General information for g3773.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor Syf2.
Parent gene
- The parent gene g3773 is located on chr_3: 27933855..27934587 (- 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 | g3773 | g3773.t4 | TTS | g3773.t4 | 27933776 | 27933776 |
| chr_3 | g3773 | g3773.t4 | isoform | g3773.t4 | 27933855 | 27934587 |
| chr_3 | g3773 | g3773.t4 | exon | g3773.t4.exon1 | 27933855 | 27934255 |
| chr_3 | g3773 | g3773.t4 | cds | g3773.t4.CDS1 | 27933855 | 27934163 |
| chr_3 | g3773 | g3773.t4 | exon | g3773.t4.exon2 | 27934363 | 27934587 |
| chr_3 | g3773 | g3773.t4 | TSS | g3773.t4 | 27934593 | 27934593 |
Sequences
>g3773.t4 Gene=g3773 Length=626
ATGGCAGATGTAAAAGCAAAAATGGCAGAGAGAATGGCCAAGTTAAAGAGTCTTCATCAA
GCAAGGAATGAAGCTCGAAATCAAAATCACAATGAAGTAAAGAAAGAAGTGGAGAGAAAT
TCTCTTCCTAAAAATTGGGAAATAAGACAACAAAAAGCAGAATGGCTTATTAAGGATAAA
GCAAAGCGTGAAGCAGTTGAAGAGAAAGGAATTGATTATGAACGAAAAAGTTGAAGAAGA
AAAGAAAAGTTGGCGATCAAGGATTTGCAGACTATGAGACACAAACAGCAAGACAATATC
AAAGATTAATTAAGGCAATGCCTCCAAAAGATTTACGCAAATATAATGAACAGAAACAAG
AATACGGAGAAGATTATTATTCGGCAAATCCTATACTTGAGGGAAAAGCTAAAGATTCAA
AAGAAGCAATTCAAAGGATGGTCGATGATCTCGATGAACAAGCTGAGAAACGTAAAAACT
TTTCACGTAGACGAATGCACAATGATGAGGCTGATATTGACTACATCAATGAAAAGAATG
CTCGTCTTAATAAGAAACTTGATAGATATTATGGAGAATATACTAAAGAGATTCGTGAAA
ATTTGGAAAGAGGAACTGCTATTTAA
>g3773.t4 Gene=g3773 Length=102
MPPKDLRKYNEQKQEYGEDYYSANPILEGKAKDSKEAIQRMVDDLDEQAEKRKNFSRRRM
HNDEADIDYINEKNARLNKKLDRYYGEYTKEIRENLERGTAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3773.t4 | Coils | Coil | Coil | 31 | 58 | - |
| 2 | g3773.t4 | PANTHER | PTHR13264:SF5 | PRE-MRNA-SPLICING FACTOR SYF2 | 3 | 102 | 2.0E-31 |
| 3 | g3773.t4 | PANTHER | PTHR13264 | GCIP-INTERACTING PROTEIN P29 | 3 | 102 | 2.0E-31 |
| 1 | g3773.t4 | Pfam | PF08231 | SYF2 splicing factor | 4 | 97 | 9.5E-29 |
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. There were no conditions that were differentially expressed