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.t8 TTS g11724.t8 18081733 18081733
chr_1 g11724 g11724.t8 isoform g11724.t8 18081772 18088387
chr_1 g11724 g11724.t8 exon g11724.t8.exon1 18081772 18082069
chr_1 g11724 g11724.t8 cds g11724.t8.CDS1 18081772 18082069
chr_1 g11724 g11724.t8 exon g11724.t8.exon2 18082134 18082266
chr_1 g11724 g11724.t8 cds g11724.t8.CDS2 18082134 18082266
chr_1 g11724 g11724.t8 exon g11724.t8.exon3 18082335 18082404
chr_1 g11724 g11724.t8 cds g11724.t8.CDS3 18082335 18082404
chr_1 g11724 g11724.t8 exon g11724.t8.exon4 18082465 18082693
chr_1 g11724 g11724.t8 cds g11724.t8.CDS4 18082465 18082605
chr_1 g11724 g11724.t8 exon g11724.t8.exon5 18088353 18088387
chr_1 g11724 g11724.t8 TSS g11724.t8 NA NA

Sequences

>g11724.t8 Gene=g11724 Length=765
TCTACAGAAAAAAAAAATAAAATTATATAAGATGTTTTGTTACCCCTTATTACACACGCC
GCAAAATAACAATTGAAATCGTGAAAAAGTTTTCAAACAAAAGATTAAATACATATTGAA
ATAATGGATATTCGTCCAAATCATACTATCTATGTGAATAATTTAAATGAAAAGGTGAAA
AAGGACGAGTTAAAAAAGTCTCTTTACGCCATTTTTAGTCAATTTGGACAAATTTTGGAT
ATTATTGCTCTTAAAACATTAAAGATGAGAGGACAAGCATTCATAATCTTTAAGGAAATA
AACAGTGCTACGAATGCATTAAGAACAATGCAAGGATTTCCATTTTATGATAAACCAATG
AAAATTAACTATGCGAAAACGGAAAGCGATGTAATTGCAAAGGCTAAAGGAACATTCAAA
GAAAGAGCAAAAAAAGTTAAATTACCGAAATCGACTGAAGAGAAGAAAGCTAAAAAGAAA
TCTGTTGATCCTGCACAAGCTGCAATTAATAGTTCTTCGATTGAGCAGCCACCTAACCAG
ATTCTTTTCCTTACGAATTTACCAGATGAAACAAATGAAATGATGCTTAGCATGCTCTTC
AATCAATTCCCAGGATTTAAAGAGGTCCGTTTGGTACCAGGTCGTCATGATATTGCATTT
GTCGAGTTTGCATCAGAAATTCAAAGTGGTGCTGCTCGTGAAGCTCTTAATGGTTTCAAA
ATAACACCAACACATGCAATGAAAATTTCATTTGCTAAGAAATAA

>g11724.t8 Gene=g11724 Length=213
MDIRPNHTIYVNNLNEKVKKDELKKSLYAIFSQFGQILDIIALKTLKMRGQAFIIFKEIN
SATNALRTMQGFPFYDKPMKINYAKTESDVIAKAKGTFKERAKKVKLPKSTEEKKAKKKS
VDPAQAAINSSSIEQPPNQILFLTNLPDETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFV
EFASEIQSGAAREALNGFKITPTHAMKISFAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11724.t8 CDD cd12246 RRM1_U1A_like 8 85 6.62069E-51
11 g11724.t8 CDD cd12479 RRM2_SNF 134 213 2.11916E-51
9 g11724.t8 Gene3D G3DSA:3.30.70.330 - 2 104 4.1E-31
8 g11724.t8 Gene3D G3DSA:3.30.70.330 - 132 213 7.5E-22
14 g11724.t8 MobiDBLite mobidb-lite consensus disorder prediction 106 121 -
15 g11724.t8 MobiDBLite mobidb-lite consensus disorder prediction 106 129 -
4 g11724.t8 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 2 128 5.4E-107
6 g11724.t8 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 2 128 5.4E-107
3 g11724.t8 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 134 213 5.4E-107
5 g11724.t8 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 134 213 5.4E-107
2 g11724.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 9 79 1.4E-10
1 g11724.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 141 200 2.7E-13
17 g11724.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 7 86 15.392
16 g11724.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 139 213 12.168
13 g11724.t8 SMART SM00360 rrm1_1 8 82 2.3E-14
12 g11724.t8 SMART SM00360 rrm1_1 140 209 8.4E-11
7 g11724.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 5 201 3.33E-27

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.

Raw TPM values