Gene loci information

Transcript annotation

  • This transcript has been annotated as U2 small nuclear ribonucleoprotein B’’.

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 g11724 g11724.t3 TTS g11724.t3 18081733 18081733
chr_1 g11724 g11724.t3 isoform g11724.t3 18081772 18082605
chr_1 g11724 g11724.t3 exon g11724.t3.exon1 18081772 18082069
chr_1 g11724 g11724.t3 cds g11724.t3.CDS1 18081772 18082069
chr_1 g11724 g11724.t3 exon g11724.t3.exon2 18082143 18082266
chr_1 g11724 g11724.t3 cds g11724.t3.CDS2 18082143 18082266
chr_1 g11724 g11724.t3 exon g11724.t3.exon3 18082335 18082404
chr_1 g11724 g11724.t3 cds g11724.t3.CDS3 18082335 18082404
chr_1 g11724 g11724.t3 exon g11724.t3.exon4 18082465 18082605
chr_1 g11724 g11724.t3 cds g11724.t3.CDS4 18082465 18082605
chr_1 g11724 g11724.t3 TSS g11724.t3 18082678 18082678

Sequences

>g11724.t3 Gene=g11724 Length=633
ATGGATATTCGTCCAAATCATACTATCTATGTGAATAATTTAAATGAAAAGGTGAAAAAG
GACGAGTTAAAAAAGTCTCTTTACGCCATTTTTAGTCAATTTGGACAAATTTTGGATATT
ATTGCTCTTAAAACATTAAAGATGAGAGGACAAGCATTCATAATCTTTAAGGAAATAAAC
AGTGCTACGAATGCATTAAGAACAATGCAAGGATTTCCATTTTATGATAAACCAATGAAA
ATTAACTATGCGAAAACGGAAAGCGATGTAATTGCAAAGGCTAAAGGAACATTCAAAGAA
AGAGCAAAAAAAGTTAAATTACCGAAATCGACTGAAGCTAAAAAGAAATCTGTTGATCCT
GCACAAGCTGCAATTAATAGTTCTTCGATTGAGCAGCCACCTAACCAGATTCTTTTCCTT
ACGAATTTACCAGATGAAACAAATGAAATGATGCTTAGCATGCTCTTCAATCAATTCCCA
GGATTTAAAGAGGTCCGTTTGGTACCAGGTCGTCATGATATTGCATTTGTCGAGTTTGCA
TCAGAAATTCAAAGTGGTGCTGCTCGTGAAGCTCTTAATGGTTTCAAAATAACACCAACA
CATGCAATGAAAATTTCATTTGCTAAGAAATAA

>g11724.t3 Gene=g11724 Length=210
MDIRPNHTIYVNNLNEKVKKDELKKSLYAIFSQFGQILDIIALKTLKMRGQAFIIFKEIN
SATNALRTMQGFPFYDKPMKINYAKTESDVIAKAKGTFKERAKKVKLPKSTEAKKKSVDP
AQAAINSSSIEQPPNQILFLTNLPDETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFA
SEIQSGAAREALNGFKITPTHAMKISFAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11724.t3 CDD cd12246 RRM1_U1A_like 8 85 0.000
15 g11724.t3 CDD cd12479 RRM2_SNF 131 210 0.000
10 g11724.t3 Gene3D G3DSA:3.30.70.330 - 2 105 0.000
11 g11724.t3 Gene3D G3DSA:3.30.70.330 - 129 210 0.000
3 g11724.t3 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 2 126 0.000
5 g11724.t3 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 2 126 0.000
4 g11724.t3 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 131 210 0.000
6 g11724.t3 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 131 210 0.000
2 g11724.t3 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 9 79 0.000
1 g11724.t3 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 138 197 0.000
13 g11724.t3 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 7 86 15.392
12 g11724.t3 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 136 210 12.168
9 g11724.t3 SMART SM00360 rrm1_1 8 82 0.000
8 g11724.t3 SMART SM00360 rrm1_1 137 206 0.000
7 g11724.t3 SUPERFAMILY SSF54928 RNA-binding domain, RBD 5 198 0.000

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

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. There were no conditions that were differentially expressed