General information for g3954.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 g3954 is located on chr_3: 29252205..29253415 (+ 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_3 | g3954 | g3954.t1 | isoform | g3954.t1 | 29252205 | 29253415 |
| chr_3 | g3954 | g3954.t1 | exon | g3954.t1.exon1 | 29252205 | 29252345 |
| chr_3 | g3954 | g3954.t1 | cds | g3954.t1.CDS1 | 29252205 | 29252345 |
| chr_3 | g3954 | g3954.t1 | exon | g3954.t1.exon2 | 29252416 | 29252536 |
| chr_3 | g3954 | g3954.t1 | cds | g3954.t1.CDS2 | 29252416 | 29252536 |
| chr_3 | g3954 | g3954.t1 | exon | g3954.t1.exon3 | 29252588 | 29252791 |
| chr_3 | g3954 | g3954.t1 | cds | g3954.t1.CDS3 | 29252588 | 29252791 |
| chr_3 | g3954 | g3954.t1 | exon | g3954.t1.exon4 | 29252857 | 29253170 |
| chr_3 | g3954 | g3954.t1 | cds | g3954.t1.CDS4 | 29252857 | 29253170 |
| chr_3 | g3954 | g3954.t1 | exon | g3954.t1.exon5 | 29253239 | 29253415 |
| chr_3 | g3954 | g3954.t1 | cds | g3954.t1.CDS5 | 29253239 | 29253415 |
| chr_3 | g3954 | g3954.t1 | TSS | g3954.t1 | NA | NA |
| chr_3 | g3954 | g3954.t1 | TTS | g3954.t1 | NA | NA |
Sequences
>g3954.t1 Gene=g3954 Length=957
ATGAATTATATAAACAGCTTTTATGCCGGCTGGCGAGATTTAATGGATAACAAATCTGAC
CCTAGAACATCAAATTGGCCACTTATGTCTTCACCTTTTCCTACAGCTATTATTTGTTTA
TCATACGTTTATATTGTTAAGGTTCTCGGTCCAAAGCTCATGGAAAATAGAAAACCATTT
AAGCTTAAGACTATTCTGATAGTTTATAACTTTTTACAAGTTATCTTCAGTGCTTGGTTG
TTCTATGAAGCTTGCGTAACAGGTTGGCTTACAACTTACAATTATCGATGTCAACCTGTT
GACTTTTCAAGATCACCAATGGCAATGAGAATGACTGTAGGATGTTATTGGTACTATATT
AGCAAATTTTCAGAATTTCTCGATACATTTTTCTTTATAATGCGAAAAAGATATGATCAA
GTATCGACTCTTCATGTTATTCATCATGGCATTATGCCATTCAGTGTTTGGTGGGGAGTA
AAATTCATGCCGGGTGGTCATAGCTCATTCTTTGGATTTATCAACACATTTGTACATATT
ATTATGTATTTTTACTATATGCTTGCCGCAATGGGACCACACATGCAAAAATATTTATGG
TGGAAAAAGTATTTGACAGTTTTACAAATGGTACAATTTGTAGCCGTCATGATTCACGCT
TTTCAATTACTCTTCCACAATCCTTGCAATTATCCAACTGCATTTATTTGGTGGATTGGA
GCTCATGCAATTATGTTTTATTTCTTATTTAGAAACTTTTATAAGAAGGCATATAAAAAG
AAAATCGAAGGTAAATTGAAGAAAGAAACAGAAAATAACAATGATTGCACAGAAAACTTC
AATGGTTCTTCAAATGATGGTGCGCAAATATATTACACGCCAACAGAAACCGGAAAAATG
GAAGAGAGTTACAGTGCAGACGCCTTTAGGAAGAGAGTATTTATTTCCAAAAATTAG
>g3954.t1 Gene=g3954 Length=318
MNYINSFYAGWRDLMDNKSDPRTSNWPLMSSPFPTAIICLSYVYIVKVLGPKLMENRKPF
KLKTILIVYNFLQVIFSAWLFYEACVTGWLTTYNYRCQPVDFSRSPMAMRMTVGCYWYYI
SKFSEFLDTFFFIMRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSSFFGFINTFVHI
IMYFYYMLAAMGPHMQKYLWWKKYLTVLQMVQFVAVMIHAFQLLFHNPCNYPTAFIWWIG
AHAIMFYFLFRNFYKKAYKKKIEGKLKKETENNNDCTENFNGSSNDGAQIYYTPTETGKM
EESYSADAFRKRVFISKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3954.t1 | Coils | Coil | Coil | 259 | 279 | - |
| 2 | g3954.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 2 | 279 | 7.1E-159 |
| 3 | g3954.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 2 | 279 | 7.1E-159 |
| 1 | g3954.t1 | Pfam | PF01151 | GNS1/SUR4 family | 28 | 262 | 2.0E-63 |
| 17 | g3954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 30 | - |
| 24 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 50 | - |
| 14 | g3954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 51 | 61 | - |
| 21 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 82 | - |
| 19 | g3954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 83 | 101 | - |
| 20 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 120 | - |
| 13 | g3954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 121 | 140 | - |
| 23 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 158 | - |
| 18 | g3954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 159 | 169 | - |
| 26 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 192 | - |
| 15 | g3954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 193 | 203 | - |
| 22 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 225 | - |
| 16 | g3954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 226 | 230 | - |
| 25 | g3954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 250 | - |
| 12 | g3954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 251 | 318 | - |
| 6 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 50 | - |
| 8 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 93 | - |
| 5 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 134 | - |
| 4 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 160 | - |
| 10 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 192 | - |
| 9 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 223 | - |
| 7 | g3954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 250 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
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.
