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.t1 TSS g9998.t1 6489537 6489537
chr_1 g9998 g9998.t1 isoform g9998.t1 6489677 6492334
chr_1 g9998 g9998.t1 exon g9998.t1.exon1 6489677 6489680
chr_1 g9998 g9998.t1 cds g9998.t1.CDS1 6489677 6489680
chr_1 g9998 g9998.t1 exon g9998.t1.exon2 6489778 6489865
chr_1 g9998 g9998.t1 cds g9998.t1.CDS2 6489778 6489865
chr_1 g9998 g9998.t1 exon g9998.t1.exon3 6489931 6490334
chr_1 g9998 g9998.t1 cds g9998.t1.CDS3 6489931 6490334
chr_1 g9998 g9998.t1 exon g9998.t1.exon4 6490397 6490581
chr_1 g9998 g9998.t1 cds g9998.t1.CDS4 6490397 6490581
chr_1 g9998 g9998.t1 exon g9998.t1.exon5 6491676 6492099
chr_1 g9998 g9998.t1 cds g9998.t1.CDS5 6491676 6492099
chr_1 g9998 g9998.t1 exon g9998.t1.exon6 6492177 6492334
chr_1 g9998 g9998.t1 cds g9998.t1.CDS6 6492177 6492334
chr_1 g9998 g9998.t1 TTS g9998.t1 6493093 6493093

Sequences

>g9998.t1 Gene=g9998 Length=1263
ATGTCTGACCGAGAGAGAGACCGTCGAAGACGCAATTCGAGAGATAGAGGAATGGATCGA
AGAAGATCAAGATCTAGAGATAGACGTCGAAGTCGATCAAAAGACCGAAACTCTCGAATG
TCTCGTCGAAGAAAAGCATCACTTTATTGGGACGTTCCACCACCAGGTTTTGAACACATC
ACACCGCTTCAATATAAAGCTATGCAAGCGGCCGGTCAAATTCCGGCAAATATTGTTGCT
GATACTCCTCAAGCTGCTGTTCCAGTTGTTGGTTCTACAATAACTCGTCAAGCAAGAAGA
TTATATGTAGGAAATATTCCTTTTGGTGTAACAGAAGAAGAAATGATGGAATTCTTTAAT
CAACAAATGCATCTCTCTGGACTTGCACAAGCTGCTGGAAATCCAGTGCTTGCATGTCAG
ATAAATCTGGATAAAAATTTTGCATTCTTGGAATTTAGATCAATTGATGAAACAACACAA
GCAATGGCTTTTGATGGAATAAATTTCAAAGGTCAAAGTTTGAAAATTCGTCGCCCACAT
GATTATCAGCCGATGCCTGGTATGACAGATTCAGTGCCAGTTGCAGCTGCTCCTGTTCTT
GGTGTCATTTCTACTGTTGTGCCCGATTCACCTCATAAAATCTTCATTGGTGGTTTACCT
AATTATTTAAATGAAGATCAGGTCAAAGAATTACTTTTATCTTTTGGACAATTGAAAGCA
TTCAATTTAGTAAAAGATGCAGCAACTGGATTATCAAAGGGATATGCTTTTGCCGAATAC
GTTGAATATGCAATTACAGATCAAGCAATTGCAGGATTGAATGGAATGCAGCTAGGTGAT
AAGAAATTGATTGTACAGAGAGCAAGTGTTGGTGCAAAAAATGCAGCAACAGTCGGACAA
GTTGCACCTGTACAAATTCAAGTTCCTGGATTGTCAATCGTTGGAGCATCTGGTCCTGCT
ACTGAAGTTCTATGTCTTTTGAATATGGTCACACCGGACGAATTGAAGGATGAAGAAGAA
TATGAGGATATTCTTGAAGATATCAAAGAGGAATGTAACAAATATGGTGTTGTTCGCTCA
ATTGAGATTCCGAGACCCATTGAAGGTGTCGACGTGCCAGGTTGTGGTAAAGTATTTGTT
GAATTTAATTCAATTATGGATTGTCAGCATGCTCAGCAAGCACTAACTGGACGTAAATTT
AGCGATCGTGTTGTGGTGACATCTTATTTTGATCCAGATAAATACCATCGTCGTGAATTT
TAA

>g9998.t1 Gene=g9998 Length=420
MSDRERDRRRRNSRDRGMDRRRSRSRDRRRSRSKDRNSRMSRRRKASLYWDVPPPGFEHI
TPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTITRQARRLYVGNIPFGVTEEEMMEFFN
QQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINFKGQSLKIRRPH
DYQPMPGMTDSVPVAAAPVLGVISTVVPDSPHKIFIGGLPNYLNEDQVKELLLSFGQLKA
FNLVKDAATGLSKGYAFAEYVEYAITDQAIAGLNGMQLGDKKLIVQRASVGAKNAATVGQ
VAPVQIQVPGLSIVGASGPATEVLCLLNMVTPDELKDEEEYEDILEDIKEECNKYGVVRS
IEIPRPIEGVDVPGCGKVFVEFNSIMDCQHAQQALTGRKFSDRVVVTSYFDPDKYHRREF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g9998.t1 CDD cd12230 RRM1_U2AF65 98 179 2.82016E-51
12 g9998.t1 CDD cd12231 RRM2_U2AF65 212 288 9.35303E-51
11 g9998.t1 CDD cd12232 RRM3_U2AF65 321 408 1.01884E-45
8 g9998.t1 Gene3D G3DSA:3.30.70.330 - 99 285 8.2E-61
10 g9998.t1 Gene3D G3DSA:3.30.70.330 - 185 263 8.2E-61
9 g9998.t1 Gene3D G3DSA:3.30.70.330 - 318 420 3.1E-33
18 g9998.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 47 -
19 g9998.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
20 g9998.t1 MobiDBLite mobidb-lite consensus disorder prediction 23 43 -
4 g9998.t1 PANTHER PTHR23139:SF9 SPLICING FACTOR U2AF 65 KDA SUBUNIT 4 417 1.5E-175
5 g9998.t1 PANTHER PTHR23139 RNA-BINDING PROTEIN 4 417 1.5E-175
1 g9998.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 101 174 4.4E-6
2 g9998.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 214 283 1.4E-15
3 g9998.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 346 405 2.3E-5
22 g9998.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 99 181 13.942
23 g9998.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 212 290 15.562
24 g9998.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 322 412 8.791
17 g9998.t1 SMART SM00360 rrm1_1 100 177 9.5E-14
16 g9998.t1 SMART SM00360 rrm1_1 213 286 2.3E-17
14 g9998.t1 SMART SM00361 rrm2_1 323 408 0.0027
15 g9998.t1 SMART SM00360 rrm1_1 323 408 0.37
7 g9998.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 99 184 4.3E-20
6 g9998.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 208 415 2.45E-27
21 g9998.t1 TIGRFAM TIGR01642 U2AF_lg: U2 snRNP auxilliary factor, large subunit, splicing factor 4 420 9.8E-139

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

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.

Raw TPM values