General information for g5143.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.
Parent gene
- The parent gene g5143 is located on chr_2: 7260309..7268647 (- 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_2 | g5143 | g5143.t1 | TTS | g5143.t1 | 7259954 | 7259954 |
| chr_2 | g5143 | g5143.t1 | isoform | g5143.t1 | 7260309 | 7266723 |
| chr_2 | g5143 | g5143.t1 | exon | g5143.t1.exon1 | 7260309 | 7260787 |
| chr_2 | g5143 | g5143.t1 | cds | g5143.t1.CDS1 | 7260309 | 7260787 |
| chr_2 | g5143 | g5143.t1 | exon | g5143.t1.exon2 | 7260861 | 7261188 |
| chr_2 | g5143 | g5143.t1 | cds | g5143.t1.CDS2 | 7260861 | 7261188 |
| chr_2 | g5143 | g5143.t1 | exon | g5143.t1.exon3 | 7266583 | 7266723 |
| chr_2 | g5143 | g5143.t1 | cds | g5143.t1.CDS3 | 7266583 | 7266723 |
| chr_2 | g5143 | g5143.t1 | TSS | g5143.t1 | NA | NA |
Sequences
>g5143.t1 Gene=g5143 Length=948
ATGAACATAATCAACAAATTCTACCATGAATGGAGGGATCTGATGGATAACAAATCTGAT
CAGAGAACGACAAATTGGATGCTAATGTCATCGCCAATTCCAACAGTCATCATTTGCTTG
TCTTATGTTTATATTGTCAAGGTACTTGGACCACGATTTATGCAAGACAGAAAACCATTC
AAGCTTCGAAAAATTATAATTGTTTATAATTTTTTGCAAGTGCTATTTAGTTTGTATCTA
TTTCTCGAAGTAGCAAGCGTTGGATGGATAGGAGGTGGATATAGCTGGAGATGTCAACCA
GTTAATCACTCAACAGATGCAGACACAATGAGAATGGTCAGCGTATGCTGGTGGTATTAT
TTCAGTAAATTCACAGAGTTCTTTGATACATTCTTCTTCGTCTTAAGAAAACGATATGAT
CAAGTTTCAACTTTGCACGTTATTCATCATGGAATCATGCCATTCAGCGTTTGGTGGGGA
GTAAAATTCATGCCAGGTGGTCACAGTTCATTCTTTGGATTCCTCAACACTTTCGTTCAT
ATTGTTATGTATACTTACTACATGTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTC
TGGTGGAAAAAGTATTTGACAATGTTCCAAATGATTCAATTTATTGGAATTTTCACACAT
GCATTCCAATTGTTCTTCCACAATCCATGCAACTATCCAATTGTGTTGGCTTACTGGATC
GGCGGTCATGGCGTTTTGTTCTTGTTCCTCTTTGCAAATTTCTATAAGCAAGCTTATACA
AAGAAGGAAGTCAAGGTAAAAGTTGATCGAGATATCAACGAAAATGCACTGAACGGAGGC
AATGGACTTTATGAAGCAAAACAGAAAGCAGCAACTGCATTTGATCAAAATGGAAATCAT
GCATACAGTAATGGAGTGCGAAATAGAATCACTGCAGTGGCGGAATAA
>g5143.t1 Gene=g5143 Length=315
MNIINKFYHEWRDLMDNKSDQRTTNWMLMSSPIPTVIICLSYVYIVKVLGPRFMQDRKPF
KLRKIIIVYNFLQVLFSLYLFLEVASVGWIGGGYSWRCQPVNHSTDADTMRMVSVCWWYY
FSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSSFFGFLNTFVH
IVMYTYYMLAAMGPEMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVLAYWI
GGHGVLFLFLFANFYKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQKAATAFDQNGNH
AYSNGVRNRITAVAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5143.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 3 | 277 | 1.1E-142 |
| 3 | g5143.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 3 | 277 | 1.1E-142 |
| 1 | g5143.t1 | Pfam | PF01151 | GNS1/SUR4 family | 28 | 265 | 2.8E-64 |
| 18 | g5143.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 20 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 45 | - |
| 14 | g5143.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 46 | 65 | - |
| 24 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 90 | - |
| 15 | g5143.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 91 | 116 | - |
| 19 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 135 | - |
| 13 | g5143.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 136 | 141 | - |
| 22 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 17 | g5143.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 162 | 172 | - |
| 21 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 193 | - |
| 11 | g5143.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 204 | - |
| 25 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 226 | - |
| 16 | g5143.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 231 | - |
| 23 | g5143.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 255 | - |
| 12 | g5143.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 256 | 315 | - |
| 9 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 46 | - |
| 4 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 89 | - |
| 7 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 135 | - |
| 8 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 5 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 6 | g5143.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 227 | - |
| 10 | g5143.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.
Data is missing for g5143/g5143.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.t1.fa.iupred3.txt does not exist
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.
