General information for g3956.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 AAEL008004.
Parent gene
- The parent gene g3956 is located on chr_3: 29267122..29268675 (+ 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 | g3956 | g3956.t1 | isoform | g3956.t1 | 29263016 | 29267122 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon1 | 29263016 | 29263073 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS1 | 29263016 | 29263073 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon2 | 29263536 | 29263618 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS2 | 29263536 | 29263618 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon3 | 29263682 | 29263789 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS3 | 29263682 | 29263789 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon4 | 29265124 | 29265207 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS4 | 29265124 | 29265207 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon5 | 29266161 | 29266217 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS5 | 29266161 | 29266217 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon6 | 29266280 | 29266358 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS6 | 29266280 | 29266358 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon7 | 29266433 | 29266596 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS7 | 29266433 | 29266596 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon8 | 29266655 | 29266807 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS8 | 29266655 | 29266807 |
| chr_3 | g3956 | g3956.t1 | exon | g3956.t1.exon9 | 29266874 | 29267122 |
| chr_3 | g3956 | g3956.t1 | cds | g3956.t1.CDS9 | 29266874 | 29267122 |
| chr_3 | g3956 | g3956.t1 | TTS | g3956.t1 | 29267500 | 29267500 |
| chr_3 | g3956 | g3956.t1 | TSS | g3956.t1 | NA | NA |
Sequences
>g3956.t1 Gene=g3956 Length=1035
ATGGCCTTAATAATGAAATATATTGACAGTTTGCACCATTATATGGATAAGTATGGTGAT
CCTCGCACTAAAGACTGGCCCCTTATGTCTTCTCCATTCCATACGCTAGGGATCTGTTTA
GGATATGTCTATATTGTGAAGTACCTAGGTCCGCGTCTTATGGAAAATAGAAAACCATTC
CAACTGAAAAATACGCTAGTTATTTATAATTTAATGCAAGTTATTTTTAGTACGTGGTTA
TTTTACGAGATCGGAATATCCGGTTGGCTAACAGGTCATTACAATTTTCGATGTCAACCT
GTTGATTATAGCAATCATCCTAGCACATTGAGGATGTGCCACGCATGCTGGTGGTATTAT
TTCTCAAAATTCACCGAATTTTTTGACACTTTCTTCTTTGTGCTTCGCAAAAAGACAAGT
CAAGTGTCAACACTTCATGTAATACATCATGGAGTTATGCCAATGTCTGTATGGTTCGGT
GTCAAATTCACTCCAGGCGGTCATAGCACATTCTTTGGTCTTTTGAATACATTCGTGCAT
ATTATCATGTACACTTATTATCTACTCACTGCAATGGGTCCACAATATCAAAAGTATTTA
TGGTGGAAAAAATACCTCACTGCCCTTCAAATGGTCCAATTTATACTCATTATGGTTCAC
GCTTTTCAACTTCTATTTGTGGATTGCAATTATCCAAAAGCTTTCGTTTGGTGGATTGGT
ATGCATGCAGTCATGTTCTTCTTTTTATTTAAAGAGTTTTATATTCAATCATACAATGCA
CGAAAATTCAAAGGGAAAAATCAATCAAATGGTTCAATTACAACAAACGATAAAAAGCAT
GACGGAGATGCAGCAATAATCTTGAATGGTCACTGTAATGGCATTTGTAAAAATACTTCA
CATCAAAACGGCACAATAAAGATGGATGCAACTGGATGCAATAAAGCATCATCTTATTAT
GTGAAAAGCGATGATATCACTGCCATTAGAACAACGAATCTAACGCAAAGAATAAGAGTC
ACTTCACCTGAGTAA
>g3956.t1 Gene=g3956 Length=344
MALIMKYIDSLHHYMDKYGDPRTKDWPLMSSPFHTLGICLGYVYIVKYLGPRLMENRKPF
QLKNTLVIYNLMQVIFSTWLFYEIGISGWLTGHYNFRCQPVDYSNHPSTLRMCHACWWYY
FSKFTEFFDTFFFVLRKKTSQVSTLHVIHHGVMPMSVWFGVKFTPGGHSTFFGLLNTFVH
IIMYTYYLLTAMGPQYQKYLWWKKYLTALQMVQFILIMVHAFQLLFVDCNYPKAFVWWIG
MHAVMFFFLFKEFYIQSYNARKFKGKNQSNGSITTNDKKHDGDAAIILNGHCNGICKNTS
HQNGTIKMDATGCNKASSYYVKSDDITAIRTTNLTQRIRVTSPE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3956.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 2 | 271 | 1.8E-155 |
| 3 | g3956.t1 | PANTHER | PTHR11157:SF119 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 2 | 271 | 1.8E-155 |
| 1 | g3956.t1 | Pfam | PF01151 | GNS1/SUR4 family | 28 | 264 | 2.1E-65 |
| 18 | g3956.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 23 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 45 | - |
| 14 | g3956.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 46 | 65 | - |
| 21 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 82 | - |
| 15 | g3956.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 83 | 116 | - |
| 19 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 135 | - |
| 12 | g3956.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 136 | 146 | - |
| 25 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 147 | 165 | - |
| 17 | g3956.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 166 | 170 | - |
| 20 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 11 | g3956.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 204 | - |
| 24 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 223 | - |
| 16 | g3956.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 224 | 234 | - |
| 22 | g3956.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 254 | - |
| 13 | g3956.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 255 | 344 | - |
| 7 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 45 | - |
| 6 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 5 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 135 | - |
| 9 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 161 | - |
| 4 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 8 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 227 | - |
| 10 | g3956.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 237 | 255 | - |
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 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.
