General information for g4412.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Splicing factor 3A subunit 3.
Parent gene
- The parent gene g4412 is located on chr_2: 2028535..2028898 (+ 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 | g4412 | g4412.t2 | isoform | g4412.t2 | 2028535 | 2028898 |
| chr_2 | g4412 | g4412.t2 | exon | g4412.t2.exon1 | 2028535 | 2028898 |
| chr_2 | g4412 | g4412.t2 | cds | g4412.t2.CDS1 | 2028695 | 2028898 |
| chr_2 | g4412 | g4412.t2 | TTS | g4412.t2 | 2029078 | 2029078 |
| chr_2 | g4412 | g4412.t2 | TSS | g4412.t2 | NA | NA |
Sequences
>g4412.t2 Gene=g4412 Length=364
AAATCTGCCATTAGGTTGGGATGGTAAACCAATTCCTTATTGGCTTTATAAATTACATGG
ACTTAATATAAGTTATAATTGTGAAATTTGTGGAAATTATACTTACAAAAGACCAAAAGC
TTTTCAACGTCATTTTAGTGAATGGAGGCATGCTCATGGTATGCGTTGTCTTGGAATTCC
AAACACTGCTCATCTTATTTTCATCACTCAAATCGAAGATGCAATTCAGCTTTGGGAAAA
AATCAAGCAACAAAAGAATCAAGAGCGATGGGTTCCAGAGCAAAGTGAAGAGTTTGAAGA
CTCACTTGGCAATGTTGTGACAAAGAAAACATATGAAGATCTAAAAAGACAAGGTTTATT
GTAA
>g4412.t2 Gene=g4412 Length=67
MRCLGIPNTAHLIFITQIEDAIQLWEKIKQQKNQERWVPEQSEEFEDSLGNVVTKKTYED
LKRQGLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4412.t2 | Coils | Coil | Coil | 15 | 35 | - |
| 2 | g4412.t2 | PANTHER | PTHR12786:SF2 | SPLICING FACTOR 3A SUBUNIT 3 | 1 | 67 | 2.3E-26 |
| 3 | g4412.t2 | PANTHER | PTHR12786 | SPLICING FACTOR SF3A-RELATED | 1 | 67 | 2.3E-26 |
| 1 | g4412.t2 | Pfam | PF11931 | Domain of unknown function (DUF3449) | 1 | 66 | 2.5E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003723 | RNA binding | MF |
| GO:0005681 | spliceosomal complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
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.
