General information for g11061.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U1 small nuclear ribonucleoprotein 70 kDa.
Parent gene
- The parent gene g11061 is located on chr_1: 13739132..13741509 (+ 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 | g11061 | g11061.t2 | TSS | g11061.t2 | 13736261 | 13736261 |
| chr_1 | g11061 | g11061.t2 | isoform | g11061.t2 | 13736448 | 13737044 |
| chr_1 | g11061 | g11061.t2 | exon | g11061.t2.exon1 | 13736448 | 13736591 |
| chr_1 | g11061 | g11061.t2 | cds | g11061.t2.CDS1 | 13736448 | 13736591 |
| chr_1 | g11061 | g11061.t2 | exon | g11061.t2.exon2 | 13736654 | 13736836 |
| chr_1 | g11061 | g11061.t2 | cds | g11061.t2.CDS2 | 13736654 | 13736836 |
| chr_1 | g11061 | g11061.t2 | exon | g11061.t2.exon3 | 13736900 | 13737044 |
| chr_1 | g11061 | g11061.t2 | cds | g11061.t2.CDS3 | 13736900 | 13737043 |
| chr_1 | g11061 | g11061.t2 | TTS | g11061.t2 | NA | NA |
Sequences
>g11061.t2 Gene=g11061 Length=472
ATGACTCAATATCTGCCAGCCAATTTATTGGCTTTATTCGCTGCTCGCGATCCTATTCCA
TTTTTGCCACCTCCTGATAAACTTCCACATGAGAAAAAGACGCGAGGATATTTAGGAGTT
GGTTCATTTTTAGATCAATTTGAGGATCCTAAAGATACACCACCACCCACAAGAGTCGAA
ACAAAAGAAGAACGAATGGAAAGACGTCGAAGAGAAAAAGCTGAGCAAGTAGCTTACAAG
CTTGAACGAGAAATAGCACTTTGGGATCCAACATCGATCGAAAATACAACAGAAGATCCT
TTCAAAACACTTTTTGTTGCTCGTATAAATTATGACACATCAGAATCGAAATTAAGAAGA
GAATTTGAAGTGTATGGACCAATAAGGAAAATTATAATGATCCACGATCAAGATTCAGGC
AAACCTCGTGGTTATGCGTTTATTGAGTACGAACATGAAAGAGACATGCATT
>g11061.t2 Gene=g11061 Length=157
MTQYLPANLLALFAARDPIPFLPPPDKLPHEKKTRGYLGVGSFLDQFEDPKDTPPPTRVE
TKEERMERRRREKAEQVAYKLEREIALWDPTSIENTTEDPFKTLFVARINYDTSESKLRR
EFEVYGPIRKIIMIHDQDSGKPRGYAFIEYEHERDMH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11061.t2 | Gene3D | G3DSA:3.30.70.330 | - | 56 | 157 | 4.2E-18 |
| 6 | g11061.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 74 | - |
| 7 | g11061.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 74 | - |
| 3 | g11061.t2 | PANTHER | PTHR13952:SF16 | - | 1 | 157 | 1.4E-65 |
| 4 | g11061.t2 | PANTHER | PTHR13952 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD | 1 | 157 | 1.4E-65 |
| 1 | g11061.t2 | Pfam | PF12220 | U1 small nuclear ribonucleoprotein of 70kDa MW N terminal | 4 | 91 | 2.6E-25 |
| 2 | g11061.t2 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 104 | 156 | 2.0E-12 |
| 9 | g11061.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 102 | 157 | 14.044 |
| 5 | g11061.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 85 | 156 | 2.71E-18 |
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 K11093 (U1 small nuclear ribonucleoprotein 70kDa)
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.
