General information for g13539.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13539 is located on chr_1: 30768093..30768479 (+ 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_1 | g13539 | g13539.t4 | TSS | g13539.t4 | 30767291 | 30767291 |
| chr_1 | g13539 | g13539.t4 | isoform | g13539.t4 | 30767345 | 30768339 |
| chr_1 | g13539 | g13539.t4 | exon | g13539.t4.exon1 | 30767345 | 30767693 |
| chr_1 | g13539 | g13539.t4 | cds | g13539.t4.CDS1 | 30767345 | 30767693 |
| chr_1 | g13539 | g13539.t4 | exon | g13539.t4.exon2 | 30767899 | 30768339 |
| chr_1 | g13539 | g13539.t4 | cds | g13539.t4.CDS2 | 30767899 | 30767915 |
| chr_1 | g13539 | g13539.t4 | TTS | g13539.t4 | 30768552 | 30768552 |
Sequences
>g13539.t4 Gene=g13539 Length=790
ATGGAGTCGATGATATTAAAAGCTATTTGGTTCATCATACACTTCATTGTTGATCTGATA
GAATCACTTTTTTATTACGGCTTGGAATTTCGCGAGAATTTCATCTATTTCATCAAAAAT
ATCAGCATAGACAGTCTCAGTAGAAGTAAAAAGAATGAGTTGGCATATATCGAGGCACGA
ATCAATGATTTGAAGAAACTGCCGAAACATATAGCTGTAATATTAAACATAAATAATAAA
AAAGACGTGGACCTATCAAAATTAGTTAATTTAGTCTCATGGTCAATGAACAGTAATGTG
AATTTTATCAGCTTTTACGATTATAAAGGTGAGAAAGTGATAATCAAAACAACTTATAAA
GGATAAACTAACCCTTAACAATGATGAAAATTTAGTTTGGGGTCCAGATTATAATCTAAA
AGCATCCTTAAACGAAGGAGTAGAATTTCCTCATCGCAATGGATTTATAAAGCACCTCGT
TATCAACATTTATTCATCTTACGACAGTTATAGTTTATTCAATAAACTGCTGACAGATGA
TGAACTAAGTAGCAAAGATATAAAAATAGAAAACGTTAATAAAAAGATTAGCAAACTCTA
TGGAAATATACCAGAACCAGAGTTAGCTTTATACATTGGAAAAACCACCTGCACAGCTGG
ATTTCTGCCATGGCATATAAGACTTACCGAATTTATTCAAATAAGCTATAAATTGAAAAA
TCTAACGCTTGATAAGTATATTCGAGTGCTCTATAAATATGCCAAGTGTGAGCAACGTTA
TGGGAAATGA
>g13539.t4 Gene=g13539 Length=121
MESMILKAIWFIIHFIVDLIESLFYYGLEFRENFIYFIKNISIDSLSRSKKNELAYIEAR
INDLKKLPKHIAVILNINNKKDVDLSKLVNLVSWSMNSNVNFISFYDYKGEKVIIKTTYK
G
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g13539.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 5 | g13539.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 28 | - |
| 3 | g13539.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 29 | 121 | - |
| 2 | g13539.t4 | SUPERFAMILY | SSF64005 | Undecaprenyl diphosphate synthase | 62 | 111 | 8.5E-7 |
| 1 | g13539.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
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:0016765 | transferase activity, transferring alkyl or aryl (other than methyl) groups | MF |
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.
