General information for g11061.t3
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.t3 | TSS | g11061.t3 | 13736261 | 13736261 |
| chr_1 | g11061 | g11061.t3 | isoform | g11061.t3 | 13736448 | 13739132 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon1 | 13736448 | 13736591 |
| chr_1 | g11061 | g11061.t3 | cds | g11061.t3.CDS1 | 13736448 | 13736591 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon2 | 13736654 | 13736836 |
| chr_1 | g11061 | g11061.t3 | cds | g11061.t3.CDS2 | 13736654 | 13736836 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon3 | 13736900 | 13737852 |
| chr_1 | g11061 | g11061.t3 | cds | g11061.t3.CDS3 | 13736900 | 13737058 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon4 | 13738147 | 13738386 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon5 | 13738580 | 13738797 |
| chr_1 | g11061 | g11061.t3 | exon | g11061.t3.exon6 | 13739002 | 13739132 |
| chr_1 | g11061 | g11061.t3 | TTS | g11061.t3 | 13739293 | 13739293 |
Sequences
>g11061.t3 Gene=g11061 Length=1869
ATGACTCAATATCTGCCAGCCAATTTATTGGCTTTATTCGCTGCTCGCGATCCTATTCCA
TTTTTGCCACCTCCTGATAAACTTCCACATGAGAAAAAGACGCGAGGATATTTAGGAGTT
GGTTCATTTTTAGATCAATTTGAGGATCCTAAAGATACACCACCACCCACAAGAGTCGAA
ACAAAAGAAGAACGAATGGAAAGACGTCGAAGAGAAAAAGCTGAGCAAGTAGCTTACAAG
CTTGAACGAGAAATAGCACTTTGGGATCCAACATCGATCGAAAATACAACAGAAGATCCT
TTCAAAACACTTTTTGTTGCTCGTATAAATTATGACACATCAGAATCGAAATTAAGAAGA
GAATTTGAAGTGTATGGACCAATAAGGAAAATTATAATGATCCACGATCAAGATTCAGGC
AAACCTCGTGGTTATGCGTTTATTGAGTACGAACATGAAAGAGACATGCATTGTAAGTAC
ATATAAGTAAGATAGAAAAAGTTTCTCTTATTCAGAGAAATCTGTGGCATCAAAAATGAA
AAGTATGGAAGTTGTTAAATCAAATTTTTAAAAATTAGTCAATTGGGTATTCCAAGCTTT
TCTTAAAAGAGATGCAATTCAACTAAAGTAAAAGATTCGGTTTGTTTTTCCGTACGAGAT
TAAAGAGGGTGTCTTTTGTAAGTTATCCAATAATAATTTGTTACATCGCTCCGTAAAAAA
ACTTTTCAATATAAATTAATGAAAAATTTTTCACAACGTAAGATAGACTCATATTAATGT
ATTTAATGATTGATAAAAGCCGTGATTTAGGTTTGTATTGTGTTTTTGGTAAGAAACTTT
ATATAACAAAAAAATTTTCTTTTACTACTTCATATTAGTAGCCAAAAACTTTTATTTTAT
GATTTCATTTCCTTTAACAAGACACAGTATCTTAAAAATTAATTTCTATAAAAACTTAGC
GCAATACGTAAGTATTTAAGCGCTCCAGGTAAAAATAATGAAATTATTCACGGATAATGT
AAAAATGGAAATCAAAAAACACAGAAAGAATGAACGCTTCGAGTCTTATCGTTCGGGGTT
TTACGTAAAAATAGAGATAAAATGTATGAAAATAAGTTGTGTGTAGGTATGATTGTTGTT
TTGGTTGGGTAGGTATCTCAAAAAAAATTTTTCTCGCTCTCTAACATCTCAATGACTTTT
TCAATTGCAAGTTCCTTCAAATCAGCTTCAATTATAAAAAAGCCCAACCAAGCAGTTTAG
AGAGCAATTACGGTGAAAAGCTGCATACAAACATGCTGATGGTAAAAAAATTGATGGTAG
AAGGGTATTGGTTGACGTTGAACGTGCAAGAACAGTTAAAGGATGGTTACCTCGAAGACT
TGGAGGTGGTTTAGGTGGAACAAGACGTGGTGGTGCTGAGGTAAATATTAAGCACAGTGG
ACGAGAAGATAATGTACGTGAAAAGGAGAGATATCGTCTTGAAAGAGAAAGAGAAGATAA
TCGTCGTCTTGATGATAGAAAAGAAACGCCGAAGAACACGTTCTAGAGATCGGTTAGTTT
TCTTTTGAAACTTCAAATAAATTTATTTATTAAAGAACAAATTTCAATTGTAGAGATCGT
TCTGAACGTAAACGCGATAAACGTGATCGTTCTAGATCACGTGAAAGACGCCGTGATAAG
GACAAGAAAGAGCGTAAACCAGAGTTCGATATTAAAATTAAGGAAGAACCCATTGATGAT
TATCCGGACTACACGCAACATGATTATGGTCAATATGCCAATCAAGTTAAGTATGAATCA
GGTGATGAAGAAAAATATAGACCAAATGAGCAAGATGGAGCCGCTTATGGTTATCGACAA
GATTATTAA
>g11061.t3 Gene=g11061 Length=161
MTQYLPANLLALFAARDPIPFLPPPDKLPHEKKTRGYLGVGSFLDQFEDPKDTPPPTRVE
TKEERMERRRREKAEQVAYKLEREIALWDPTSIENTTEDPFKTLFVARINYDTSESKLRR
EFEVYGPIRKIIMIHDQDSGKPRGYAFIEYEHERDMHCKYI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11061.t3 | Gene3D | G3DSA:3.30.70.330 | - | 56 | 158 | 3.9E-18 |
| 7 | g11061.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 73 | - |
| 8 | g11061.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 73 | - |
| 3 | g11061.t3 | PANTHER | PTHR13952:SF16 | - | 1 | 158 | 4.6E-66 |
| 4 | g11061.t3 | PANTHER | PTHR13952 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD | 1 | 158 | 4.6E-66 |
| 1 | g11061.t3 | Pfam | PF12220 | U1 small nuclear ribonucleoprotein of 70kDa MW N terminal | 4 | 91 | 2.8E-25 |
| 2 | g11061.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 104 | 156 | 2.1E-12 |
| 10 | g11061.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 102 | 161 | 13.413 |
| 6 | g11061.t3 | SMART | SM00360 | rrm1_1 | 103 | 159 | 1.3E-6 |
| 5 | g11061.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 85 | 156 | 2.44E-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.
