Gene loci information

Transcript annotation

  • This transcript has been annotated as Splicing factor U2AF 50 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_1 g9998 g9998.t5 TSS g9998.t5 6489537 6489537
chr_1 g9998 g9998.t5 isoform g9998.t5 6489677 6492334
chr_1 g9998 g9998.t5 exon g9998.t5.exon1 6489677 6489680
chr_1 g9998 g9998.t5 cds g9998.t5.CDS1 6489677 6489680
chr_1 g9998 g9998.t5 exon g9998.t5.exon2 6489778 6489865
chr_1 g9998 g9998.t5 cds g9998.t5.CDS2 6489778 6489865
chr_1 g9998 g9998.t5 exon g9998.t5.exon3 6489931 6490334
chr_1 g9998 g9998.t5 cds g9998.t5.CDS3 6489931 6490334
chr_1 g9998 g9998.t5 exon g9998.t5.exon4 6490397 6490581
chr_1 g9998 g9998.t5 cds g9998.t5.CDS4 6490397 6490581
chr_1 g9998 g9998.t5 exon g9998.t5.exon5 6491676 6492103
chr_1 g9998 g9998.t5 cds g9998.t5.CDS5 6491676 6492103
chr_1 g9998 g9998.t5 exon g9998.t5.exon6 6492177 6492334
chr_1 g9998 g9998.t5 cds g9998.t5.CDS6 6492177 6492201
chr_1 g9998 g9998.t5 TTS g9998.t5 6493093 6493093

Sequences

>g9998.t5 Gene=g9998 Length=1267
ATGTCTGACCGAGAGAGAGACCGTCGAAGACGCAATTCGAGAGATAGAGGAATGGATCGA
AGAAGATCAAGATCTAGAGATAGACGTCGAAGTCGATCAAAAGACCGAAACTCTCGAATG
TCTCGTCGAAGAAAAGCATCACTTTATTGGGACGTTCCACCACCAGGTTTTGAACACATC
ACACCGCTTCAATATAAAGCTATGCAAGCGGCCGGTCAAATTCCGGCAAATATTGTTGCT
GATACTCCTCAAGCTGCTGTTCCAGTTGTTGGTTCTACAATAACTCGTCAAGCAAGAAGA
TTATATGTAGGAAATATTCCTTTTGGTGTAACAGAAGAAGAAATGATGGAATTCTTTAAT
CAACAAATGCATCTCTCTGGACTTGCACAAGCTGCTGGAAATCCAGTGCTTGCATGTCAG
ATAAATCTGGATAAAAATTTTGCATTCTTGGAATTTAGATCAATTGATGAAACAACACAA
GCAATGGCTTTTGATGGAATAAATTTCAAAGGTCAAAGTTTGAAAATTCGTCGCCCACAT
GATTATCAGCCGATGCCTGGTATGACAGATTCAGTGCCAGTTGCAGCTGCTCCTGTTCTT
GGTGTCATTTCTACTGTTGTGCCCGATTCACCTCATAAAATCTTCATTGGTGGTTTACCT
AATTATTTAAATGAAGATCAGGTCAAAGAATTACTTTTATCTTTTGGACAATTGAAAGCA
TTCAATTTAGTAAAAGATGCAGCAACTGGATTATCAAAGGGATATGCTTTTGCCGAATAC
GTTGAATATGCAATTACAGATCAAGCAATTGCAGGATTGAATGGAATGCAGCTAGGTGAT
AAGAAATTGATTGTACAGAGAGCAAGTGTTGGTGCAAAAAATGCAGCAACAGTCGGACAA
GTTGCACCTGTACAAATTCAAGTTCCTGGATTGTCAATCGTTGGAGCATCTGGTCCTGCT
ACTGAAGTTCTATGTCTTTTGAATATGGTCACACCGGACGAATTGAAGGATGAAGAAGAA
TATGAGGATATTCTTGAAGATATCAAAGAGGAATGTAACAAATATGGTGTTGTTCGCTCA
ATTGAGATTCCGAGACCCATTGAAGGCAAGTGTCGACGTGCCAGGTTGTGGTAAAGTATT
TGTTGAATTTAATTCAATTATGGATTGTCAGCATGCTCAGCAAGCACTAACTGGACGTAA
ATTTAGCGATCGTGTTGTGGTGACATCTTATTTTGATCCAGATAAATACCATCGTCGTGA
ATTTTAA

>g9998.t5 Gene=g9998 Length=377
MSDRERDRRRRNSRDRGMDRRRSRSRDRRRSRSKDRNSRMSRRRKASLYWDVPPPGFEHI
TPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTITRQARRLYVGNIPFGVTEEEMMEFFN
QQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINFKGQSLKIRRPH
DYQPMPGMTDSVPVAAAPVLGVISTVVPDSPHKIFIGGLPNYLNEDQVKELLLSFGQLKA
FNLVKDAATGLSKGYAFAEYVEYAITDQAIAGLNGMQLGDKKLIVQRASVGAKNAATVGQ
VAPVQIQVPGLSIVGASGPATEVLCLLNMVTPDELKDEEEYEDILEDIKEECNKYGVVRS
IEIPRPIEGKCRRARLW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g9998.t5 CDD cd12230 RRM1_U2AF65 98 179 1.09398E-51
12 g9998.t5 CDD cd12231 RRM2_U2AF65 212 288 1.67046E-51
11 g9998.t5 CDD cd12232 RRM3_U2AF65 321 369 1.34256E-25
8 g9998.t5 Gene3D G3DSA:3.30.70.330 - 99 285 6.3E-61
10 g9998.t5 Gene3D G3DSA:3.30.70.330 - 185 263 6.3E-61
9 g9998.t5 Gene3D G3DSA:3.30.70.330 - 318 375 1.1E-15
16 g9998.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 47 -
17 g9998.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
18 g9998.t5 MobiDBLite mobidb-lite consensus disorder prediction 23 43 -
3 g9998.t5 PANTHER PTHR23139:SF9 SPLICING FACTOR U2AF 65 KDA SUBUNIT 4 369 9.1E-151
4 g9998.t5 PANTHER PTHR23139 RNA-BINDING PROTEIN 4 369 9.1E-151
1 g9998.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 101 174 3.7E-6
2 g9998.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 214 283 1.1E-15
20 g9998.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 99 181 13.942
21 g9998.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 212 290 15.562
15 g9998.t5 SMART SM00360 rrm1_1 100 177 9.5E-14
14 g9998.t5 SMART SM00360 rrm1_1 213 286 2.3E-17
7 g9998.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 99 184 3.49E-20
6 g9998.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 207 294 4.84E-21
5 g9998.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 320 366 2.19E-6
19 g9998.t5 TIGRFAM TIGR01642 U2AF_lg: U2 snRNP auxilliary factor, large subunit, splicing factor 4 368 3.9E-116

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:0006397 mRNA processing BP
GO:0005634 nucleus CC
GO:0003723 RNA binding MF
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