Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine/arginine-rich splicing factor 2.

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 g5936 g5936.t3 TSS g5936.t3 12907087 12907087
chr_2 g5936 g5936.t3 isoform g5936.t3 12907278 12908639
chr_2 g5936 g5936.t3 exon g5936.t3.exon1 12907278 12907460
chr_2 g5936 g5936.t3 exon g5936.t3.exon2 12907746 12907850
chr_2 g5936 g5936.t3 cds g5936.t3.CDS1 12907797 12907850
chr_2 g5936 g5936.t3 exon g5936.t3.exon3 12907924 12908069
chr_2 g5936 g5936.t3 cds g5936.t3.CDS2 12907924 12908069
chr_2 g5936 g5936.t3 exon g5936.t3.exon4 12908135 12908194
chr_2 g5936 g5936.t3 cds g5936.t3.CDS3 12908135 12908194
chr_2 g5936 g5936.t3 exon g5936.t3.exon5 12908253 12908324
chr_2 g5936 g5936.t3 cds g5936.t3.CDS4 12908253 12908324
chr_2 g5936 g5936.t3 exon g5936.t3.exon6 12908389 12908436
chr_2 g5936 g5936.t3 cds g5936.t3.CDS5 12908389 12908436
chr_2 g5936 g5936.t3 exon g5936.t3.exon7 12908492 12908639
chr_2 g5936 g5936.t3 cds g5936.t3.CDS6 12908492 12908639
chr_2 g5936 g5936.t3 TTS g5936.t3 12909252 12909252

Sequences

>g5936.t3 Gene=g5936 Length=762
AGTGCTGACTCCTATCTAAAATCAAATTTAAGCTACTTTATTTCTTCATGAATTTTTTGC
ATTATCTTACTTTGACAATTTCATGACATTTCTTCAAAACGTTTGCTGCAATCGTGCAAC
TTTCTCTGAGTTTAGCTATATCATCCTCAGATTTTATTTCAATGCATCCAGACATGTCAG
CAGTAATTGATATTTCATCATCAAAACGAATTCAAGAACAAAAGAACAACAAACATGTCA
TATTCAGCTAGACCACCGCCCAAAATTGAGGGCATGATTTCTTTAAAAGTTGACAATTTG
ACTTATCGAACTACTCCCGAAGACTTGAGACGAGTTTTTGAGCGATGCGGTGATGTTGGT
GACATTTATATTCCAAGAGATAGACATACTCGTGAGTCGAGAGGATTTGCTTTTGTTCGA
TTTTATGACAAACGTGATGCTGAGGAAGCTCTTCAAGAAATGGATGGAAGAATGCTTGAT
GGACGTGAATTGAGAGTGCAAATGGCCAGATATGGGAGACCTACATCTCCACAAAGACGT
TCTAACAGACACGATCGTCGCCGAAGATCCCGTTCGAGAGACCGTAGAGGAGGTGGAGGT
GGAAGACGCTCAAGATCACGTTCAAGAGACCGAAGAGGACGCCGTCGTTCATACTCACGT
TCCAAATCTCGTTCAAGATCAGCAAATAGTCGCAGCAACAGCAAATCTTCACGCGATCGT
TCACGCTCTCCAGTTCGTAAGAATCGCAGCTCAAGCAATTAA

>g5936.t3 Gene=g5936 Length=175
MSYSARPPPKIEGMISLKVDNLTYRTTPEDLRRVFERCGDVGDIYIPRDRHTRESRGFAF
VRFYDKRDAEEALQEMDGRMLDGRELRVQMARYGRPTSPQRRSNRHDRRRRSRSRDRRGG
GGGRRSRSRSRDRRGRRRSYSRSKSRSRSANSRSNSKSSRDRSRSPVRKNRSSSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5936.t3 CDD cd12311 RRM_SRSF2_SRSF8 17 89 5.52768E-41
5 g5936.t3 Gene3D G3DSA:3.30.70.330 - 4 130 2.7E-28
9 g5936.t3 MobiDBLite mobidb-lite consensus disorder prediction 87 175 -
10 g5936.t3 MobiDBLite mobidb-lite consensus disorder prediction 102 118 -
8 g5936.t3 MobiDBLite mobidb-lite consensus disorder prediction 127 144 -
2 g5936.t3 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 6 171 2.6E-42
3 g5936.t3 PANTHER PTHR23147:SF145 SERINE/ARGININE-RICH SPLICING FACTOR 2 6 171 2.6E-42
1 g5936.t3 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 18 87 1.9E-22
11 g5936.t3 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 15 93 19.621
7 g5936.t3 SMART SM00360 rrm1_1 16 89 1.1E-26
4 g5936.t3 SUPERFAMILY SSF54928 RNA-binding domain, RBD 7 123 7.93E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5936/g5936.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5936.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003723 RNA binding MF
GO:0000381 regulation of alternative mRNA splicing, via spliceosome BP
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