General information for g5019.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor U2af 38 kDa subunit.
Parent gene
- The parent gene g5019 is located on chr_2: 6478452..6478848 (+ 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 | g5019 | g5019.t1 | TSS | g5019.t1 | 6477811 | 6477811 |
| chr_2 | g5019 | g5019.t1 | isoform | g5019.t1 | 6477914 | 6478848 |
| chr_2 | g5019 | g5019.t1 | exon | g5019.t1.exon1 | 6477914 | 6477957 |
| chr_2 | g5019 | g5019.t1 | cds | g5019.t1.CDS1 | 6477914 | 6477957 |
| chr_2 | g5019 | g5019.t1 | exon | g5019.t1.exon2 | 6478026 | 6478180 |
| chr_2 | g5019 | g5019.t1 | cds | g5019.t1.CDS2 | 6478026 | 6478180 |
| chr_2 | g5019 | g5019.t1 | exon | g5019.t1.exon3 | 6478236 | 6478390 |
| chr_2 | g5019 | g5019.t1 | cds | g5019.t1.CDS3 | 6478236 | 6478390 |
| chr_2 | g5019 | g5019.t1 | exon | g5019.t1.exon4 | 6478452 | 6478666 |
| chr_2 | g5019 | g5019.t1 | cds | g5019.t1.CDS4 | 6478452 | 6478666 |
| chr_2 | g5019 | g5019.t1 | exon | g5019.t1.exon5 | 6478728 | 6478848 |
| chr_2 | g5019 | g5019.t1 | cds | g5019.t1.CDS5 | 6478728 | 6478848 |
| chr_2 | g5019 | g5019.t1 | TTS | g5019.t1 | 6479061 | 6479061 |
Sequences
>g5019.t1 Gene=g5019 Length=690
ATGGCCGAATATCTAGCATCTATTTTTGGAACAGAAAAAGACAAAGTAAATTGTTCATTT
TACTTCAAAATAGGAGCATGTCGTCACGGAGATAGATGTTCTCGCATTCACAATAAACCA
ACATTCTCACAAACGGTTCTTTTGCAAAATTTATATGTAAATCCACAAAATTCTGCAAAA
TCTGCCGATGGCTCTCACTTGGTTGCAAATGTTTCTGATGAGGAAATGCAAGAGCATTAT
GATAATTTCTTTGAAGATGTGTTTGTAGAGCTTGAAGACAAGTATGGAGAAATTGAAGAG
ATGAATGTTTGCGATAATCTAGGAGATCATCTTGTTGGAAATGTTTACATTAAATTTCGA
CGTGAAGAAGATGCTGAAAGAGCAGCAAAAGAACTGAATAATCGTTGGTTTGGTGGACGA
CCAGTGTATGCAGAATTATCTCCCGTTACTGACTTTCGAGAAGCATGTTGTCGTCAATAT
GAAATGGGTGAATGCACTCGCTCTGGTTTTTGTAATTTCATGCATTTGAAACCAATATCT
CGTGAGCTTCGTCGTTATTTGTATTCTAGACGAAGAGGTCGTTCACGCTCAAGATCAAAA
TCACCAAGGCGTCGATCAAGATCAAGAAATCGTGATCGTCATTCAAGAGACAGAGACCGT
GGAGATAGAGATCGTCGGGGACGTTATTAA
>g5019.t1 Gene=g5019 Length=229
MAEYLASIFGTEKDKVNCSFYFKIGACRHGDRCSRIHNKPTFSQTVLLQNLYVNPQNSAK
SADGSHLVANVSDEEMQEHYDNFFEDVFVELEDKYGEIEEMNVCDNLGDHLVGNVYIKFR
REEDAERAAKELNNRWFGGRPVYAELSPVTDFREACCRQYEMGECTRSGFCNFMHLKPIS
RELRRYLYSRRRGRSRSRSKSPRRRSRSRNRDRHSRDRDRGDRDRRGRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5019.t1 | CDD | cd12538 | RRM_U2AF35 | 43 | 148 | 1.09623E-70 |
| 13 | g5019.t1 | Gene3D | G3DSA:3.30.70.330 | - | 43 | 148 | 1.8E-36 |
| 18 | g5019.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 229 | - |
| 19 | g5019.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 211 | - |
| 20 | g5019.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 212 | 229 | - |
| 4 | g5019.t1 | PANTHER | PTHR12620:SF11 | SPLICING FACTOR U2AF 35 KDA SUBUNIT-RELATED | 1 | 227 | 7.5E-119 |
| 5 | g5019.t1 | PANTHER | PTHR12620 | U2 SNRNP AUXILIARY FACTOR, SMALL SUBUNIT | 1 | 227 | 7.5E-119 |
| 7 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 18 | 37 | 4.9E-59 |
| 9 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 37 | 57 | 4.9E-59 |
| 8 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 77 | 92 | 4.9E-59 |
| 11 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 106 | 128 | 4.9E-59 |
| 10 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 133 | 157 | 4.9E-59 |
| 6 | g5019.t1 | PRINTS | PR01848 | U2 auxiliary factor small subunit signature | 168 | 180 | 4.9E-59 |
| 2 | g5019.t1 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 15 | 38 | 2.4E-7 |
| 1 | g5019.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 93 | 142 | 4.5E-6 |
| 3 | g5019.t1 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 152 | 176 | 1.8E-5 |
| 21 | g5019.t1 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 12 | 40 | 12.305 |
| 23 | g5019.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 44 | 149 | 11.673 |
| 22 | g5019.t1 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 151 | 178 | 10.906 |
| 16 | g5019.t1 | SMART | SM00356 | c3hfinal6 | 13 | 39 | 0.0051 |
| 17 | g5019.t1 | SMART | SM00361 | rrm2_1 | 68 | 145 | 3.5E-21 |
| 15 | g5019.t1 | SMART | SM00356 | c3hfinal6 | 151 | 177 | 0.29 |
| 12 | g5019.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 80 | 152 | 3.09E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5019/g5019.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5019.t1.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 transcript has been annotated with K12836 (splicing factor U2AF 35 kDa subunit)
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.
