General information for g12608.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation of very long chain fatty acids protein 4.
Parent gene
- The parent gene g12608 is located on chr_1: 24780011..24783615 (+ 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 | g12608 | g12608.t1 | TSS | g12608.t1 | 24778323 | 24778323 |
| chr_1 | g12608 | g12608.t1 | isoform | g12608.t1 | 24778345 | 24780011 |
| chr_1 | g12608 | g12608.t1 | exon | g12608.t1.exon1 | 24778345 | 24778511 |
| chr_1 | g12608 | g12608.t1 | cds | g12608.t1.CDS1 | 24778345 | 24778511 |
| chr_1 | g12608 | g12608.t1 | exon | g12608.t1.exon2 | 24778913 | 24779247 |
| chr_1 | g12608 | g12608.t1 | cds | g12608.t1.CDS2 | 24778913 | 24779247 |
| chr_1 | g12608 | g12608.t1 | exon | g12608.t1.exon3 | 24779311 | 24779438 |
| chr_1 | g12608 | g12608.t1 | cds | g12608.t1.CDS3 | 24779311 | 24779438 |
| chr_1 | g12608 | g12608.t1 | exon | g12608.t1.exon4 | 24779628 | 24779735 |
| chr_1 | g12608 | g12608.t1 | cds | g12608.t1.CDS4 | 24779628 | 24779735 |
| chr_1 | g12608 | g12608.t1 | exon | g12608.t1.exon5 | 24779940 | 24780011 |
| chr_1 | g12608 | g12608.t1 | cds | g12608.t1.CDS5 | 24779940 | 24780011 |
| chr_1 | g12608 | g12608.t1 | TTS | g12608.t1 | NA | NA |
Sequences
>g12608.t1 Gene=g12608 Length=810
ATGATCGGAAGTTTAGTTGTGAAAATTAACGAAACTTATCAATGGTTGGATCAATATTCT
GATCCACGAACAAAGTCTTTACCATTGATTGAGAATCCATTTACTGTTTTGTGGGTTGTT
TCGGGATATTTTATTGGAATATGGTGTCTATTGAAGTTTATGGAAAATCAAAAACCATTC
AAACTCAACAAGATCATGGTATTTTATAATCTCTCATTAGCTTTGCTAAATCTCAAGATT
TTCATAACAGCAATAAAATATTCTTATATTCTTAACTACAACTTTGTATGCGAACCGTAT
CGAGTTAGTTACCATCCAATGGAATTGATTCTCATCGATAATAATTGGCTATATTACATT
AGCAAAATTGTTGAATTTTGTGACACGATGTTTTTCATATTGCGTAAAAAGAACACTCAA
CTCTCCTTCCTCCACGTGTATCATCACTCATCTGTTTTTGTTTTGTCATGGGTTGTCATG
AAATGGACGCCTTCTGGATCTGTTATCAGTGCATTGAAATTGAATTCTTTTGTGCATATT
GTAATGTATTCTTATTATGGACTTGCTGCTGTTGGACCACATATGGCTAAATATTTAACA
TGGAAAAAACATTTGACGAAAATTCAAATTATTCAATTTTTGATTGCTTTTTACATTGCG
GCTTCAAATATGTTAAACGGTTGCCAATATCCGATTGGATTGAAAATTTGTGCTCTTTTC
TATGCTGTTTCTTATCTGATTCTTTTCGGAAATTTTTACTGGAAATCATATTTAAAAGGA
GCAAAGAAGCAAATTCTAAAAGAAGCTTAA
>g12608.t1 Gene=g12608 Length=269
MIGSLVVKINETYQWLDQYSDPRTKSLPLIENPFTVLWVVSGYFIGIWCLLKFMENQKPF
KLNKIMVFYNLSLALLNLKIFITAIKYSYILNYNFVCEPYRVSYHPMELILIDNNWLYYI
SKIVEFCDTMFFILRKKNTQLSFLHVYHHSSVFVLSWVVMKWTPSGSVISALKLNSFVHI
VMYSYYGLAAVGPHMAKYLTWKKHLTKIQIIQFLIAFYIAASNMLNGCQYPIGLKICALF
YAVSYLILFGNFYWKSYLKGAKKQILKEA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12608.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 9 | 262 | 2.1E-71 |
| 3 | g12608.t1 | PANTHER | PTHR11157:SF12 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 4 | 9 | 262 | 2.1E-71 |
| 1 | g12608.t1 | Pfam | PF01151 | GNS1/SUR4 family | 29 | 263 | 9.9E-56 |
| 17 | g12608.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 34 | - |
| 23 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 54 | - |
| 12 | g12608.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 55 | 65 | - |
| 22 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 85 | - |
| 16 | g12608.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 86 | 115 | - |
| 24 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 134 | - |
| 14 | g12608.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 135 | 145 | - |
| 21 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 164 | - |
| 19 | g12608.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 165 | 175 | - |
| 20 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 196 | - |
| 15 | g12608.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 197 | 207 | - |
| 26 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 226 | - |
| 18 | g12608.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 231 | - |
| 25 | g12608.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 254 | - |
| 13 | g12608.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 255 | 269 | - |
| 11 | g12608.t1 | ProSitePatterns | PS01188 | ELO family signature. | 141 | 149 | - |
| 8 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 34 | 53 | - |
| 6 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 85 | - |
| 7 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 134 | - |
| 4 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 160 | - |
| 10 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 175 | 192 | - |
| 5 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 222 | - |
| 9 | g12608.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 254 | - |
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