | g5142.t6.exon3 | 7253172 | 7253322 |
| chr_2 | g5142 | g5142.t6 | exon | g5142.t6.exon4 | 7253518 | 7253658 |
| chr_2 | g5142 | g5142.t6 | exon | g5142.t6.exon5 | 7256267 | 7256277 |
| chr_2 | g5142 | g5142.t6 | TSS | g5142.t6 | 7256375 | 7256375 |
Sequences
>g5142.t6 Gene=g5142 Length=1183
AGTTTTAAAAAATGGATATTATCACTCGTATACATGCCGGATGGAGAGATCTAATGGATA
ACAAAACAGACCCGCGAGTCGCTAAATGGCCATTGGCAGCATCTCCGTTTCCCACATTGT
TTATCTGCTTAGCTTATGTTTACATTGTCAAGGTTCTTGGACCACGATTTATGCAAGACA
GAAAGCCATTTAATCTTCGGAAAGTGATAATTTTTTATAACTTTTTGCAAGTCATGCTGA
GTTTCTATCTATTTTGGGAAGTGTCCGTTGTTGGATGGATAGGAGGTGGTTACAATTGGC
GCTTAAATTCACAGAATTTTTCGACACATTCTTCTTTGTTTTGAGAAAAAGATACGACCA
AGTTTCAACACTTCATATCATTCATCACAGAATTATGCCATTTAGTGTTTGGTGGGGTTT
AAAGTTTATGCCTGGAGGTCATAGCACGTTTTTTTTCTTTCTTAATACATTCGTTCATAT
TGTGATGTATACTTACTACATGTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTCTG
GTGGAAACGATATTTGACAATGTTCCAAATGATTCAATTTATTGGAATTTTCACACATGC
ATTCCAATTGTTCTTCCACAATCCATGCAACTATCCGATTGTTTTCTCTTACTGGATTGG
TGGTCATGGTGTTTTGTTCTTGTTCCTTTTCGCTAATTTCTATGTACAAACTTATACAAA
GAAAAAGAGCAAGAAAACTTTAGAAAATGGAAAAGTTAATGGTTTAATTAAGAAAGAAAT
TGAAACAAATGGATTGAAAAAGGAACTGTAAAATGAATTTATTAATTAGTATTTGCCATT
TGAGGAGTTCTAAGTTTTCTTATTTGAAAAAGCTTAATGATTATTTTAAGATGTTAGTCA
GAAATTAGAAAATTAAGATAAATATTGATTAAAGGAACAAAAATCGACTGAAGAGAACTG
CTTTTAAAGAGCAGCACCAAAGGTCATTTTTTAATTAATTAAACTCTGGCGATTTGGTTC
CATTTAAAGGATAATTTTAGCATTTTTTACTTTGATGAACTTTATAAAATTTAATACGCA
TGACAAGTGATATAATTGCTAAATAAATTTTTATTAAACAGCACTTTTAATAAATAGAAA
TTGGTGTGAAATATTTATTGCTAATAAAAATTATTTTTTATCA
>g5142.t6 Gene=g5142 Length=138
MPFSVWWGLKFMPGGHSTFFFFLNTFVHIVMYTYYMLAAMGPEMQKYLWWKRYLTMFQMI
QFIGIFTHAFQLFFHNPCNYPIVFSYWIGGHGVLFLFLFANFYVQTYTKKKSKKTLENGK
VNGLIKKEIETNGLKKEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5142.t6 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 1 | 118 | 2.0E-57 |
| 3 | g5142.t6 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 1 | 118 | 2.0E-57 |
| 1 | g5142.t6 | Pfam | PF01151 | GNS1/SUR4 family | 2 | 114 | 4.1E-28 |
| 9 | g5142.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 19 | - |
| 13 | g5142.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 41 | - |
| 8 | g5142.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 42 | 52 | - |
| 12 | g5142.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 74 | - |
| 10 | g5142.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 75 | 85 | - |
| 11 | g5142.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 104 | - |
| 7 | g5142.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 105 | 138 | - |
| 6 | g5142.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 5 | g5142.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 4 | g5142.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 104 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5142/g5142.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5142.t6.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