General information for g5326.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g5326 is located on chr_2: 8864493..8865197 (+ 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 | g5326 | g5326.t1 | TSS | g5326.t1 | 8864401 | 8864401 |
| chr_2 | g5326 | g5326.t1 | isoform | g5326.t1 | 8864493 | 8865197 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon1 | 8864493 | 8864520 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS1 | 8864493 | 8864520 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon2 | 8864587 | 8864645 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS2 | 8864587 | 8864645 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon3 | 8864703 | 8864782 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS3 | 8864703 | 8864782 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon4 | 8864839 | 8864866 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS4 | 8864839 | 8864866 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon5 | 8864929 | 8864963 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS5 | 8864929 | 8864963 |
| chr_2 | g5326 | g5326.t1 | exon | g5326.t1.exon6 | 8865167 | 8865197 |
| chr_2 | g5326 | g5326.t1 | cds | g5326.t1.CDS6 | 8865167 | 8865197 |
| chr_2 | g5326 | g5326.t1 | TTS | g5326.t1 | 8865285 | 8865285 |
Sequences
>g5326.t1 Gene=g5326 Length=261
ATGGATAACAGAACAGTGGTTGTTCAACAATCTGGAGTTTCAGTTGGTCCTCAATCTACA
AGACTTACTTGTCCAAGTTGTCATGCAGTGATTAATTCTCGTGTAGAACATGAAGCATCA
ACTAAAACTCATATTATCGCATTGGTTTTATGTTTATTGACAGGATGTTTATGCTGCATT
CCTTATTGTGTTGATTCTTGTAAGAATGCAAATCATTATTGCCCCAATTGCCAATCTTTC
TTGGGATCATATAACAATTAA
>g5326.t1 Gene=g5326 Length=86
MDNRTVVVQQSGVSVGPQSTRLTCPSCHAVINSRVEHEASTKTHIIALVLCLLTGCLCCI
PYCVDSCKNANHYCPNCQSFLGSYNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5326.t1 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 4 | 86 | 4.7E-31 |
| 3 | g5326.t1 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 4 | 86 | 4.7E-31 |
| 1 | g5326.t1 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 18 | 84 | 3.0E-24 |
| 8 | g5326.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 44 | - |
| 9 | g5326.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 7 | g5326.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 86 | - |
| 6 | g5326.t1 | ProSiteProfiles | PS51837 | LITAF domain profile. | 3 | 86 | 18.348 |
| 5 | g5326.t1 | SMART | SM00714 | litaf | 19 | 86 | 3.9E-21 |
| 4 | g5326.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5326/g5326.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5326.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K19363 (lipopolysaccharide-induced tumor necrosis factor-alpha factor)
Pathway
- This transcript belongs to the following pathways
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.
