General information for g12190.t12
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.t12 | TTS | g12190.t12 | 21658510 | 21658510 |
| chr_1 | g12190 | g12190.t12 | isoform | g12190.t12 | 21658682 | 21664887 |
| chr_1 | g12190 | g12190.t12 | exon | g12190.t12.exon1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t12 | cds | g12190.t12.CDS1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t12 | exon | g12190.t12.exon2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t12 | cds | g12190.t12.CDS2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t12 | exon | g12190.t12.exon3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t12 | cds | g12190.t12.CDS3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t12 | exon | g12190.t12.exon4 | 21661922 | 21662062 |
| chr_1 | g12190 | g12190.t12 | cds | g12190.t12.CDS4 | 21661922 | 21662062 |
| chr_1 | g12190 | g12190.t12 | exon | g12190.t12.exon5 | 21664628 | 21664887 |
| chr_1 | g12190 | g12190.t12 | cds | g12190.t12.CDS5 | 21664628 | 21664630 |
| chr_1 | g12190 | g12190.t12 | TSS | g12190.t12 | 21664861 | 21664861 |
Sequences
>g12190.t12 Gene=g12190 Length=1190
GTGAGTGTTAAATTATTCGGATTTTCAGTCTTTCATTAGCGTTTAAATCGCACGCATCAT
TCTCCAGTTTTATTAAAAGTGAAGAAGTGAAATAGACACTTGAAAAATATTTTTATAAAT
ATTATTTATGTGATGAATTTACTTTAATAAAAAGAATAATTATTTAAACAACTGCAAGAA
AATAAATTTAGAAGTGAAATAAAAATAGTGAAATTATTTTTAAATTATAACATTCAGAAA
GAATTAATAAAAAATAGATGATGGATGCTCTAAACAAAATTAGTGCCACATGGCAAGACT
TAATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTTCCTTATGTCATCGCCACTTC
CCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGATAGTTGGTCCTGCGCTTA
TGGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTATAATTTTCTGCAAG
TACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATGGTTCACAAATTATA
GTTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCATACAGATGACACACT
TTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTGTTT
TGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATTATGCCTT
TTAGTGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCC
TCAACACATTTGTGCATATCATAATGTATACTTATTATATGTTAGCTGCAATGGGACCAC
AAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCAGATGATCCAATTTG
TTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTGCAATTACTCTTATA
TTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGCTTCT
ATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAA
AGACATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAAACATTATGAGACAA
AAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCTTTAA
>g12190.t12 Gene=g12190 Length=310
MMDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKP
FQLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYY
FSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVH
IIMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWI
GGHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSIT
QINKALAKHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12190.t12 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 5 | 282 | 1.2E-143 |
| 3 | g12190.t12 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 5 | 282 | 1.2E-143 |
| 1 | g12190.t12 | Pfam | PF01151 | GNS1/SUR4 family | 29 | 265 | 1.9E-59 |
| 15 | g12190.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 26 | - |
| 25 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 46 | - |
| 14 | g12190.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 47 | 65 | - |
| 21 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 83 | - |
| 18 | g12190.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 84 | 102 | - |
| 24 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 103 | 121 | - |
| 13 | g12190.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 122 | 141 | - |
| 22 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 17 | g12190.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 162 | 172 | - |
| 20 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 193 | - |
| 12 | g12190.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 204 | - |
| 23 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 226 | - |
| 16 | g12190.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 231 | - |
| 19 | g12190.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 251 | - |
| 11 | g12190.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 252 | 310 | - |
| 9 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 25 | 47 | - |
| 8 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 86 | - |
| 6 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 135 | - |
| 7 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 4 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 5 | g12190.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 227 | - |
| 10 | g12190.t12 | 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 K10250 (elongation of very long chain fatty acids protein 7)
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