General information for g12296.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12296 is located on chr_1: 22242124..22243213 (+ 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 | g12296 | g12296.t3 | isoform | g12296.t3 | 22219325 | 22229939 |
| chr_1 | g12296 | g12296.t3 | exon | g12296.t3.exon1 | 22219325 | 22219482 |
| chr_1 | g12296 | g12296.t3 | exon | g12296.t3.exon2 | 22219967 | 22220124 |
| chr_1 | g12296 | g12296.t3 | exon | g12296.t3.exon3 | 22223481 | 22223645 |
| chr_1 | g12296 | g12296.t3 | cds | g12296.t3.CDS1 | 22223588 | 22223645 |
| chr_1 | g12296 | g12296.t3 | exon | g12296.t3.exon4 | 22223703 | 22223829 |
| chr_1 | g12296 | g12296.t3 | cds | g12296.t3.CDS2 | 22223703 | 22223829 |
| chr_1 | g12296 | g12296.t3 | exon | g12296.t3.exon5 | 22229531 | 22229939 |
| chr_1 | g12296 | g12296.t3 | cds | g12296.t3.CDS3 | 22229531 | 22229651 |
| chr_1 | g12296 | g12296.t3 | TTS | g12296.t3 | 22229937 | 22229937 |
| chr_1 | g12296 | g12296.t3 | TSS | g12296.t3 | NA | NA |
Sequences
>g12296.t3 Gene=g12296 Length=1017
CTTTCTTTTTTTTCTCTTTATTATTCTCTACAAAAATAACAAAATAAGATAGAAGCGACA
CTAATGTTGAAACTGTAAACTAAGCCATTCTCTCAATTTTCGATTTTATGAAATGAAGAA
ATATGCGCTCAGTGTGAGTTCGCAATTGATTGAGAGAGCTTTTGTTGTGTTGTTCTTTCT
ATGAAAGAAGTGGAAATATAAGAAACTGATTTTGAGAATCAACGATAGTTGTGATAAAAA
GAAATTAGCGATACACATACTATAAGAAACAAAAAAATAGAGAGTAATTCTCTTTGGATT
ATTTAACTACGAACAGATAACTCATTTTTTAATTTTAATTTTGAAACAAAATTAAAACAG
AAATCACGACATACGAGAATTTTATAAGTTGAACTTTAGGTTAAGTTAATATAAAATATA
AAAATGTGGCGATCAAGTTTTATTTTGGTCGTTGCATTGACCGTAACATCATATGCAATA
ATTCATTCACCGCCTCGGATAACAAAACAACCAATTGCTGAGGAAATGCTGTTTCAAGTT
GCACAATTTGGTGATACAGAAAAACTGTTTATAATTGAATGTGAAGCAGAAGGAGAACCG
GCGCCAAATTACAGACTATTACAGACAGAAGATGAAGGTGTAGTAAAGTGTGGCACGCTG
TTTTGGTTGCGACAATATTCGAGCAACAAATCAAAGTCAATTGAAGAATCGTATACGGCA
CACGTTTAAAATAAAATTAAAAGCATTGTTAGCGGCGAGAGAGCGGATGATGTCATACAA
ATTTATTCTCTAGAATACCACCCTCCTTTATTGAATGCATTTTTTTTGTATATTCATACT
AAGTGTCGCCGCTGCATATGCCAACGATATGAATAAGAGAGAAAATTTATTGGATTAAAT
TTGTATGACATTTGCTTCGTGTGCAGGATTACATTTTTTGATAATAATAATAATCCACTC
ACCGTGTGATTGCGGGAATAAAAATAATAAAGTACTTCGGCTTGATGCCTAAAATGA
>g12296.t3 Gene=g12296 Length=101
MWRSSFILVVALTVTSYAIIHSPPRITKQPIAEEMLFQVAQFGDTEKLFIIECEAEGEPA
PNYRLLQTEDEGVVKCGTLFWLRQYSSNKSKSIEESYTAHV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g12296.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 4 | g12296.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 5 | g12296.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 6 | g12296.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 2 | g12296.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 101 | - |
| 1 | g12296.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
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.
