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.t2 TTS g5308.t2 8649364 8649364
chr_2 g5308 g5308.t2 isoform g5308.t2 8649460 8650450
chr_2 g5308 g5308.t2 exon g5308.t2.exon1 8649460 8650450
chr_2 g5308 g5308.t2 cds g5308.t2.CDS1 8649822 8650406
chr_2 g5308 g5308.t2 TSS g5308.t2 8650794 8650794

Sequences

>g5308.t2 Gene=g5308 Length=991
TTTTCTAAACGTTTATTTTTCTCTGTTTTGCAGTAAATGTGCATATGCCTAAAGATCGAG
TAACACAATTACATCAAGGCTATGGATTTGTGGAATTTCTCGGTGAAGAAGATGCTGATT
ATGCAATCAAAATCATGAATATGATCAAATTATATGGAAAGCCAATTAGAGTAAATAAAG
CTTCTGCTCATCAAAAGAATCTGGATGTTGGTGCAAATATTTTCATTGGAAATCTTGATC
CAGAAGTCGATGAAAAGCTTCTCTATGATACATTCTCAGCATTTGGTGTTATTTTACAAA
CACCAAAAATCATGAGAGATCCAGAAACAGGAAATTCAAAAGGATTTGCATTTATAAATT
TTGCTAGTTTTGAAGCTTCAGATGCAGCAATGGATGCAATGAATGGACAATATCTTTGTA
ATAGACCGATTTCAGTGTCGTATGCATTTAAAAAAGATTCAAAGGGTGAACGTCACGGTT
CTGCAGCTGAACGATTACTTGCAGCACAAAATCCTCTATCTCATGCTGATAGACCGCATC
AATTATTTGCAGATGCTCCTGTACCAATGATTCCAATGATGAATCAAATGATGCCACCAC
CACCACTTATTGTGCCACCTCCAGCGTGAGTTAAATTTAAAAGAATTTTACATGATTAAA
ATTTAATTATTTTCTTTTTTTTTTTGCAGACATATTCCAAATCCACCAATGTTTCCTCCT
GCAATGCCACCGTTAGTACTCTGATTAATTTTGCATTTAACTAAAGTTTTTCAATTAATT
CTTCTTTTCTTTTTTAGTCAAATGCCACCACCACCTCAATTACCACCATCACTTGCACCT
CCTCCTTTACCAAGGTAACTTTCATTCTTTTCTAATTTTATCAGTACATTATTTTAATTA
ACTCGACATTCATTTTTTTCATTTTTAAAACAGCTCCAATTGGCCTGCAAATATGCCACC
TATTCCACCACCACCACAAACATACTTTTAA

>g5308.t2 Gene=g5308 Length=194
MPKDRVTQLHQGYGFVEFLGEEDADYAIKIMNMIKLYGKPIRVNKASAHQKNLDVGANIF
IGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPETGNSKGFAFINFASFEASDAAMDAMN
GQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFADAPVPMIPMMN
QMMPPPPLIVPPPA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5308.t2 CDD cd12335 RRM2_SF3B4 56 138 0.0000000
8 g5308.t2 Gene3D G3DSA:3.30.70.330 - 1 57 0.0000000
7 g5308.t2 Gene3D G3DSA:3.30.70.330 - 58 146 0.0000000
3 g5308.t2 PANTHER PTHR48030 SPLICING FACTOR 3B SUBUNIT 4 1 185 0.0000000
4 g5308.t2 PANTHER PTHR48030:SF4 SPLICING FACTOR 3B SUBUNIT 4 1 185 0.0000000
2 g5308.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2 42 0.0000032
1 g5308.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 59 129 0.0000000
9 g5308.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 1 48 10.1900000
10 g5308.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 57 136 17.4210000
6 g5308.t2 SMART SM00360 rrm1_1 58 132 0.0000000
5 g5308.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 1 139 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5308/g5308.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5308.t2.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.

Raw TPM values