General information for g4412.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g4412.t1 | 2027258 | 2027258 |
| chr_2 | g4412 | g4412.t1 | isoform | g4412.t1 | 2027324 | 2028898 |
| chr_2 | g4412 | g4412.t1 | exon | g4412.t1.exon1 | 2027324 | 2027467 |
| chr_2 | g4412 | g4412.t1 | cds | g4412.t1.CDS1 | 2027324 | 2027467 |
| chr_2 | g4412 | g4412.t1 | exon | g4412.t1.exon2 | 2027528 | 2028898 |
| chr_2 | g4412 | g4412.t1 | cds | g4412.t1.CDS2 | 2027528 | 2028898 |
| chr_2 | g4412 | g4412.t1 | TTS | g4412.t1 | 2029078 | 2029078 |
Sequences
>g4412.t1 Gene=g4412 Length=1515
ATGGAAAGTTTATTAGAAATTCAAAGAAGGTGTCATGAAGAAAGAGAGCGATTACAAAAG
CTTATGGTTGACGAGTTTATGGAAAAGAAATTGTCAGAAAAAGACCGAATTTTTTCAGAA
CATCGTGTAAAAATTTATTTGGATCAATATATTGAAACAACAGCGCGTTTAGCTGACTTA
TATGAAGATAAAGAAGGCGAAAGAAAAGCAGAAATTTCAGCTCTTTCTGGGCCTAATGAA
TTTACAGAATTTTATTCTCGTCTAAAGAACATAAAAGAGTTTCATAAGAAACATCCTGAC
GAAATTAGTGTACCACTTTCGACTGAGTTTGAGCAAATGGCTAAAGCTTATCAACAATCG
GATGCTATGAATTTGCTCGTTGAATTCACTGATGAAGAAGGTTTTGGCAAATACTTGGAT
TTGCACGAATCTTATGATAGATACATCAATTTGAAGGGAATCGAAAAAACTGACTATATA
ACATATTTGATGATTTTTGATCATCTTTATGATATTCCAAAAGATCGAAAAAATGCCGAG
TATAAAAAGTACATTGATGCACTTTTTGAATATTTATACAATTTTAATCAACGTGTTAAA
CCATTAATGGATCTTGAGAAAAGTTTAGAACAAACAAAAGCGGACTTTGAAAAACAATGG
ATTAGTGGCACTTTTCCAGGATGGCCAAAAGAAACTGAAAGTGCTTTGGCAAATGTTGGA
GCACCGCTTGATTTATCCGCATTTACTAGTTGGGAAGAATTAGCTTCACTTGGTCTTGAT
CGTTTGAAATCAGCTTTGATGGCGTTAAATATGAAATGTGGAGGAACTCTTGAAGAACGT
GCACAAAGACTTTTCTCAACGAAAGGCATGAAACAAATTGATCAATCGCTTCTCGCCAAG
AAATCTAATCTTGGTAAAAACTCGTCAAGTGCTGCAAAAGAACAAGCACGTCAAAAAGAA
ATTGCACTTGTTGAATCTCAAATTTACTATCTCTGTGAATTGATAAAAGAGCAGCGAGCG
GCAACAAAAGAAAATGTGCAGCGTAAGCAAGCAAGAGGTGCTGGTGAGAGAAATGACAGT
GATGTCGAAGCTAGCGATTCAGAATCGGAAGAGGAAGAAGATGACAATGATGATGTTCCA
TATAATCCTAAAAATCTGCCATTAGGTTGGGATGGTAAACCAATTCCTTATTGGCTTTAT
AAATTACATGGACTTAATATAAGTTATAATTGTGAAATTTGTGGAAATTATACTTACAAA
AGACCAAAAGCTTTTCAACGTCATTTTAGTGAATGGAGGCATGCTCATGGTATGCGTTGT
CTTGGAATTCCAAACACTGCTCATCTTATTTTCATCACTCAAATCGAAGATGCAATTCAG
CTTTGGGAAAAAATCAAGCAACAAAAGAATCAAGAGCGATGGGTTCCAGAGCAAAGTGAA
GAGTTTGAAGACTCACTTGGCAATGTTGTGACAAAGAAAACATATGAAGATCTAAAAAGA
CAAGGTTTATTGTAA
>g4412.t1 Gene=g4412 Length=504
MESLLEIQRRCHEERERLQKLMVDEFMEKKLSEKDRIFSEHRVKIYLDQYIETTARLADL
YEDKEGERKAEISALSGPNEFTEFYSRLKNIKEFHKKHPDEISVPLSTEFEQMAKAYQQS
DAMNLLVEFTDEEGFGKYLDLHESYDRYINLKGIEKTDYITYLMIFDHLYDIPKDRKNAE
YKKYIDALFEYLYNFNQRVKPLMDLEKSLEQTKADFEKQWISGTFPGWPKETESALANVG
APLDLSAFTSWEELASLGLDRLKSALMALNMKCGGTLEERAQRLFSTKGMKQIDQSLLAK
KSNLGKNSSSAAKEQARQKEIALVESQIYYLCELIKEQRAATKENVQRKQARGAGERNDS
DVEASDSESEEEEDDNDDVPYNPKNLPLGWDGKPIPYWLYKLHGLNISYNCEICGNYTYK
RPKAFQRHFSEWRHAHGMRCLGIPNTAHLIFITQIEDAIQLWEKIKQQKNQERWVPEQSE
EFEDSLGNVVTKKTYEDLKRQGLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4412.t1 | Coils | Coil | Coil | 4 | 24 | - |
| 12 | g4412.t1 | Coils | Coil | Coil | 332 | 352 | - |
| 11 | g4412.t1 | Coils | Coil | Coil | 452 | 472 | - |
| 8 | g4412.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 346 | 385 | - |
| 9 | g4412.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 346 | 362 | - |
| 7 | g4412.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 363 | 378 | - |
| 5 | g4412.t1 | PANTHER | PTHR12786:SF3 | SPLICING FACTOR 3A SUBUNIT 3 | 1 | 504 | 1.0E-221 |
| 6 | g4412.t1 | PANTHER | PTHR12786 | SPLICING FACTOR SF3A-RELATED | 1 | 504 | 1.0E-221 |
| 2 | g4412.t1 | Pfam | PF12108 | Splicing factor SF3a60 binding domain | 74 | 100 | 9.2E-14 |
| 3 | g4412.t1 | Pfam | PF16837 | Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 | 128 | 206 | 3.3E-22 |
| 1 | g4412.t1 | Pfam | PF13297 | Telomere stability C-terminal | 243 | 300 | 8.8E-25 |
| 4 | g4412.t1 | Pfam | PF11931 | Domain of unknown function (DUF3449) | 325 | 503 | 2.4E-71 |
| 13 | g4412.t1 | ProSiteProfiles | PS50171 | Zinc finger matrin-type profile. | 409 | 440 | 9.543 |
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:0005634 | nucleus | CC |
| GO:0003723 | RNA binding | MF |
| GO:0005681 | spliceosomal complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12827 (splicing factor 3A subunit 3)
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.
