General information for g5308.t1
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.t1 | TTS | g5308.t1 | 8649364 | 8649364 |
| chr_2 | g5308 | g5308.t1 | isoform | g5308.t1 | 8649460 | 8650717 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon1 | 8649460 | 8649517 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS1 | 8649460 | 8649517 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon2 | 8649597 | 8649653 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS2 | 8649597 | 8649653 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon3 | 8649720 | 8649761 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS3 | 8649720 | 8649761 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon4 | 8649826 | 8650417 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS4 | 8649826 | 8650417 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon5 | 8650484 | 8650567 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS5 | 8650484 | 8650567 |
| chr_2 | g5308 | g5308.t1 | exon | g5308.t1.exon6 | 8650684 | 8650717 |
| chr_2 | g5308 | g5308.t1 | cds | g5308.t1.CDS6 | 8650684 | 8650717 |
| chr_2 | g5308 | g5308.t1 | TSS | g5308.t1 | 8650794 | 8650794 |
Sequences
>g5308.t1 Gene=g5308 Length=867
ATGGCAAGTGGACCAATAGCTGAAAGAAATCAAGATGCAACAATTTATGTTGGTGGTCTT
GATGAGAAAGTAACAGAAACATTGCTTTGGGAGCTTTTTGTGCAAGCTGGTCCAGTTGTA
AATGTGCATATGCCTAAAGATCGAGTAACACAATTACATCAAGGCTATGGATTTGTGGAA
TTTCTCGGTGAAGAAGATGCTGATTATGCAATCAAAATCATGAATATGATCAAATTATAT
GGAAAGCCAATTAGAGTAAATAAAGCTTCTGCTCATCAAAAGAATCTGGATGTTGGTGCA
AATATTTTCATTGGAAATCTTGATCCAGAAGTCGATGAAAAGCTTCTCTATGATACATTC
TCAGCATTTGGTGTTATTTTACAAACACCAAAAATCATGAGAGATCCAGAAACAGGAAAT
TCAAAAGGATTTGCATTTATAAATTTTGCTAGTTTTGAAGCTTCAGATGCAGCAATGGAT
GCAATGAATGGACAATATCTTTGTAATAGACCGATTTCAGTGTCGTATGCATTTAAAAAA
GATTCAAAGGGTGAACGTCACGGTTCTGCAGCTGAACGATTACTTGCAGCACAAAATCCT
CTATCTCATGCTGATAGACCGCATCAATTATTTGCAGATGCTCCTGTACCAATGATTCCA
ATGATGAATCAAATGATGCCACCACCACCACTTATTGTGCCACCTCCAGCACATATTCCA
AATCCACCAATGTTTCCTCCTGCAATGCCACCTCAAATGCCACCACCACCTCAATTACCA
CCATCACTTGCACCTCCTCCTTTACCAAGCTCCAATTGGCCTGCAAATATGCCACCTATT
CCACCACCACCACAAACATACTTTTAA
>g5308.t1 Gene=g5308 Length=288
MASGPIAERNQDATIYVGGLDEKVTETLLWELFVQAGPVVNVHMPKDRVTQLHQGYGFVE
FLGEEDADYAIKIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTF
SAFGVILQTPKIMRDPETGNSKGFAFINFASFEASDAAMDAMNGQYLCNRPISVSYAFKK
DSKGERHGSAAERLLAAQNPLSHADRPHQLFADAPVPMIPMMNQMMPPPPLIVPPPAHIP
NPPMFPPAMPPQMPPPPQLPPSLAPPPLPSSNWPANMPPIPPPPQTYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5308.t1 | CDD | cd12334 | RRM1_SF3B4 | 15 | 88 | 2.83087E-57 |
| 9 | g5308.t1 | CDD | cd12335 | RRM2_SF3B4 | 99 | 181 | 2.70587E-61 |
| 6 | g5308.t1 | Gene3D | G3DSA:3.30.70.330 | - | 6 | 94 | 2.3E-28 |
| 7 | g5308.t1 | Gene3D | G3DSA:3.30.70.330 | - | 95 | 188 | 1.0E-25 |
| 12 | g5308.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 248 | 288 | - |
| 3 | g5308.t1 | PANTHER | PTHR48030 | SPLICING FACTOR 3B SUBUNIT 4 | 1 | 272 | 1.3E-141 |
| 4 | g5308.t1 | PANTHER | PTHR48030:SF4 | SPLICING FACTOR 3B SUBUNIT 4 | 1 | 272 | 1.3E-141 |
| 1 | g5308.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 15 | 85 | 4.0E-17 |
| 2 | g5308.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 102 | 172 | 3.1E-20 |
| 14 | g5308.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 13 | 91 | 17.609 |
| 13 | g5308.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 100 | 179 | 17.421 |
| 11 | g5308.t1 | SMART | SM00360 | rrm1_1 | 14 | 87 | 3.5E-24 |
| 10 | g5308.t1 | SMART | SM00360 | rrm1_1 | 101 | 175 | 1.0E-24 |
| 5 | g5308.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 12 | 182 | 3.04E-50 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5308/g5308.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5308.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12831 (splicing factor 3B subunit 4)
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.
