General information for g5140.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 g5140 is located on chr_2: 7246495..7247573 (- 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 | g5140 | g5140.t1 | TTS | g5140.t1 | 7246308 | 7246308 |
| chr_2 | g5140 | g5140.t1 | isoform | g5140.t1 | 7246495 | 7247573 |
| chr_2 | g5140 | g5140.t1 | exon | g5140.t1.exon1 | 7246495 | 7246886 |
| chr_2 | g5140 | g5140.t1 | cds | g5140.t1.CDS1 | 7246495 | 7246886 |
| chr_2 | g5140 | g5140.t1 | exon | g5140.t1.exon2 | 7246956 | 7247091 |
| chr_2 | g5140 | g5140.t1 | cds | g5140.t1.CDS2 | 7246956 | 7247091 |
| chr_2 | g5140 | g5140.t1 | exon | g5140.t1.exon3 | 7247250 | 7247573 |
| chr_2 | g5140 | g5140.t1 | cds | g5140.t1.CDS3 | 7247250 | 7247573 |
| chr_2 | g5140 | g5140.t1 | TSS | g5140.t1 | 7247736 | 7247736 |
Sequences
>g5140.t1 Gene=g5140 Length=852
ATGCTTCACAAAATTCAAGCAATTTGGCAAGATTTAATGCAAAATAAATCTGATCCAAGA
GTGGCAAATTTTTTTTTAATGTCATCGCCTTTTCCGACAATAATAATTTGCCTTACTTAT
GTTTATCTCGTGAAAGTTCTATTGCCAAAATTTATGGAAAATCGAAAACCTTTCAAACTA
CAGAAGATATTGATAGTTTACAATTTTGCCCAAGCTTTATTCAGTTTATATTTATTTTCT
GAGGCAGGTCGATATGGGTGGTTCAGGCACTACAGCTGGCGATGCCAAGCAGTTGATTAC
TCACATAACAAACTTGCTATGAAAATGGTCATTGGCAGTTACCTCTATTATTTGAGTAAA
TTTTCTGAATTCTTTGACACTTTCTTTTTTGTTTTGAGAAAGAAATATGATCAAGTTTCA
ACTTTACACGTCATTCATCATGGAATTATGCCTTTTAGTGTTTGGTGGGGAGCGAAATTT
TTACCAGGTGGTCACAGCTCATTCTTTGCTTTTCTCAATACTTTCATTCATTTCGTTATG
TACACTTACTACATGTTAGCAGCAATGGGACCAAAAGTGCAGAAATATCTCTGGTGGAAA
AAATATTTGACTTTGATGCAAATGGCTCAATTTGTGGCAATTTTTGTTCATGCATTTCAA
CTGTTCTTTCACAATCCTTGCAATTATCCAATTATTTTTGCTTATTGGATCGGCGGTCAT
GGAGTTTTGTTCTTAGTTCTTTTTATGAACTTTTATAAACAAGCATATTTAAAGAAGGAT
AAAAAAATCAAAGCAGTTGATTTGAATGAAAATTCTGAATATATTTCAATTGAAGGAAAG
AAAATTAAGTAA
>g5140.t1 Gene=g5140 Length=283
MLHKIQAIWQDLMQNKSDPRVANFFLMSSPFPTIIICLTYVYLVKVLLPKFMENRKPFKL
QKILIVYNFAQALFSLYLFSEAGRYGWFRHYSWRCQAVDYSHNKLAMKMVIGSYLYYLSK
FSEFFDTFFFVLRKKYDQVSTLHVIHHGIMPFSVWWGAKFLPGGHSSFFAFLNTFIHFVM
YTYYMLAAMGPKVQKYLWWKKYLTLMQMAQFVAIFVHAFQLFFHNPCNYPIIFAYWIGGH
GVLFLVLFMNFYKQAYLKKDKKIKAVDLNENSEYISIEGKKIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5140.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 3 | 269 | 7.3E-132 |
| 3 | g5140.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 3 | 269 | 7.3E-132 |
| 1 | g5140.t1 | Pfam | PF01151 | GNS1/SUR4 family | 26 | 262 | 1.3E-61 |
| 14 | g5140.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 20 | - |
| 23 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 13 | g5140.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 44 | 62 | - |
| 24 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 80 | - |
| 15 | g5140.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 81 | 113 | - |
| 22 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 114 | 132 | - |
| 12 | g5140.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 133 | 143 | - |
| 18 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 144 | 162 | - |
| 17 | g5140.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 163 | 167 | - |
| 21 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 190 | - |
| 10 | g5140.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 191 | 201 | - |
| 20 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 223 | - |
| 16 | g5140.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 224 | 228 | - |
| 19 | g5140.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 252 | - |
| 11 | g5140.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 253 | 283 | - |
| 7 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 9 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 80 | - |
| 6 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 110 | 132 | - |
| 5 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 190 | - |
| 8 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
| 4 | g5140.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 251 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5140/g5140.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5140.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. There were no conditions that were differentially expressed