General information for g5308.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3B subunit 4.
Parent gene
- The parent gene g5308 is located on chr_2: 8649846..8650717 (- 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 | g5308 | g5308.t3 | TTS | g5308.t3 | 8649364 | 8649364 |
| chr_2 | g5308 | g5308.t3 | isoform | g5308.t3 | 8649460 | 8650717 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon1 | 8649460 | 8649517 |
| chr_2 | g5308 | g5308.t3 | cds | g5308.t3.CDS1 | 8649460 | 8649517 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon2 | 8649597 | 8649653 |
| chr_2 | g5308 | g5308.t3 | cds | g5308.t3.CDS2 | 8649597 | 8649653 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon3 | 8649720 | 8649761 |
| chr_2 | g5308 | g5308.t3 | cds | g5308.t3.CDS3 | 8649720 | 8649761 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon4 | 8649826 | 8650417 |
| chr_2 | g5308 | g5308.t3 | cds | g5308.t3.CDS4 | 8649826 | 8650406 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon5 | 8650484 | 8650567 |
| chr_2 | g5308 | g5308.t3 | exon | g5308.t3.exon6 | 8650680 | 8650717 |
| chr_2 | g5308 | g5308.t3 | TSS | g5308.t3 | 8650794 | 8650794 |
Sequences
>g5308.t3 Gene=g5308 Length=871
ATGGCAAGTGGACCAATAGCTGAAAGAAATCAAGGCAAATGCAACAATTTATGTTGGTGG
TCTTGATGAGAAAGTAACAGAAACATTGCTTTGGGAGCTTTTTGTGCAAGCTGGTCCAGT
TGTAAATGTGCATATGCCTAAAGATCGAGTAACACAATTACATCAAGGCTATGGATTTGT
GGAATTTCTCGGTGAAGAAGATGCTGATTATGCAATCAAAATCATGAATATGATCAAATT
ATATGGAAAGCCAATTAGAGTAAATAAAGCTTCTGCTCATCAAAAGAATCTGGATGTTGG
TGCAAATATTTTCATTGGAAATCTTGATCCAGAAGTCGATGAAAAGCTTCTCTATGATAC
ATTCTCAGCATTTGGTGTTATTTTACAAACACCAAAAATCATGAGAGATCCAGAAACAGG
AAATTCAAAAGGATTTGCATTTATAAATTTTGCTAGTTTTGAAGCTTCAGATGCAGCAAT
GGATGCAATGAATGGACAATATCTTTGTAATAGACCGATTTCAGTGTCGTATGCATTTAA
AAAAGATTCAAAGGGTGAACGTCACGGTTCTGCAGCTGAACGATTACTTGCAGCACAAAA
TCCTCTATCTCATGCTGATAGACCGCATCAATTATTTGCAGATGCTCCTGTACCAATGAT
TCCAATGATGAATCAAATGATGCCACCACCACCACTTATTGTGCCACCTCCAGCACATAT
TCCAAATCCACCAATGTTTCCTCCTGCAATGCCACCTCAAATGCCACCACCACCTCAATT
ACCACCATCACTTGCACCTCCTCCTTTACCAAGCTCCAATTGGCCTGCAAATATGCCACC
TATTCCACCACCACCACAAACATACTTTTAA
>g5308.t3 Gene=g5308 Length=245
MPKDRVTQLHQGYGFVEFLGEEDADYAIKIMNMIKLYGKPIRVNKASAHQKNLDVGANIF
IGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPETGNSKGFAFINFASFEASDAAMDAMN
GQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFADAPVPMIPMMN
QMMPPPPLIVPPPAHIPNPPMFPPAMPPQMPPPPQLPPSLAPPPLPSSNWPANMPPIPPP
PQTYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5308.t3 | CDD | cd12335 | RRM2_SF3B4 | 56 | 138 | 1.28373E-60 |
| 7 | g5308.t3 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 56 | 3.2E-13 |
| 6 | g5308.t3 | Gene3D | G3DSA:3.30.70.330 | - | 57 | 146 | 5.2E-26 |
| 10 | g5308.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 205 | 245 | - |
| 3 | g5308.t3 | PANTHER | PTHR48030 | SPLICING FACTOR 3B SUBUNIT 4 | 1 | 229 | 2.5E-113 |
| 4 | g5308.t3 | PANTHER | PTHR48030:SF4 | SPLICING FACTOR 3B SUBUNIT 4 | 1 | 229 | 2.5E-113 |
| 2 | g5308.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 2 | 42 | 4.7E-6 |
| 1 | g5308.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 59 | 129 | 2.3E-20 |
| 11 | g5308.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 48 | 10.19 |
| 12 | g5308.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 57 | 136 | 17.421 |
| 9 | g5308.t3 | SMART | SM00360 | rrm1_1 | 58 | 132 | 1.0E-24 |
| 5 | g5308.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 140 | 3.78E-37 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5308/g5308.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5308.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| 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. There were no conditions that were differentially expressed