Gene loci information

Transcript annotation

  • This transcript has been annotated as Splicing factor 3B subunit 4.

Parent gene

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.t4 TTS g5308.t4 8649364 8649364
chr_2 g5308 g5308.t4 isoform g5308.t4 8649846 8650717
chr_2 g5308 g5308.t4 exon g5308.t4.exon1 8649846 8650417
chr_2 g5308 g5308.t4 cds g5308.t4.CDS1 8649846 8650406
chr_2 g5308 g5308.t4 exon g5308.t4.exon2 8650484 8650567
chr_2 g5308 g5308.t4 exon g5308.t4.exon3 8650680 8650717
chr_2 g5308 g5308.t4 TSS g5308.t4 8650794 8650794

Sequences

>g5308.t4 Gene=g5308 Length=694
ATGGCAAGTGGACCAATAGCTGAAAGAAATCAAGGCAAATGCAACAATTTATGTTGGTGG
TCTTGATGAGAAAGTAACAGAAACATTGCTTTGGGAGCTTTTTGTGCAAGCTGGTCCAGT
TGTAAATGTGCATATGCCTAAAGATCGAGTAACACAATTACATCAAGGCTATGGATTTGT
GGAATTTCTCGGTGAAGAAGATGCTGATTATGCAATCAAAATCATGAATATGATCAAATT
ATATGGAAAGCCAATTAGAGTAAATAAAGCTTCTGCTCATCAAAAGAATCTGGATGTTGG
TGCAAATATTTTCATTGGAAATCTTGATCCAGAAGTCGATGAAAAGCTTCTCTATGATAC
ATTCTCAGCATTTGGTGTTATTTTACAAACACCAAAAATCATGAGAGATCCAGAAACAGG
AAATTCAAAAGGATTTGCATTTATAAATTTTGCTAGTTTTGAAGCTTCAGATGCAGCAAT
GGATGCAATGAATGGACAATATCTTTGTAATAGACCGATTTCAGTGTCGTATGCATTTAA
AAAAGATTCAAAGGGTGAACGTCACGGTTCTGCAGCTGAACGATTACTTGCAGCACAAAA
TCCTCTATCTCATGCTGATAGACCGCATCAATTATTTGCAGATGCTCCTGTACCAATGAT
TCCAATGATGAATCAAATGATGCCACCACCACCA

>g5308.t4 Gene=g5308 Length=187
MPKDRVTQLHQGYGFVEFLGEEDADYAIKIMNMIKLYGKPIRVNKASAHQKNLDVGANIF
IGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPETGNSKGFAFINFASFEASDAAMDAMN
GQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFADAPVPMIPMMN
QMMPPPP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5308.t4 CDD cd12335 RRM2_SF3B4 56 138 0.000000
8 g5308.t4 Gene3D G3DSA:3.30.70.330 - 1 57 0.000000
7 g5308.t4 Gene3D G3DSA:3.30.70.330 - 58 146 0.000000
3 g5308.t4 PANTHER PTHR48030 SPLICING FACTOR 3B SUBUNIT 4 1 175 0.000000
4 g5308.t4 PANTHER PTHR48030:SF4 SPLICING FACTOR 3B SUBUNIT 4 1 175 0.000000
2 g5308.t4 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2 42 0.000003
1 g5308.t4 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 59 129 0.000000
9 g5308.t4 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 1 48 10.190000
10 g5308.t4 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 57 136 17.421000
6 g5308.t4 SMART SM00360 rrm1_1 58 132 0.000000
5 g5308.t4 SUPERFAMILY SSF54928 RNA-binding domain, RBD 1 140 0.000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5308/g5308.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5308.t4.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