General information for g3227.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3A subunit 1.
Parent gene
- The parent gene g3227 is located on chr_3: 23833987..23835499 (- 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 | g3227 | g3227.t4 | TTS | g3227.t4 | 23833070 | 23833070 |
| chr_3 | g3227 | g3227.t4 | isoform | g3227.t4 | 23833987 | 23835036 |
| chr_3 | g3227 | g3227.t4 | exon | g3227.t4.exon1 | 23833987 | 23835036 |
| chr_3 | g3227 | g3227.t4 | cds | g3227.t4.CDS1 | 23833988 | 23834878 |
| chr_3 | g3227 | g3227.t4 | TSS | g3227.t4 | 23835557 | 23835557 |
Sequences
>g3227.t4 Gene=g3227 Length=1050
TGAAACAAGCAACTGAACAGCAGTTTCAACCAAAAGATCCACCACCCGAATTTGAATTTA
TTGCTGATCCACCTTCAATTTCAGCACTAGATCTTGATATTGTTAAACTCACAGCACAAT
TTGTAGCACGTAATGGACGTCAATTTCTTACAAACTTGATGAATCGTGAACAGAGAAACT
TTCAATTTGATTTCTTACGTCCTCAACATTCACTCTTTCAATATTTCACAAAATTACTTG
AACAATACACTAAAATTTTGATTCCACCCAAGGATTTATTGCCAAAATTGAGAGCTGAAA
TTGATATTAATAAAGAAGGAAGTGTTAATGCTATACTGGATTCAGTAAAATATCGAGCAA
ATTGGCTCAAACATGAGGAAGCACAAAAAAGACGCGAAGAAGAGAAGGTTGAACGTGAAC
GAGTTGCATATGCTCAAATAGATTGGCATGATTTTGTTGTAGTAGAAGTTGTAGAATATC
AACCATTTGAAAGCGGTAATTTTCCAGCGCCCACAACTCCTGAAGAAGTCGGTGCTCGTG
TTATAATGGAACAACGATATCAAGAAGATGATAACGATATAGAAATGCAAATTGAATCAG
ATGAAGAAGTGCCAAATGATCAGCAAGTACCTCATCAAAATGTCAAGTTATCAGTTATGG
AGAATCGTGTTAAAGATAATACACAAGTGCAAGACATGGATGAAGCATCAAGTGATGATG
ATGCAGGTCCTAGTCAACCAACACAAGTTGCTCCTGTCATGCCACCGACTCATGATAAAG
TTATTGTCAAGAAATATGATCCTAAACAAGCTCAAAAAGTCACTAAACCTGTGTCAACTA
CAGATGAATATCTCATTTCTCCAATCACAGGTGAAAAAATACCAGCAAGTAAAGTTGCTG
AACATATGCGAATTGGATTACTTGATCCTCGTTGGGTTGAACAACGTGACAAGTTGATGG
AAAAAGTTCGTGAAGAAAATGTTTATGCACCAGGAGCTGCAATTGAAGCAAGCTTGAAAC
AATTGGCTGAACGTCGTACTGATATTTTCG
>g3227.t4 Gene=g3227 Length=297
MNREQRNFQFDFLRPQHSLFQYFTKLLEQYTKILIPPKDLLPKLRAEIDINKEGSVNAIL
DSVKYRANWLKHEEAQKRREEEKVERERVAYAQIDWHDFVVVEVVEYQPFESGNFPAPTT
PEEVGARVIMEQRYQEDDNDIEMQIESDEEVPNDQQVPHQNVKLSVMENRVKDNTQVQDM
DEASSDDDAGPSQPTQVAPVMPPTHDKVIVKKYDPKQAQKVTKPVSTTDEYLISPITGEK
IPASKVAEHMRIGLLDPRWVEQRDKLMEKVREENVYAPGAAIEASLKQLAERRTDIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3227.t4 | Coils | Coil | Coil | 70 | 90 | - |
| 7 | g3227.t4 | Gene3D | G3DSA:1.10.10.790 | - | 1 | 32 | 1.2E-8 |
| 6 | g3227.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 178 | 202 | - |
| 3 | g3227.t4 | PANTHER | PTHR15316:SF1 | SPLICING FACTOR 3A SUBUNIT 1 | 1 | 297 | 1.2E-81 |
| 4 | g3227.t4 | PANTHER | PTHR15316 | SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED | 1 | 297 | 1.2E-81 |
| 2 | g3227.t4 | Pfam | PF01805 | Surp module | 1 | 30 | 5.4E-7 |
| 1 | g3227.t4 | Pfam | PF12230 | Pre-mRNA splicing factor PRP21 like protein | 57 | 292 | 4.1E-45 |
| 9 | g3227.t4 | ProSiteProfiles | PS50128 | SURP motif repeat profile. | 1 | 23 | 9.209 |
| 5 | g3227.t4 | SUPERFAMILY | SSF109905 | Surp module (SWAP domain) | 1 | 38 | 3.6E-8 |
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:0006396 | RNA processing | BP |
| GO:0003723 | RNA binding | MF |
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. There were no conditions that were differentially expressed