General information for g9998.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor U2AF 50 kDa subunit.
Parent gene
- The parent gene g9998 is located on chr_1: 6492178..6492702 (+ 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_1 | g9998 | g9998.t4 | TSS | g9998.t4 | 6489537 | 6489537 |
| chr_1 | g9998 | g9998.t4 | isoform | g9998.t4 | 6489677 | 6491149 |
| chr_1 | g9998 | g9998.t4 | exon | g9998.t4.exon1 | 6489677 | 6489680 |
| chr_1 | g9998 | g9998.t4 | cds | g9998.t4.CDS1 | 6489677 | 6489680 |
| chr_1 | g9998 | g9998.t4 | exon | g9998.t4.exon2 | 6489778 | 6489865 |
| chr_1 | g9998 | g9998.t4 | cds | g9998.t4.CDS2 | 6489778 | 6489865 |
| chr_1 | g9998 | g9998.t4 | exon | g9998.t4.exon3 | 6489931 | 6490334 |
| chr_1 | g9998 | g9998.t4 | cds | g9998.t4.CDS3 | 6489931 | 6490334 |
| chr_1 | g9998 | g9998.t4 | exon | g9998.t4.exon4 | 6490397 | 6491149 |
| chr_1 | g9998 | g9998.t4 | cds | g9998.t4.CDS4 | 6490397 | 6490611 |
| chr_1 | g9998 | g9998.t4 | TTS | g9998.t4 | 6491505 | 6491505 |
Sequences
>g9998.t4 Gene=g9998 Length=1249
ATGTCTGACCGAGAGAGAGACCGTCGAAGACGCAATTCGAGAGATAGAGGAATGGATCGA
AGAAGATCAAGATCTAGAGATAGACGTCGAAGTCGATCAAAAGACCGAAACTCTCGAATG
TCTCGTCGAAGAAAAGCATCACTTTATTGGGACGTTCCACCACCAGGTTTTGAACACATC
ACACCGCTTCAATATAAAGCTATGCAAGCGGCCGGTCAAATTCCGGCAAATATTGTTGCT
GATACTCCTCAAGCTGCTGTTCCAGTTGTTGGTTCTACAATAACTCGTCAAGCAAGAAGA
TTATATGTAGGAAATATTCCTTTTGGTGTAACAGAAGAAGAAATGATGGAATTCTTTAAT
CAACAAATGCATCTCTCTGGACTTGCACAAGCTGCTGGAAATCCAGTGCTTGCATGTCAG
ATAAATCTGGATAAAAATTTTGCATTCTTGGAATTTAGATCAATTGATGAAACAACACAA
GCAATGGCTTTTGATGGAATAAATTTCAAAGGTCAAAGTTTGAAAATTCGTCGCCCACAT
GATTATCAGCCGATGCCTGGTATGACAGATTCAGTGCCAGTTGCAGCTGCTCCTGTTCTT
GGTGTCATTTCTACTGTTGTGCCCGATTCACCTCATAAAATCTTCATTGGTGGTTTACCT
AATTATTTAAATGAAGATCAGGTATGTTTTTCAATTTTCATGCGTGTTTAATTTTGATGA
TAAAAAAATTATGTGAAAGTTCAGATGCATTCATATCAAAGAATTTAATTGAAAAGCTCA
TTTAAATCTTCTAATGTGTCAGCAGTTTATGTTAAAATTTTTAATAATTGCTTCAATGTA
ATCGAGTTTTTCGTAAATTTCCTTTATTGCATACTGAACTGTTTTCACACACAATGAGAT
TTTTTCAACGTTAGTTTTACCTTACATAAAAACAATTTTTTGTCTCAGGTGCTTTACAGT
TATACACTCGCCACAAACAAAAGTGCACCAAGTAAAGCTGAACAGCTTTTTTTGTTAAAA
CACATTTTTATTCCACTTTAGCAAAATTAGGGAAATTGTGCGGGAAAAATGTAAAGTATG
AAAAGTTTTGTTTAACAGCTTTGTCCACAGCGTTTTAGGATTTCGTACCGTCCAGAGTCC
TTAAAACAGCATTTTAAATTTCCTTTAGGTTTTATTCTAGTGCTTAAACTTTCAATTGTG
AAATTCTACGTACGTACAATTTTCAGCCAAGAATCATTATTTTAATTTT
>g9998.t4 Gene=g9998 Length=236
MSDRERDRRRRNSRDRGMDRRRSRSRDRRRSRSKDRNSRMSRRRKASLYWDVPPPGFEHI
TPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTITRQARRLYVGNIPFGVTEEEMMEFFN
QQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINFKGQSLKIRRPH
DYQPMPGMTDSVPVAAAPVLGVISTVVPDSPHKIFIGGLPNYLNEDQVCFSIFMRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9998.t4 | CDD | cd12230 | RRM1_U2AF65 | 98 | 179 | 1.53427E-52 |
| 5 | g9998.t4 | Gene3D | G3DSA:3.30.70.330 | - | 94 | 192 | 1.1E-32 |
| 8 | g9998.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 47 | - |
| 9 | g9998.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 10 | g9998.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 43 | - |
| 2 | g9998.t4 | PANTHER | PTHR23139:SF9 | SPLICING FACTOR U2AF 65 KDA SUBUNIT | 4 | 228 | 2.3E-82 |
| 3 | g9998.t4 | PANTHER | PTHR23139 | RNA-BINDING PROTEIN | 4 | 228 | 2.3E-82 |
| 1 | g9998.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 101 | 174 | 1.6E-6 |
| 11 | g9998.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 99 | 181 | 13.942 |
| 7 | g9998.t4 | SMART | SM00360 | rrm1_1 | 100 | 177 | 9.5E-14 |
| 4 | g9998.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 99 | 184 | 1.34E-20 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
