General information for g12190.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 g12190 is located on chr_1: 21659344..21665041 (- 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_1 | g12190 | g12190.t2 | TTS | g12190.t2 | 21658510 | 21658510 |
| chr_1 | g12190 | g12190.t2 | isoform | g12190.t2 | 21658682 | 21659110 |
| chr_1 | g12190 | g12190.t2 | exon | g12190.t2.exon1 | 21658682 | 21659110 |
| chr_1 | g12190 | g12190.t2 | cds | g12190.t2.CDS1 | 21658682 | 21659041 |
| chr_1 | g12190 | g12190.t2 | TSS | g12190.t2 | 21659757 | 21659757 |
Sequences
>g12190.t2 Gene=g12190 Length=429
AGCACCTTCTTTGGACTCCTCAACACATTTGTGCATATCATAATGTATACTTATTATATG
TTAGCTGCAATGGGACCACAAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATT
TTGCAGATGATCCAATTTGTTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAAT
CCCTGCAATTACTCTTATATTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTAT
TTCCTCTTTAGAAGCTTCTATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAAT
GATGAACCAAATGACAAAAAGACATTAATTGTAGATGACAATGAAAATATTGTAGAATAC
AAGAAACATTATGAGACAAAAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAG
CATCTTTAA
>g12190.t2 Gene=g12190 Length=119
MGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIGGHGVLFYFLF
RSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSITQINKALAKHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12190.t2 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 1 | 93 | 1.0E-31 |
| 3 | g12190.t2 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 1 | 93 | 1.0E-31 |
| 1 | g12190.t2 | Pfam | PF01151 | GNS1/SUR4 family | 7 | 74 | 3.6E-10 |
| 7 | g12190.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 13 | - |
| 10 | g12190.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 14 | 35 | - |
| 8 | g12190.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 40 | - |
| 9 | g12190.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 41 | 60 | - |
| 6 | g12190.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 61 | 119 | - |
| 5 | g12190.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 4 | g12190.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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