General information for g11679.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3B subunit 6.
Parent gene
- The parent gene g11679 is located on chr_1: 17763149..17763651 (- 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_1 | g11679 | g11679.t1 | TTS | g11679.t1 | 17763087 | 17763087 |
| chr_1 | g11679 | g11679.t1 | isoform | g11679.t1 | 17763149 | 17763651 |
| chr_1 | g11679 | g11679.t1 | exon | g11679.t1.exon1 | 17763149 | 17763357 |
| chr_1 | g11679 | g11679.t1 | cds | g11679.t1.CDS1 | 17763149 | 17763357 |
| chr_1 | g11679 | g11679.t1 | exon | g11679.t1.exon2 | 17763419 | 17763560 |
| chr_1 | g11679 | g11679.t1 | cds | g11679.t1.CDS2 | 17763419 | 17763560 |
| chr_1 | g11679 | g11679.t1 | exon | g11679.t1.exon3 | 17763622 | 17763651 |
| chr_1 | g11679 | g11679.t1 | cds | g11679.t1.CDS3 | 17763622 | 17763651 |
| chr_1 | g11679 | g11679.t1 | TSS | g11679.t1 | 17763786 | 17763786 |
Sequences
>g11679.t1 Gene=g11679 Length=381
ATGGCGTTGGCGATGCAAAAGCGGAATAATGTTCGACTTCCTCCAGAAGTTAATAGAATA
TTATATGTAAGAAACCTTCCCTATAAAATCACTAGTGATGAAATGTATGATATTTTTGGT
AAATATGGTGCAATCAGACAAATTAGAGTTGGAAATATTCCAGAAACAAAAGGAACGGCT
TTTGTGGTATATGAAGATATTTGGGATGCAAAAAATGCATGTGATCATTTGTCTGGTTTT
AATGTCTGCAATCGCTATCTCATTGTATTATATTATCAAGCATCGAAAGCATTCAAAACT
ACTGACATAAATGCAAAACAAGATGAAATTGAAAAAATGAAGGCAAAATACAACATAAAT
TCCGATGATTTACGAAAGTGA
>g11679.t1 Gene=g11679 Length=126
MALAMQKRNNVRLPPEVNRILYVRNLPYKITSDEMYDIFGKYGAIRQIRVGNIPETKGTA
FVVYEDIWDAKNACDHLSGFNVCNRYLIVLYYQASKAFKTTDINAKQDEIEKMKAKYNIN
SDDLRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11679.t1 | CDD | cd12241 | RRM_SF3B14 | 17 | 93 | 0.000 |
| 6 | g11679.t1 | Gene3D | G3DSA:3.30.70.330 | - | 15 | 122 | 0.000 |
| 2 | g11679.t1 | PANTHER | PTHR12785 | SPLICING FACTOR 3B | 5 | 116 | 0.000 |
| 3 | g11679.t1 | PANTHER | PTHR12785:SF7 | SPLICING FACTOR 3B SUBUNIT 6 | 5 | 116 | 0.000 |
| 1 | g11679.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 21 | 87 | 0.000 |
| 7 | g11679.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 19 | 94 | 14.778 |
| 5 | g11679.t1 | SMART | SM00360 | rrm1_1 | 20 | 90 | 0.000 |
| 4 | g11679.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 18 | 96 | 0.000 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12833 (pre-mRNA branch site protein p14)
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.
