General information for g3773.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g3773.t1 | 27933776 | 27933776 |
| chr_3 | g3773 | g3773.t1 | isoform | g3773.t1 | 27933855 | 27934587 |
| chr_3 | g3773 | g3773.t1 | exon | g3773.t1.exon1 | 27933855 | 27934262 |
| chr_3 | g3773 | g3773.t1 | cds | g3773.t1.CDS1 | 27933855 | 27934262 |
| chr_3 | g3773 | g3773.t1 | exon | g3773.t1.exon2 | 27934327 | 27934587 |
| chr_3 | g3773 | g3773.t1 | cds | g3773.t1.CDS2 | 27934327 | 27934587 |
| chr_3 | g3773 | g3773.t1 | TSS | g3773.t1 | 27934593 | 27934593 |
Sequences
>g3773.t1 Gene=g3773 Length=669
ATGGCAGATGTAAAAGCAAAAATGGCAGAGAGAATGGCCAAGTTAAAGAGTCTTCATCAA
GCAAGGAATGAAGCTCGAAATCAAAATCACAATGAAGTAAAGAAAGAAGTGGAGAGAAAT
TCTCTTCCTAAAAATTGGGAAATAAGACAACAAAAAGCAGAATGGCTTATTAAGGATAAA
GCAAAGCGTGAAGCAGTTGAAGAGAAAGGAATTGATTATGAACGAGTAAAATTATTAAAT
GTCTCTGCATTAGAACAGGATAGATTAGAAAAGTTGAAGAAGAAAAGAAAAGTTGGCGAT
CAAGGATTTGCAGACTATGAGACACAAACAGCAAGACAATATCAAAGATTAATTAAGGCA
ATGCCTCCAAAAGATTTACGCAAATATAATGAACAGAAACAAGAATACGGAGAAGATTAT
TATTCGGCAAATCCTATACTTGAGGGAAAAGCTAAAGATTCAAAAGAAGCAATTCAAAGG
ATGGTCGATGATCTCGATGAACAAGCTGAGAAACGTAAAAACTTTTCACGTAGACGAATG
CACAATGATGAGGCTGATATTGACTACATCAATGAAAAGAATGCTCGTCTTAATAAGAAA
CTTGATAGATATTATGGAGAATATACTAAAGAGATTCGTGAAAATTTGGAAAGAGGAACT
GCTATTTAA
>g3773.t1 Gene=g3773 Length=222
MADVKAKMAERMAKLKSLHQARNEARNQNHNEVKKEVERNSLPKNWEIRQQKAEWLIKDK
AKREAVEEKGIDYERVKLLNVSALEQDRLEKLKKKRKVGDQGFADYETQTARQYQRLIKA
MPPKDLRKYNEQKQEYGEDYYSANPILEGKAKDSKEAIQRMVDDLDEQAEKRKNFSRRRM
HNDEADIDYINEKNARLNKKLDRYYGEYTKEIRENLERGTAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3773.t1 | Coils | Coil | Coil | 151 | 178 | - |
| 5 | g3773.t1 | Coils | Coil | Coil | 222 | 222 | - |
| 4 | g3773.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 38 | - |
| 2 | g3773.t1 | PANTHER | PTHR13264:SF5 | PRE-MRNA-SPLICING FACTOR SYF2 | 5 | 222 | 4.5E-52 |
| 3 | g3773.t1 | PANTHER | PTHR13264 | GCIP-INTERACTING PROTEIN P29 | 5 | 222 | 4.5E-52 |
| 1 | g3773.t1 | Pfam | PF08231 | SYF2 splicing factor | 68 | 217 | 1.8E-42 |
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 transcript has been annotated with K12868 (pre-mRNA-splicing factor SYF2)
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.
