General information for g5936.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine/arginine-rich splicing factor 2.
Parent gene
- The parent gene g5936 is located on chr_2: 12908497..12909940 (+ 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 | g5936 | g5936.t8 | TSS | g5936.t8 | 12907679 | 12907679 |
| chr_2 | g5936 | g5936.t8 | isoform | g5936.t8 | 12907797 | 12909285 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon1 | 12907797 | 12907850 |
| chr_2 | g5936 | g5936.t8 | cds | g5936.t8.CDS1 | 12907797 | 12907850 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon2 | 12907924 | 12908069 |
| chr_2 | g5936 | g5936.t8 | cds | g5936.t8.CDS2 | 12907924 | 12908069 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon3 | 12908135 | 12908194 |
| chr_2 | g5936 | g5936.t8 | cds | g5936.t8.CDS3 | 12908135 | 12908194 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon4 | 12908255 | 12908324 |
| chr_2 | g5936 | g5936.t8 | cds | g5936.t8.CDS4 | 12908255 | 12908303 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon5 | 12908389 | 12908436 |
| chr_2 | g5936 | g5936.t8 | exon | g5936.t8.exon6 | 12908492 | 12909285 |
| chr_2 | g5936 | g5936.t8 | TTS | g5936.t8 | 12909252 | 12909252 |
Sequences
>g5936.t8 Gene=g5936 Length=1172
ATGTCATATTCAGCTAGACCACCGCCCAAAATTGAGGGCATGATTTCTTTAAAAGTTGAC
AATTTGACTTATCGAACTACTCCCGAAGACTTGAGACGAGTTTTTGAGCGATGCGGTGAT
GTTGGTGACATTTATATTCCAAGAGATAGACATACTCGTGAGTCGAGAGGATTTGCTTTT
GTTCGATTTTATGACAAACGTGATGCTGAGGAAGCTCTTCAAGAAATGGATGGAAGAATG
CTTGATGGACGTGAATTGAGTGCAAATGGCCAGATATGGGAGACCTACATCTCCACAAAG
ACGTTCTAACAGACACGATCGTCGCCGAAGATCCCGTTCGAGAGACCGTAGAGGAGGTGG
AGGTGGAAGACGCTCAAGATCACGTTCAAGAGACCGAAGAGGACGCCGTCGTTCATACTC
ACGTTCCAAATCTCGTTCAAGATCAGCAAATAGTCGCAGCAACAGCAAATCTTCACGCGA
TCGTTCACGCTCTCCAGTTCGTAAGAATCGCAGCTCAAGCAATTAAGCAGAGGTGACACT
TAAAATTGTTTGACAGCCGACTGCTAATGTGCTTCTGCAAAATATTATATTTGCGTTCAA
AAGGTACAATCGTTTTTCTATACATTTTTTTTCCTCCTAATTACTTTAATGAGTTTAAAA
ATTTGTCTAAACAGTAAAAAAATCGTAACAAAATTTGATAAAGAAATGAAATATCTAATA
CTATAACTACTACTCTTTTGTTTGATAGAAAAATAAGCAAATTTCTTGATAGATTTTAAG
CATTTTCAAGTTTTCCTATTTTAAAATAGACATTAAAACATACTTTATGAAATTATACGT
GTGCTAAGGCAATTTATTTGTATTATTCTGTCATCTTTTAAAAACGAACAATCAGTTCTT
TTTTTAACAAATATAATCATTTTGTAATTTTAGCAATTATAAATGTCGCTATAATGAACA
CATGTCCTATCTTACACTTCCTTTAGAATACATTTTTTTTCTGTAAGGTTCAATATATAT
TTTGAGTTTATAAGACAAGAGAATTAACTTTTCTTGTCATAATAACATTTAATGAAGAAA
TTAATTGATATATACCAATCAATAATAATATGCATAAAAATATCAACATTTTAAAAAATA
AAAAATAATATTTTATCCTACTTTTACCTACA
>g5936.t8 Gene=g5936 Length=102
MSYSARPPPKIEGMISLKVDNLTYRTTPEDLRRVFERCGDVGDIYIPRDRHTRESRGFAF
VRFYDKRDAEEALQEMDGRMLDGRELSANGQIWETYISTKTF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5936.t8 | CDD | cd12311 | RRM_SRSF2_SRSF8 | 17 | 86 | 0.000 |
| 6 | g5936.t8 | Gene3D | G3DSA:3.30.70.330 | - | 3 | 91 | 0.000 |
| 2 | g5936.t8 | PANTHER | PTHR23147 | SERINE/ARGININE RICH SPLICING FACTOR | 6 | 87 | 0.000 |
| 3 | g5936.t8 | PANTHER | PTHR23147:SF145 | SERINE/ARGININE-RICH SPLICING FACTOR 2 | 6 | 87 | 0.000 |
| 1 | g5936.t8 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 18 | 86 | 0.000 |
| 7 | g5936.t8 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 15 | 89 | 17.643 |
| 5 | g5936.t8 | SMART | SM00360 | rrm1_1 | 16 | 89 | 0.000 |
| 4 | g5936.t8 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 7 | 87 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5936/g5936.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5936.t8.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003723 | RNA binding | MF |
| GO:0000381 | regulation of alternative mRNA splicing, via spliceosome | BP |
| GO:0003676 | nucleic acid 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.
