General information for g1883.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1883 is located on chr_3: 13643439..13644848 (+ 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_3 | g1883 | g1883.t4 | isoform | g1883.t4 | 13643439 | 13644442 |
| chr_3 | g1883 | g1883.t4 | exon | g1883.t4.exon1 | 13643439 | 13643446 |
| chr_3 | g1883 | g1883.t4 | exon | g1883.t4.exon2 | 13643504 | 13643739 |
| chr_3 | g1883 | g1883.t4 | exon | g1883.t4.exon3 | 13643798 | 13644008 |
| chr_3 | g1883 | g1883.t4 | cds | g1883.t4.CDS1 | 13643851 | 13644008 |
| chr_3 | g1883 | g1883.t4 | exon | g1883.t4.exon4 | 13644061 | 13644442 |
| chr_3 | g1883 | g1883.t4 | cds | g1883.t4.CDS2 | 13644061 | 13644247 |
| chr_3 | g1883 | g1883.t4 | TTS | g1883.t4 | 13644869 | 13644869 |
| chr_3 | g1883 | g1883.t4 | TSS | g1883.t4 | NA | NA |
Sequences
>g1883.t4 Gene=g1883 Length=837
ATTATTGGTCATATTCCTCCAGGACATGCAGATTGTTTAAAGATTTGGAGTAGAAATTAT
TATAAAATCGTTCAGCGATATGAGAGCACAATTACTGCTCAATTCTTCGGTCATACACAT
TTTGATGAATTTGAAGTCTTCTATGACTCAAATGATGTATCTCGTCCCACAAATATTGCT
TATATTGGACCCAGTGTGACTCCATATTATGATTTAAATCCTGGATATCGAATCTATTAT
ATTGATGGTGATCATGATGCAACCACAAGATTAGTAATTGATCATGAAACTTGGATTATG
AATCTCAAAGAAGCGAATCTCTATGATTTTCCAATTTATTATAAACTTTATTCAACTCGT
GCTGCATACAATCTTAAAGCACTTAGACCATCTGATTGGGATGAATTAATTAATTCAATG
ACTGATGATCAAGATAAATTTGATCTTTATTATAAACATTATTGGAAAGCATCACCAGTA
AGACCAGCATGTGATGCAGATTGCAGAAAACGAATATTATGCGATGCAAAAAGTGGCAGA
AGTCACGATCGAAAATATTTCTGTGCAGAAGTTGAATCTAAATTGGATTCATCGAACGGA
AGTTGGAGATCGTGGATTTATCGCGGAATTTCATTTTCGTAAGTTAAATGCAAAAATTAT
TTTTGAACATTTCAGAATCAATATTTTTAACATGCAAAAAACTTTCGGTGAATGGTGGCT
TTTAAAATACTAACAAAAAACATTTTCTTTTCTTTCTTCTTTGAATAAAACTTTTTTCAA
CATTTTCAAAAGTAATAAAACAATGTCTAATAATACAGCTTATCAATTATTAACTAA
>g1883.t4 Gene=g1883 Length=114
MNLKEANLYDFPIYYKLYSTRAAYNLKALRPSDWDELINSMTDDQDKFDLYYKHYWKASP
VRPACDADCRKRILCDAKSGRSHDRKYFCAEVESKLDSSNGSWRSWIYRGISFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g1883.t4 | PANTHER | PTHR10340 | SPHINGOMYELIN PHOSPHODIESTERASE | 1 | 98 | 0 |
| g1883.t4 | PANTHER | PTHR10340:SF34 | SPHINGOMYELIN PHOSPHODIESTERASE | 1 | 98 | 0 |
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.
