General information for g17623.t1
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 7.
Parent gene
- The parent gene g17623 is located on HiC_scaffold_18: 1592..2728 (+ 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_18 | g17623 | g17623.t1 | TSS | g17623.t1 | 1555 | 1555 |
| HiC_scaffold_18 | g17623 | g17623.t1 | isoform | g17623.t1 | 1592 | 2728 |
| HiC_scaffold_18 | g17623 | g17623.t1 | exon | g17623.t1.exon1 | 1592 | 1637 |
| HiC_scaffold_18 | g17623 | g17623.t1 | cds | g17623.t1.CDS1 | 1592 | 1637 |
| HiC_scaffold_18 | g17623 | g17623.t1 | exon | g17623.t1.exon2 | 1730 | 1920 |
| HiC_scaffold_18 | g17623 | g17623.t1 | cds | g17623.t1.CDS2 | 1730 | 1920 |
| HiC_scaffold_18 | g17623 | g17623.t1 | exon | g17623.t1.exon3 | 1980 | 2120 |
| HiC_scaffold_18 | g17623 | g17623.t1 | cds | g17623.t1.CDS3 | 1980 | 2120 |
| HiC_scaffold_18 | g17623 | g17623.t1 | exon | g17623.t1.exon4 | 2185 | 2427 |
| HiC_scaffold_18 | g17623 | g17623.t1 | cds | g17623.t1.CDS4 | 2185 | 2427 |
| HiC_scaffold_18 | g17623 | g17623.t1 | exon | g17623.t1.exon5 | 2549 | 2728 |
| HiC_scaffold_18 | g17623 | g17623.t1 | cds | g17623.t1.CDS5 | 2549 | 2728 |
| HiC_scaffold_18 | g17623 | g17623.t1 | TTS | g17623.t1 | NA | NA |
Sequences
>g17623.t1 Gene=g17623 Length=801
ATGGTGTCTTTGGGTTATATATCTGAAATTTGGAATAAATATGAAGATCCTAGAACAGCA
GGAAAATTTCTTATGGAAAATCCACCTACGAGATTTTTCGGATTTATAATTTCATATGTA
TTGTTCATTCACTTTGGACCAACTTTAATGAAGAAAAGAAAACCGTTTGAATTAAAATTA
GTGAAATCTGTTTACAACATTTTTCAAATTGTCATAAATGGATATTACGGACTTTATGGA
CTGTATTATGTATTTTTAACACATAATTACAATTATTCTTGCCCATCATTGGCTATTGGA
AATGATGAATATGCTCAGACAATTGCACACTTGGGACATATTTATTTCTTATCAAAACTT
TGGGATCTTTTTGATACTATTTTCATAATATTAAAAAAGAATGATCGACAGTTATCATTT
CTTCATTGCTATCATCATATGTTTATGGCTTTTGCAACTTATTTTATTATGAAATTTTAC
ATTGATACATCTTTCTGTTTGGTTGCTGTCATCAATGCTTTGATTCATAGCTGCATGTAT
TTTTACTATTTTCTCACAACGCAAAATTCGGAAGTTAAGAAATCAATCACATGGAAGAAA
CATATTACACATATTCAAATGTTACAATTCACGGTGCTTTCTATTCATTTTCTGAGACCA
GTATTTAATACAGAATGTAATAGACCGAAAGTTTGGGATATATTTATGTCTCTTCAGATT
CTTTTTATCCTTTATATGTTCATACAATTCTATATTAAAACATATTTAGTAAAGAAGAAT
TCAAATAAAAAGAAATTTTAA
>g17623.t1 Gene=g17623 Length=266
MVSLGYISEIWNKYEDPRTAGKFLMENPPTRFFGFIISYVLFIHFGPTLMKKRKPFELKL
VKSVYNIFQIVINGYYGLYGLYYVFLTHNYNYSCPSLAIGNDEYAQTIAHLGHIYFLSKL
WDLFDTIFIILKKNDRQLSFLHCYHHMFMAFATYFIMKFYIDTSFCLVAVINALIHSCMY
FYYFLTTQNSEVKKSITWKKHITHIQMLQFTVLSIHFLRPVFNTECNRPKVWDIFMSLQI
LFILYMFIQFYIKTYLVKKNSNKKKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g17623.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 29 | 259 | 8.1E-63 |
| 3 | g17623.t1 | PANTHER | PTHR11157:SF116 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN-RELATED | 29 | 259 | 8.1E-63 |
| 1 | g17623.t1 | Pfam | PF01151 | GNS1/SUR4 family | 27 | 262 | 1.3E-50 |
| 14 | g17623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 31 | - |
| 18 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 51 | - |
| 10 | g17623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 52 | 62 | - |
| 22 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 85 | - |
| 13 | g17623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 86 | 112 | - |
| 21 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 131 | - |
| 11 | g17623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 132 | 142 | - |
| 16 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 161 | - |
| 15 | g17623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 162 | 166 | - |
| 20 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 185 | - |
| 9 | g17623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 186 | 204 | - |
| 17 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 222 | - |
| 12 | g17623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 223 | 233 | - |
| 19 | g17623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 256 | - |
| 8 | g17623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 257 | 266 | - |
| 7 | g17623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 49 | - |
| 5 | g17623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 64 | 86 | - |
| 6 | g17623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 164 | 186 | - |
| 4 | g17623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 257 | - |
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 transcript has been annotated with K10245 (fatty acid elongase 2)
Pathway
- This transcript belongs to the following pathways
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