General information for g11724.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U1 small nuclear ribonucleoprotein A.
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.t6 | TTS | g11724.t6 | 18081733 | 18081733 |
| chr_1 | g11724 | g11724.t6 | isoform | g11724.t6 | 18081772 | 18082605 |
| chr_1 | g11724 | g11724.t6 | exon | g11724.t6.exon1 | 18081772 | 18082069 |
| chr_1 | g11724 | g11724.t6 | cds | g11724.t6.CDS1 | 18081772 | 18082069 |
| chr_1 | g11724 | g11724.t6 | exon | g11724.t6.exon2 | 18082134 | 18082605 |
| chr_1 | g11724 | g11724.t6 | cds | g11724.t6.CDS2 | 18082134 | 18082243 |
| chr_1 | g11724 | g11724.t6 | TSS | g11724.t6 | 18082678 | 18082678 |
Sequences
>g11724.t6 Gene=g11724 Length=770
ATGGATATTCGTCCAAATCATACTATCTATGTGAATAATTTAAATGAAAAGGTGAAAAAG
GACGAGTTAAAAAAGTCTCTTTACGCCATTTTTAGTCAATTTGGACAAATTTTGGATATT
ATTGCTCTTAAAACATTAAAGGTAAGGTAATAATTTACGTTTTAAATCAATTAATTGTCT
AAATCACTTAAGTTTATTTAGATGAGAGGACAAGCATTCATAATCTTTAAGGAAATAAAC
AGTGCTACGAATGCATTAAGAACAATGCAAGGTAAAATGAAATTATAAAAACTACTAATG
TACAAAAGTAAAAATATTCAAATATATTTTTCTTTTTAGGATTTCCATTTTATGATAAAC
CAATGAAAATTAACTATGCGAAAACGGAAAGCGATGTAATTGCAAAGGCTAAAGGAACAT
TCAAAGAAAGAGCAAAAAAAGTTAAATTACCGAAATCGACTGAAGAGAAGAAAGCTAAAA
AGAAATCTGTTGATCCTGCACAAGCTGCAATTAATAGTTCTTCGATTGAGCAGCCACCTA
ACCAGATTCTTTTCCTTACGAATTTACCAGATGAAACAAATGAAATGATGCTTAGCATGC
TCTTCAATCAATTCCCAGGATTTAAAGAGGTCCGTTTGGTACCAGGTCGTCATGATATTG
CATTTGTCGAGTTTGCATCAGAAATTCAAAGTGGTGCTGCTCGTGAAGCTCTTAATGGTT
TCAAAATAACACCAACACATGCAATGAAAATTTCATTTGCTAAGAAATAA
>g11724.t6 Gene=g11724 Length=135
MKINYAKTESDVIAKAKGTFKERAKKVKLPKSTEEKKAKKKSVDPAQAAINSSSIEQPPN
QILFLTNLPDETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFASEIQSGAAREALNGF
KITPTHAMKISFAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11724.t6 | CDD | cd12479 | RRM2_SNF | 56 | 135 | 2.34023E-51 |
| 5 | g11724.t6 | Gene3D | G3DSA:3.30.70.330 | - | 54 | 135 | 2.4E-22 |
| 8 | g11724.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 52 | - |
| 9 | g11724.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 43 | - |
| 2 | g11724.t6 | PANTHER | PTHR10501:SF61 | U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B’’ | 1 | 135 | 1.6E-52 |
| 3 | g11724.t6 | PANTHER | PTHR10501 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B | 1 | 135 | 1.6E-52 |
| 1 | g11724.t6 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 63 | 122 | 1.0E-13 |
| 10 | g11724.t6 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 61 | 135 | 12.168 |
| 7 | g11724.t6 | SMART | SM00360 | rrm1_1 | 62 | 131 | 8.4E-11 |
| 4 | g11724.t6 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 54 | 134 | 1.88E-17 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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