General information for g3955.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 g3955 is located on chr_3: 29256898..29257436 (+ 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 | g3955 | g3955.t1 | isoform | g3955.t1 | 29255622 | 29257091 |
| chr_3 | g3955 | g3955.t1 | exon | g3955.t1.exon1 | 29255622 | 29255682 |
| chr_3 | g3955 | g3955.t1 | cds | g3955.t1.CDS1 | 29255622 | 29255682 |
| chr_3 | g3955 | g3955.t1 | exon | g3955.t1.exon2 | 29255789 | 29255979 |
| chr_3 | g3955 | g3955.t1 | cds | g3955.t1.CDS2 | 29255789 | 29255979 |
| chr_3 | g3955 | g3955.t1 | exon | g3955.t1.exon3 | 29256041 | 29256415 |
| chr_3 | g3955 | g3955.t1 | cds | g3955.t1.CDS3 | 29256041 | 29256415 |
| chr_3 | g3955 | g3955.t1 | exon | g3955.t1.exon4 | 29256668 | 29256901 |
| chr_3 | g3955 | g3955.t1 | cds | g3955.t1.CDS4 | 29256668 | 29256901 |
| chr_3 | g3955 | g3955.t1 | exon | g3955.t1.exon5 | 29256969 | 29257091 |
| chr_3 | g3955 | g3955.t1 | cds | g3955.t1.CDS5 | 29256969 | 29257091 |
| chr_3 | g3955 | g3955.t1 | TTS | g3955.t1 | 29257426 | 29257426 |
| chr_3 | g3955 | g3955.t1 | TSS | g3955.t1 | NA | NA |
Sequences
>g3955.t1 Gene=g3955 Length=984
ATGGCTCACTTATTAACAGACCTGTACGATTGGTACAATGACTTGATGGACAATCGTTCA
GATTCTCGTGTCAAAGATTGGCCAATGATGCAGTCACCAATCCCAACATTACTGCTCTGC
ATGAGTTACGCATTTTTCTGTAAATCACTGGCTCCCCGCCTGATGAAAAATCGCAAACCA
TTTGATCTTAGAAAAACTCTAGTTGTATACAATCTGTTTCAAACAGTATTCAGTGCATGG
ATATTTTATGAGTATTTACAAAGTGGTTGGCTGCGTGATTATAGCTATAGATGTCAACCA
GTCGATTATTCGCCTAAAGGATTTAGAATGGCTGAAACATGCTGGTGGTACTACATCTCC
AAATTTACAGAGTTCTTCGATACATTTTTCTTCATACTGAGGAAAAAATATCAACATGTT
TCAACCCTTCATGTCATTCATCACGGTGTTATGCCATTCAGTGTATGGATGGGAATGAAG
TTCGCTCCGGGCGGTCACAGTACCTTTTTTGCAATGCTCAATGCTTTTGTACATATTGTC
ATGTATTTTTATTACATGCTGGCTGCAATGGGTCCACAAGTGCAGAAATATTTATGGTGG
AAGCGATATTTAACGGCGTTTCAAATGGTTCAATTTGTGGCCATTTTCACACATCAGTTC
CAATTATTATGGACAGAGTGCGATTATCCAAAAGGCTTCATGGTGTGGATTGGTCTGCAC
GGCATCATGTTTCTCTTTCTTTTCTCAGATTTTTATAAACAGAGTTATATTAATAAGAAG
GAAAAAGTTCGAGCTCTTAAAAAAGAGTCTGAAAATGGCAAATTATATCTCAATGGAGAT
AGCAAAATTCATAGTTCTCTGTCAAATCATCAAGAAGAACATCTAAATGGAGGAACTTAT
CTCAATGGACACATAGAGAAGAATGGACAAATCATCACAAACGGTATCAATGCAACTAAT
GGTTCAATTAGATCAAGAAAATGA
>g3955.t1 Gene=g3955 Length=327
MAHLLTDLYDWYNDLMDNRSDSRVKDWPMMQSPIPTLLLCMSYAFFCKSLAPRLMKNRKP
FDLRKTLVVYNLFQTVFSAWIFYEYLQSGWLRDYSYRCQPVDYSPKGFRMAETCWWYYIS
KFTEFFDTFFFILRKKYQHVSTLHVIHHGVMPFSVWMGMKFAPGGHSTFFAMLNAFVHIV
MYFYYMLAAMGPQVQKYLWWKRYLTAFQMVQFVAIFTHQFQLLWTECDYPKGFMVWIGLH
GIMFLFLFSDFYKQSYINKKEKVRALKKESENGKLYLNGDSKIHSSLSNHQEEHLNGGTY
LNGHIEKNGQIITNGINATNGSIRSRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3955.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 4 | 276 | 1.9E-134 |
| 3 | g3955.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 4 | 276 | 1.9E-134 |
| 1 | g3955.t1 | Pfam | PF01151 | GNS1/SUR4 family | 29 | 262 | 2.5E-64 |
| 17 | g3955.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 26 | - |
| 24 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 46 | - |
| 11 | g3955.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 47 | 66 | - |
| 22 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 86 | - |
| 15 | g3955.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 87 | 114 | - |
| 21 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 133 | - |
| 14 | g3955.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 134 | 144 | - |
| 25 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 145 | 163 | - |
| 18 | g3955.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 164 | 168 | - |
| 20 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 169 | 191 | - |
| 12 | g3955.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 192 | 202 | - |
| 19 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 221 | - |
| 16 | g3955.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 222 | 232 | - |
| 23 | g3955.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 252 | - |
| 13 | g3955.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 253 | 327 | - |
| 10 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 46 | - |
| 8 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 86 | - |
| 4 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 114 | 133 | - |
| 7 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 140 | 159 | - |
| 5 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 169 | 191 | - |
| 9 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 222 | - |
| 6 | g3955.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 249 | - |
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.
