General information for g6436.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6436 is located on chr_2: 17070271..17070903 (+ 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 | g6436 | g6436.t1 | TSS | g6436.t1 | 17070222 | 17070222 |
| chr_2 | g6436 | g6436.t1 | isoform | g6436.t1 | 17070271 | 17070903 |
| chr_2 | g6436 | g6436.t1 | exon | g6436.t1.exon1 | 17070271 | 17070382 |
| chr_2 | g6436 | g6436.t1 | cds | g6436.t1.CDS1 | 17070271 | 17070382 |
| chr_2 | g6436 | g6436.t1 | exon | g6436.t1.exon2 | 17070506 | 17070655 |
| chr_2 | g6436 | g6436.t1 | cds | g6436.t1.CDS2 | 17070506 | 17070655 |
| chr_2 | g6436 | g6436.t1 | exon | g6436.t1.exon3 | 17070759 | 17070794 |
| chr_2 | g6436 | g6436.t1 | cds | g6436.t1.CDS3 | 17070759 | 17070794 |
| chr_2 | g6436 | g6436.t1 | exon | g6436.t1.exon4 | 17070854 | 17070903 |
| chr_2 | g6436 | g6436.t1 | cds | g6436.t1.CDS4 | 17070854 | 17070903 |
| chr_2 | g6436 | g6436.t1 | TTS | g6436.t1 | 17070992 | 17070992 |
Sequences
>g6436.t1 Gene=g6436 Length=348
ATGACAGAGAAAAATCCAGAAAACCTTGCATATCAACCACCGCCACCATATTCTCCTCAA
CAACAAAGTCAACCATATCATATTCCACAAGGCACTACACAAGTCGTTACAGTGATAACA
AATGCTGCATACGGCCCTGAACCCGTTGTTATAATTTGTCCTTCGTGCCATCAACAGAAT
CAGACTAAATTGGATTATGAATCATCAACAAAGACACATCTAATGGCATTCGTTATATGT
TTACTTTGTTGGCCATGCTTTTGGATGCCATATGCTATTGACTCATGCAAAGATACAAAT
CATTATTGCTCATCTTGTGGTGCATATCTTGGAACATACCGAGGATAA
>g6436.t1 Gene=g6436 Length=115
MTEKNPENLAYQPPPPYSPQQQSQPYHIPQGTTQVVTVITNAAYGPEPVVIICPSCHQQN
QTKLDYESSTKTHLMAFVICLLCWPCFWMPYAIDSCKDTNHYCSSCGAYLGTYRG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6436.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 2 | g6436.t1 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 8 | 114 | 7.6E-33 |
| 3 | g6436.t1 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 8 | 114 | 7.6E-33 |
| 1 | g6436.t1 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 47 | 114 | 3.1E-24 |
| 8 | g6436.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 73 | - |
| 10 | g6436.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 93 | - |
| 9 | g6436.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 94 | 115 | - |
| 7 | g6436.t1 | ProSiteProfiles | PS51837 | LITAF domain profile. | 33 | 115 | 18.233 |
| 5 | g6436.t1 | SMART | SM00714 | litaf | 48 | 115 | 6.7E-24 |
| 4 | g6436.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 93 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
