General information for g11540.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein Musashi homolog Rbp6.
Parent gene
- The parent gene g11540 is located on chr_1: 16939492..16940887 (- 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 | g11540 | g11540.t1 | TTS | g11540.t1 | 16939434 | 16939434 |
| chr_1 | g11540 | g11540.t1 | isoform | g11540.t1 | 16939492 | 16940887 |
| chr_1 | g11540 | g11540.t1 | exon | g11540.t1.exon1 | 16939492 | 16939723 |
| chr_1 | g11540 | g11540.t1 | cds | g11540.t1.CDS1 | 16939492 | 16939723 |
| chr_1 | g11540 | g11540.t1 | exon | g11540.t1.exon2 | 16939780 | 16939889 |
| chr_1 | g11540 | g11540.t1 | cds | g11540.t1.CDS2 | 16939780 | 16939889 |
| chr_1 | g11540 | g11540.t1 | exon | g11540.t1.exon3 | 16939947 | 16940200 |
| chr_1 | g11540 | g11540.t1 | cds | g11540.t1.CDS3 | 16939947 | 16940200 |
| chr_1 | g11540 | g11540.t1 | exon | g11540.t1.exon4 | 16940267 | 16940534 |
| chr_1 | g11540 | g11540.t1 | cds | g11540.t1.CDS4 | 16940267 | 16940534 |
| chr_1 | g11540 | g11540.t1 | exon | g11540.t1.exon5 | 16940867 | 16940887 |
| chr_1 | g11540 | g11540.t1 | cds | g11540.t1.CDS5 | 16940867 | 16940887 |
| chr_1 | g11540 | g11540.t1 | TSS | g11540.t1 | NA | NA |
Sequences
>g11540.t1 Gene=g11540 Length=885
ATGAAGGATCCAATAACACAAGAACCCGATGCTGTAGAAAAAGTTCTCAAAGTTCCCATT
CATACACTTGATGGAAAGAAAATTGATCCGAAGCATGCAACTCCAAAGAATCGTCCGAAA
GCTGCTAACAAAACTAAAAAGATTTTTGTTGGCGGAGTATCACAAGATACAAGCGTGGAA
GAAGTTAAGGCTTATTTTAGCCAATTCGGAAAAGTTGAAGAAGCCGTAATGCTCATGGAT
CAGCAGACGAAGCGTCATCGAGGCTTTGGATTTATCACATTAGCTGATGAGGATGTTGTC
GATAGAATCTGTGAAATTCATTTTCACACAATCAAAAACAAGAAGGTAGAGTGCAAGAAA
GCTCAACCAAAAGAAACTGTAACACCAGCGACACAACTACAATTGCAAAAACGCTTATTA
CTTAGTGGATTGGGATTAAGAATGCCTCCAACAGCAGTGATGAGTGCAGCCGCAAATCCT
CACGCTGCAGCCAATGTCATGCCAACACCACTGACAGCATATCCTTTAACTGCTGCTCAT
CAGGCTCAAGCTGCAACTTTGATACCGAATCCTCTAACTAATACTGCTGCAGTTGCTACA
AATGCTGGTGGAAAATTGATTGCTACATATCCACCATCGTTTCATGCATTAAGATATACA
CCATATCCTCATTTAACTCAAGCAATTCCAACAGCAGCAGCGACTGTTTCTCAACTGACT
GCTACTCCAACACCCAGTCATCAACAACCACAAAATCCTCAACTAGCTGCTGCTGCTGCA
GCAGCAAACGCAAATCCATATCCAAGTGGTTACAATCTCGCTGGTGTTGACATGTCAAGC
TTCAATGGAATCGATTGGTCATCTATGTATGGCATGTATGTATAA
>g11540.t1 Gene=g11540 Length=294
MKDPITQEPDAVEKVLKVPIHTLDGKKIDPKHATPKNRPKAANKTKKIFVGGVSQDTSVE
EVKAYFSQFGKVEEAVMLMDQQTKRHRGFGFITLADEDVVDRICEIHFHTIKNKKVECKK
AQPKETVTPATQLQLQKRLLLSGLGLRMPPTAVMSAAANPHAAANVMPTPLTAYPLTAAH
QAQAATLIPNPLTNTAAVATNAGGKLIATYPPSFHALRYTPYPHLTQAIPTAAATVSQLT
ATPTPSHQQPQNPQLAAAAAAANANPYPSGYNLAGVDMSSFNGIDWSSMYGMYV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11540.t1 | Gene3D | G3DSA:3.30.70.330 | - | 25 | 131 | 3.1E-22 |
| 10 | g11540.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 43 | - |
| 8 | g11540.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 259 | - |
| 9 | g11540.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 258 | - |
| 3 | g11540.t1 | PANTHER | PTHR48032:SF4 | FI20028P1 | 7 | 242 | 9.2E-124 |
| 5 | g11540.t1 | PANTHER | PTHR48032 | RNA-BINDING PROTEIN MUSASHI HOMOLOG RBP6 | 7 | 242 | 9.2E-124 |
| 2 | g11540.t1 | PANTHER | PTHR48032:SF4 | FI20028P1 | 232 | 292 | 9.2E-124 |
| 4 | g11540.t1 | PANTHER | PTHR48032 | RNA-BINDING PROTEIN MUSASHI HOMOLOG RBP6 | 232 | 292 | 9.2E-124 |
| 1 | g11540.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 48 | 116 | 5.5E-13 |
| 12 | g11540.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 46 | 123 | 14.965 |
| 7 | g11540.t1 | SMART | SM00360 | rrm1_1 | 47 | 119 | 2.6E-20 |
| 6 | g11540.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 38 | 129 | 1.36E-22 |
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 K14411 (RNA-binding protein Musashi)
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.
