General information for g12190.t10
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.t10 | TTS | g12190.t10 | 21658510 | 21658510 |
| chr_1 | g12190 | g12190.t10 | isoform | g12190.t10 | 21658682 | 21664879 |
| chr_1 | g12190 | g12190.t10 | exon | g12190.t10.exon1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t10 | cds | g12190.t10.CDS1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t10 | exon | g12190.t10.exon2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t10 | cds | g12190.t10.CDS2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t10 | exon | g12190.t10.exon3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t10 | cds | g12190.t10.CDS3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t10 | exon | g12190.t10.exon4 | 21661922 | 21661997 |
| chr_1 | g12190 | g12190.t10 | cds | g12190.t10.CDS4 | 21661922 | 21661997 |
| chr_1 | g12190 | g12190.t10 | exon | g12190.t10.exon5 | 21664596 | 21664879 |
| chr_1 | g12190 | g12190.t10 | cds | g12190.t10.CDS5 | 21664596 | 21664630 |
| chr_1 | g12190 | g12190.t10 | TSS | g12190.t10 | 21664861 | 21664861 |
Sequences
>g12190.t10 Gene=g12190 Length=1149
TAAATTATTCGGATTTTCAGTCTTTCATTAGCGTTTAAATCGCACGCATCATTCTCCAGT
TTTATTAAAAGTGAAGAAGTGAAATAGACACTTGAAAAATATTTTTATAAATATTATTTA
TGTGATGAATTTACTTTAATAAAAAGAATAATTATTTAAACAACTGCAAGAAAATAAATT
TAGAAGTGAAATAAAAATAGTGAAATTATTTTTAAATTATAACATTCAGAAAGAATTAAT
AAAAAATAGATGGTAAGAGAGTGCTTTGACATTGTGAACATAAAAACGACAAATTGGTTC
CTTATGTCATCGCCACTTCCCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAG
ATAGTTGGTCCTGCGCTTATGGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTA
GTTTATAATTTTCTGCAAGTACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCG
GGATGGTTCACAAATTATAGTTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAA
GCCATACAGATGACACACTTTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTT
GACACATTTTTCTTTGTTTTGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATT
CATCATGGAATTATGCCTTTTAGTGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCAC
AGCACCTTCTTTGGACTCCTCAACACATTTGTGCATATCATAATGTATACTTATTATATG
TTAGCTGCAATGGGACCACAAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATT
TTGCAGATGATCCAATTTGTTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAAT
CCCTGCAATTACTCTTATATTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTAT
TTCCTCTTTAGAAGCTTCTATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAAT
GATGAACCAAATGACAAAAAGACATTAATTGTAGATGACAATGAAAATATTGTAGAATAC
AAGAAACATTATGAGACAAAAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAG
CATCTTTAA
>g12190.t10 Gene=g12190 Length=299
MVRECFDIVNIKTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKPFQLRKIIVVYN
FLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYYFSKFTEFFDTF
FFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVHIIMYTYYMLAA
MGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIGGHGVLFYFLF
RSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSITQINKALAKHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12190.t10 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 11 | 271 | 1.1E-134 |
| 3 | g12190.t10 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 11 | 271 | 1.1E-134 |
| 1 | g12190.t10 | Pfam | PF01151 | GNS1/SUR4 family | 18 | 254 | 1.7E-59 |
| 18 | g12190.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 15 | - |
| 19 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 16 | 35 | - |
| 12 | g12190.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 36 | 54 | - |
| 22 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 72 | - |
| 15 | g12190.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 73 | 91 | - |
| 24 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 92 | 110 | - |
| 14 | g12190.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 111 | 130 | - |
| 21 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 150 | - |
| 17 | g12190.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 151 | 161 | - |
| 20 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 182 | - |
| 13 | g12190.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 183 | 193 | - |
| 23 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 215 | - |
| 16 | g12190.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 216 | 220 | - |
| 25 | g12190.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 240 | - |
| 11 | g12190.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 241 | 299 | - |
| 10 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 36 | - |
| 5 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 56 | 75 | - |
| 8 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 124 | - |
| 7 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 150 | - |
| 6 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 160 | 182 | - |
| 9 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 216 | - |
| 4 | g12190.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 243 | - |
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