General information for g6439.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6439 is located on chr_2: 17074412..17076694 (+ 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 | g6439 | g6439.t1 | TSS | g6439.t1 | 17074212 | 17074212 |
| chr_2 | g6439 | g6439.t1 | isoform | g6439.t1 | 17074412 | 17075871 |
| chr_2 | g6439 | g6439.t1 | exon | g6439.t1.exon1 | 17074412 | 17074484 |
| chr_2 | g6439 | g6439.t1 | cds | g6439.t1.CDS1 | 17074412 | 17074484 |
| chr_2 | g6439 | g6439.t1 | exon | g6439.t1.exon2 | 17074570 | 17074598 |
| chr_2 | g6439 | g6439.t1 | cds | g6439.t1.CDS2 | 17074570 | 17074598 |
| chr_2 | g6439 | g6439.t1 | exon | g6439.t1.exon3 | 17074781 | 17074827 |
| chr_2 | g6439 | g6439.t1 | cds | g6439.t1.CDS3 | 17074781 | 17074827 |
| chr_2 | g6439 | g6439.t1 | exon | g6439.t1.exon4 | 17074887 | 17074961 |
| chr_2 | g6439 | g6439.t1 | cds | g6439.t1.CDS4 | 17074887 | 17074961 |
| chr_2 | g6439 | g6439.t1 | exon | g6439.t1.exon5 | 17075769 | 17075871 |
| chr_2 | g6439 | g6439.t1 | cds | g6439.t1.CDS5 | 17075769 | 17075871 |
| chr_2 | g6439 | g6439.t1 | TTS | g6439.t1 | 17076732 | 17076732 |
Sequences
>g6439.t1 Gene=g6439 Length=327
ATGGATGGTTTTATGAATCCACAAAAAAATATAGGTTTAAAACAACCTGATAAGCAATGG
TCTTTTGTTGAATCTGCCTTAGTTGCACGACACGCACCTGAAGTAGGACCACATCCAATT
CATATAAAATGTCCCTCATGTGGTAAAAGTATAACAACGCGTGTAGAAGCAGAAACCTAC
TCGAAGACTCATTTTTGCGCCGCTGCACTAGTTATGACAATAGTATGCTGTCCATTGGCA
TGTTTGGTTTATTTGCTAGACACATGGAAACGAAAACATCACTATTGCACTAACTGTAAA
AATTATTTGGGAACGTACGATGGATAA
>g6439.t1 Gene=g6439 Length=108
MDGFMNPQKNIGLKQPDKQWSFVESALVARHAPEVGPHPIHIKCPSCGKSITTRVEAETY
SKTHFCAAALVMTIVCCPLACLVYLLDTWKRKHHYCTNCKNYLGTYDG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6439.t1 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 5 | 107 | 7.9E-24 |
| 3 | g6439.t1 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 5 | 107 | 7.9E-24 |
| 1 | g6439.t1 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 38 | 106 | 3.2E-18 |
| 8 | g6439.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 66 | - |
| 9 | g6439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 86 | - |
| 7 | g6439.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 87 | 108 | - |
| 6 | g6439.t1 | ProSiteProfiles | PS51837 | LITAF domain profile. | 23 | 108 | 13.254 |
| 5 | g6439.t1 | SMART | SM00714 | litaf | 39 | 108 | 4.9E-17 |
| 4 | g6439.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 64 | 86 | - |
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 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.
