General information for g12190.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t16 | TTS | g12190.t16 | 21658510 | 21658510 |
| chr_1 | g12190 | g12190.t16 | isoform | g12190.t16 | 21659052 | 21664669 |
| chr_1 | g12190 | g12190.t16 | exon | g12190.t16.exon1 | 21659052 | 21659145 |
| chr_1 | g12190 | g12190.t16 | cds | g12190.t16.CDS1 | 21659054 | 21659145 |
| chr_1 | g12190 | g12190.t16 | exon | g12190.t16.exon2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t16 | cds | g12190.t16.CDS2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t16 | exon | g12190.t16.exon3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t16 | cds | g12190.t16.CDS3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t16 | exon | g12190.t16.exon4 | 21661922 | 21662039 |
| chr_1 | g12190 | g12190.t16 | cds | g12190.t16.CDS4 | 21661922 | 21662020 |
| chr_1 | g12190 | g12190.t16 | exon | g12190.t16.exon5 | 21664628 | 21664669 |
| chr_1 | g12190 | g12190.t16 | TSS | g12190.t16 | 21664861 | 21664861 |
Sequences
>g12190.t16 Gene=g12190 Length=579
TTTAAATTATAACATTCAGAAAGAATTAATAAAAAATAGATGTGCCACATGGCAAGACTT
AATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTTCCTTATGTCATCGCCACTTCC
CACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGATAGTTGGTCCTGCGCTTAT
GGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTATAATTTTCTGCAAGT
ACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATGGTTCACAAATTATAG
TTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCATACAGATGACACACTT
TTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTGTTTT
GAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATTATGCCTTT
TAGTGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCCT
CAACACATTTGTGCATATCATAATGTATACTTATTATAT
>g12190.t16 Gene=g12190 Length=172
MDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKPFQLRKIIVVYNFLQV
LLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYYFSKFTEFFDTFFFVL
RKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVHIIMYTYY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12190.t16 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 1 | 172 | 8.5E-96 |
| 3 | g12190.t16 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 1 | 172 | 8.5E-96 |
| 1 | g12190.t16 | Pfam | PF01151 | GNS1/SUR4 family | 14 | 172 | 8.1E-44 |
| 10 | g12190.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 17 | g12190.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 31 | - |
| 9 | g12190.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 32 | 50 | - |
| 16 | g12190.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 51 | 68 | - |
| 12 | g12190.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 69 | 87 | - |
| 14 | g12190.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 106 | - |
| 8 | g12190.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 107 | 126 | - |
| 15 | g12190.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 146 | - |
| 11 | g12190.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 147 | 151 | - |
| 13 | g12190.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 152 | 171 | - |
| 7 | g12190.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 172 | 172 | - |
| 6 | g12190.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
| 5 | g12190.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 52 | 71 | - |
| 4 | g12190.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 149 | 171 | - |
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