General information for g5325.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5325 is located on chr_2: 8862019..8862938 (+ 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 | g5325 | g5325.t20 | TSS | g5325.t20 | 8861795 | 8861795 |
| chr_2 | g5325 | g5325.t20 | isoform | g5325.t20 | 8861899 | 8862938 |
| chr_2 | g5325 | g5325.t20 | exon | g5325.t20.exon1 | 8861899 | 8861926 |
| chr_2 | g5325 | g5325.t20 | cds | g5325.t20.CDS1 | 8861899 | 8861926 |
| chr_2 | g5325 | g5325.t20 | exon | g5325.t20.exon2 | 8862012 | 8862070 |
| chr_2 | g5325 | g5325.t20 | cds | g5325.t20.CDS2 | 8862012 | 8862070 |
| chr_2 | g5325 | g5325.t20 | exon | g5325.t20.exon3 | 8862137 | 8862216 |
| chr_2 | g5325 | g5325.t20 | cds | g5325.t20.CDS3 | 8862137 | 8862216 |
| chr_2 | g5325 | g5325.t20 | exon | g5325.t20.exon4 | 8862284 | 8862349 |
| chr_2 | g5325 | g5325.t20 | cds | g5325.t20.CDS4 | 8862284 | 8862349 |
| chr_2 | g5325 | g5325.t20 | exon | g5325.t20.exon5 | 8862556 | 8862938 |
| chr_2 | g5325 | g5325.t20 | cds | g5325.t20.CDS5 | 8862556 | 8862622 |
| chr_2 | g5325 | g5325.t20 | TTS | g5325.t20 | 8862940 | 8862940 |
Sequences
>g5325.t20 Gene=g5325 Length=616
ATGCAACAACCTACAGTAATAATTCAACATTCAAATGTTGCTGTTGGACCAAATTCAACT
CGACTCACTTGCCCATCATGTCATGCAGTAATTTCTACGCGTGTTGAACGTAAATCATCG
GCTAAAACTTATATAGTTGCGGTACTTCTATGTGTGTTCTTATGCTGGCCATGTGTATGC
GTTCCGTTTTGCACAAATTCCTGCCGGAATGCTAACCATTATTGCCCCAATTGCATTCTT
GGGAACCTACAACTGAAAATTCAAGGTATTATTCATCTGTATTACTTCATTAATTTTTAA
GTTAAAAAGAGTTCGATTTGCTCCATTAGATATTAAGATTGTGCTCCAAAAAGTGAATCA
TATAAAGCAAATTACTAATTCATTCTAGAAACAAGTGCTATATAAGAAAATTTATTTATC
ATAAACAAGATAACAACGACTGTCTCATTACGAAATGAGTGCGAATATTGTCAGGTGATA
AGAATATTTATTTTTTACTTACTTAATTGTCGCATTCAAAGATAAAAACGTAATAAAAGT
TAAAAGAAGTTAGAACAAAAATTTTGATTTTAAATGTTAAAAATAATGAATTTAATAAAA
AATATTTTTTAAAAAT
>g5325.t20 Gene=g5325 Length=99
MQQPTVIIQHSNVAVGPNSTRLTCPSCHAVISTRVERKSSAKTYIVAVLLCVFLCWPCVC
VPFCTNSCRNANHYCPNCILGNLQLKIQGIIHLYYFINF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5325.t20 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 2 | 78 | 5.2E-28 |
| 3 | g5325.t20 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 2 | 78 | 5.2E-28 |
| 1 | g5325.t20 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 18 | 78 | 1.3E-19 |
| 8 | g5325.t20 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 43 | - |
| 9 | g5325.t20 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 64 | - |
| 7 | g5325.t20 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 99 | - |
| 6 | g5325.t20 | ProSiteProfiles | PS51837 | LITAF domain profile. | 3 | 87 | 16.784 |
| 5 | g5325.t20 | SMART | SM00714 | litaf | 19 | 88 | 5.4E-11 |
| 4 | g5325.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 65 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5325/g5325.t20; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5325.t20.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.
