General information for g11724.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U2 small nuclear ribonucleoprotein B’’.
Parent gene
- The parent gene g11724 is located on chr_1: 18081772..18088387 (- strand)
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.t1 | TTS | g11724.t1 | 18081733 | 18081733 |
| chr_1 | g11724 | g11724.t1 | isoform | g11724.t1 | 18081772 | 18082605 |
| chr_1 | g11724 | g11724.t1 | exon | g11724.t1.exon1 | 18081772 | 18082069 |
| chr_1 | g11724 | g11724.t1 | cds | g11724.t1.CDS1 | 18081772 | 18082069 |
| chr_1 | g11724 | g11724.t1 | exon | g11724.t1.exon2 | 18082134 | 18082266 |
| chr_1 | g11724 | g11724.t1 | cds | g11724.t1.CDS2 | 18082134 | 18082266 |
| chr_1 | g11724 | g11724.t1 | exon | g11724.t1.exon3 | 18082335 | 18082404 |
| chr_1 | g11724 | g11724.t1 | cds | g11724.t1.CDS3 | 18082335 | 18082404 |
| chr_1 | g11724 | g11724.t1 | exon | g11724.t1.exon4 | 18082465 | 18082605 |
| chr_1 | g11724 | g11724.t1 | cds | g11724.t1.CDS4 | 18082465 | 18082605 |
| chr_1 | g11724 | g11724.t1 | TSS | g11724.t1 | 18082678 | 18082678 |
Sequences
>g11724.t1 Gene=g11724 Length=642
ATGGATATTCGTCCAAATCATACTATCTATGTGAATAATTTAAATGAAAAGGTGAAAAAG
GACGAGTTAAAAAAGTCTCTTTACGCCATTTTTAGTCAATTTGGACAAATTTTGGATATT
ATTGCTCTTAAAACATTAAAGATGAGAGGACAAGCATTCATAATCTTTAAGGAAATAAAC
AGTGCTACGAATGCATTAAGAACAATGCAAGGATTTCCATTTTATGATAAACCAATGAAA
ATTAACTATGCGAAAACGGAAAGCGATGTAATTGCAAAGGCTAAAGGAACATTCAAAGAA
AGAGCAAAAAAAGTTAAATTACCGAAATCGACTGAAGAGAAGAAAGCTAAAAAGAAATCT
GTTGATCCTGCACAAGCTGCAATTAATAGTTCTTCGATTGAGCAGCCACCTAACCAGATT
CTTTTCCTTACGAATTTACCAGATGAAACAAATGAAATGATGCTTAGCATGCTCTTCAAT
CAATTCCCAGGATTTAAAGAGGTCCGTTTGGTACCAGGTCGTCATGATATTGCATTTGTC
GAGTTTGCATCAGAAATTCAAAGTGGTGCTGCTCGTGAAGCTCTTAATGGTTTCAAAATA
ACACCAACACATGCAATGAAAATTTCATTTGCTAAGAAATAA
>g11724.t1 Gene=g11724 Length=213
MDIRPNHTIYVNNLNEKVKKDELKKSLYAIFSQFGQILDIIALKTLKMRGQAFIIFKEIN
SATNALRTMQGFPFYDKPMKINYAKTESDVIAKAKGTFKERAKKVKLPKSTEEKKAKKKS
VDPAQAAINSSSIEQPPNQILFLTNLPDETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFV
EFASEIQSGAAREALNGFKITPTHAMKISFAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11724.t1 | CDD | cd12246 | RRM1_U1A_like | 8 | 85 | 6.62069E-51 |
| 11 | g11724.t1 | CDD | cd12479 | RRM2_SNF | 134 | 213 | 2.11916E-51 |
| 9 | g11724.t1 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 104 | 4.1E-31 |
| 8 | g11724.t1 | Gene3D | G3DSA:3.30.70.330 | - | 132 | 213 | 7.5E-22 |
| 14 | g11724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 121 | - |
| 15 | g11724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 129 | - |
| 4 | g11724.t1 | PANTHER | PTHR10501:SF63 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A | 2 | 128 | 5.4E-107 |
| 6 | g11724.t1 | PANTHER | PTHR10501 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B | 2 | 128 | 5.4E-107 |
| 3 | g11724.t1 | PANTHER | PTHR10501:SF63 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A | 134 | 213 | 5.4E-107 |
| 5 | g11724.t1 | PANTHER | PTHR10501 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B | 134 | 213 | 5.4E-107 |
| 2 | g11724.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 9 | 79 | 1.4E-10 |
| 1 | g11724.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 141 | 200 | 2.7E-13 |
| 17 | g11724.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 7 | 86 | 15.392 |
| 16 | g11724.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 139 | 213 | 12.168 |
| 13 | g11724.t1 | SMART | SM00360 | rrm1_1 | 8 | 82 | 2.3E-14 |
| 12 | g11724.t1 | SMART | SM00360 | rrm1_1 | 140 | 209 | 8.4E-11 |
| 7 | g11724.t1 | 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
- This transcript has been annotated with K11094 (U2 small nuclear ribonucleoprotein B’’)
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.
