Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Splicing factor U2af 38 kDa subunit.

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 g5019 g5019.t7 TSS g5019.t7 6477811 6477811
chr_2 g5019 g5019.t7 isoform g5019.t7 6478023 6478848
chr_2 g5019 g5019.t7 exon g5019.t7.exon1 6478023 6478180
chr_2 g5019 g5019.t7 exon g5019.t7.exon2 6478236 6478390
chr_2 g5019 g5019.t7 cds g5019.t7.CDS1 6478262 6478390
chr_2 g5019 g5019.t7 exon g5019.t7.exon3 6478452 6478666
chr_2 g5019 g5019.t7 cds g5019.t7.CDS2 6478452 6478666
chr_2 g5019 g5019.t7 exon g5019.t7.exon4 6478728 6478848
chr_2 g5019 g5019.t7 cds g5019.t7.CDS3 6478728 6478848
chr_2 g5019 g5019.t7 TTS g5019.t7 6479061 6479061

Sequences

>g5019.t7 Gene=g5019 Length=649
CAGAGTAAATTGTTCATTTTACTTCAAAATAGGAGCATGTCGTCACGGAGATAGATGTTC
TCGCATTCACAATAAACCAACATTCTCACAAACGGTTCTTTTGCAAAATTTATATGTAAA
TCCACAAAATTCTGCAAAATCTGCCGATGGCTCTCACTTGGTTGCAAATGTTTCTGATGA
GGAAATGCAAGAGCATTATGATAATTTCTTTGAAGATGTGTTTGTAGAGCTTGAAGACAA
GTATGGAGAAATTGAAGAGATGAATGTTTGCGATAATCTAGGAGATCATCTTGTTGGAAA
TGTTTACATTAAATTTCGACGTGAAGAAGATGCTGAAAGAGCAGCAAAAGAACTGAATAA
TCGTTGGTTTGGTGGACGACCAGTGTATGCAGAATTATCTCCCGTTACTGACTTTCGAGA
AGCATGTTGTCGTCAATATGAAATGGGTGAATGCACTCGCTCTGGTTTTTGTAATTTCAT
GCATTTGAAACCAATATCTCGTGAGCTTCGTCGTTATTTGTATTCTAGACGAAGAGGTCG
TTCACGCTCAAGATCAAAATCACCAAGGCGTCGATCAAGATCAAGAAATCGTGATCGTCA
TTCAAGAGACAGAGACCGTGGAGATAGAGATCGTCGGGGACGTTATTAA

>g5019.t7 Gene=g5019 Length=154
MQEHYDNFFEDVFVELEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAERAAKELNNR
WFGGRPVYAELSPVTDFREACCRQYEMGECTRSGFCNFMHLKPISRELRRYLYSRRRGRS
RSRSKSPRRRSRSRNRDRHSRDRDRGDRDRRGRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5019.t7 Gene3D G3DSA:3.30.70.330 - 1 73 1.2E-28
12 g5019.t7 MobiDBLite mobidb-lite consensus disorder prediction 115 154 -
14 g5019.t7 MobiDBLite mobidb-lite consensus disorder prediction 115 136 -
13 g5019.t7 MobiDBLite mobidb-lite consensus disorder prediction 137 154 -
3 g5019.t7 PANTHER PTHR12620:SF11 SPLICING FACTOR U2AF 35 KDA SUBUNIT-RELATED 1 152 2.2E-74
4 g5019.t7 PANTHER PTHR12620 U2 SNRNP AUXILIARY FACTOR, SMALL SUBUNIT 1 152 2.2E-74
6 g5019.t7 PRINTS PR01848 U2 auxiliary factor small subunit signature 2 17 7.6E-36
7 g5019.t7 PRINTS PR01848 U2 auxiliary factor small subunit signature 31 53 7.6E-36
8 g5019.t7 PRINTS PR01848 U2 auxiliary factor small subunit signature 58 82 7.6E-36
5 g5019.t7 PRINTS PR01848 U2 auxiliary factor small subunit signature 93 105 7.6E-36
1 g5019.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 18 67 2.1E-6
2 g5019.t7 Pfam PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) 77 101 9.8E-6
16 g5019.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 1 74 10.65
15 g5019.t7 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 76 103 10.906
11 g5019.t7 SMART SM00361 rrm2_1 1 70 1.9E-16
9 g5019.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 6 77 1.88E-17

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5019/g5019.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5019.t7.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0046872 metal ion binding MF
GO:0003723 RNA binding MF
GO:0089701 U2AF complex CC
GO:0000398 mRNA splicing, via spliceosome BP
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