General information for g5142.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 g5142 is located on chr_2: 7252456..7256378 (- 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 | g5142 | g5142.t1 | TTS | g5142.t1 | 7252080 | 7252080 |
| chr_2 | g5142 | g5142.t1 | isoform | g5142.t1 | 7252456 | 7253658 |
| chr_2 | g5142 | g5142.t1 | exon | g5142.t1.exon1 | 7252456 | 7252859 |
| chr_2 | g5142 | g5142.t1 | cds | g5142.t1.CDS1 | 7252456 | 7252859 |
| chr_2 | g5142 | g5142.t1 | exon | g5142.t1.exon2 | 7252928 | 7253063 |
| chr_2 | g5142 | g5142.t1 | cds | g5142.t1.CDS2 | 7252928 | 7253063 |
| chr_2 | g5142 | g5142.t1 | exon | g5142.t1.exon3 | 7253131 | 7253322 |
| chr_2 | g5142 | g5142.t1 | cds | g5142.t1.CDS3 | 7253131 | 7253322 |
| chr_2 | g5142 | g5142.t1 | exon | g5142.t1.exon4 | 7253518 | 7253658 |
| chr_2 | g5142 | g5142.t1 | cds | g5142.t1.CDS4 | 7253518 | 7253658 |
| chr_2 | g5142 | g5142.t1 | TSS | g5142.t1 | NA | NA |
Sequences
>g5142.t1 Gene=g5142 Length=873
ATGGATATTATCACTCGTATACATGCCGGATGGAGAGATCTAATGGATAACAAAACAGAC
CCGCGAGTCGCTAAATGGCCATTGGCAGCATCTCCGTTTCCCACATTGTTTATCTGCTTA
GCTTATGTTTACATTGTCAAGGTTCTTGGACCACGATTTATGCAAGACAGAAAGCCATTT
AATCTTCGGAAAGTGATAATTTTTTATAACTTTTTGCAAGTCATGCTGAGTTTCTATCTA
TTTTGGGAAGTGTCCGTTGTTGGATGGATAGGAGGTGGTTACAATTGGCGCTGTCAACCT
GTCGACTTTTCTCGCAATGAAATGCCAATGAGAATGGCAAGAGTTTGTTGGCTATATTTT
ATTAGTAAATTCACAGAATTTTTCGACACATTCTTCTTTGTTTTGAGAAAAAGATACGAC
CAAGTTTCAACACTTCATATCATTCATCACAGAATTATGCCATTTAGTGTTTGGTGGGGT
TTAAAGTTTATGCCTGGAGGTCATAGCACGTTTTTTTTCTTTCTTAATACATTCGTTCAT
ATTGTGATGTATACTTACTACATGTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTC
TGGTGGAAACGATATTTGACAATGTTCCAAATGATTCAATTTATTGGAATTTTCACACAT
GCATTCCAATTGTTCTTCCACAATCCATGCAACTATCCGATTGTTTTCTCTTACTGGATT
GGTGGTCATGGTGTTTTGTTCTTGTTCCTTTTCGCTAATTTCTATGTACAAACTTATACA
AAGAAAAAGAGCAAGAAAACTTTAGAAAATGGAAAAGTTAATGGTTTAATTAAGAAAGAA
ATTGAAACAAATGGATTGAAAAAGGAACTGTAA
>g5142.t1 Gene=g5142 Length=290
MDIITRIHAGWRDLMDNKTDPRVAKWPLAASPFPTLFICLAYVYIVKVLGPRFMQDRKPF
NLRKVIIFYNFLQVMLSFYLFWEVSVVGWIGGGYNWRCQPVDFSRNEMPMRMARVCWLYF
ISKFTEFFDTFFFVLRKRYDQVSTLHIIHHRIMPFSVWWGLKFMPGGHSTFFFFLNTFVH
IVMYTYYMLAAMGPEMQKYLWWKRYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVFSYWI
GGHGVLFLFLFANFYVQTYTKKKSKKTLENGKVNGLIKKEIETNGLKKEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5142.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 3 | 269 | 6.2E-137 |
| 3 | g5142.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 3 | 269 | 6.2E-137 |
| 1 | g5142.t1 | Pfam | PF01151 | GNS1/SUR4 family | 28 | 266 | 4.9E-64 |
| 18 | g5142.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 20 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 45 | - |
| 14 | g5142.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 46 | 65 | - |
| 19 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 92 | - |
| 15 | g5142.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 93 | 111 | - |
| 24 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 135 | - |
| 12 | g5142.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 136 | 141 | - |
| 23 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 17 | g5142.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 162 | 172 | - |
| 21 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 193 | - |
| 11 | g5142.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 204 | - |
| 25 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 226 | - |
| 16 | g5142.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 237 | - |
| 22 | g5142.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 238 | 256 | - |
| 13 | g5142.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 257 | 290 | - |
| 6 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 50 | - |
| 9 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 93 | - |
| 5 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 135 | - |
| 8 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 4 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 7 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 224 | - |
| 10 | g5142.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 256 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5142/g5142.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5142.t1.fa.iupred3.txt does not exist
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.
