Gene loci information

Transcript annotation

  • This transcript has been annotated as RNA-binding protein Musashi homolog Rbp6.

Parent gene

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_2 g6869 g6869.t1 isoform g6869.t1 19386702 19460118
chr_2 g6869 g6869.t1 exon g6869.t1.exon1 19386702 19386766
chr_2 g6869 g6869.t1 cds g6869.t1.CDS1 19386702 19386766
chr_2 g6869 g6869.t1 exon g6869.t1.exon2 19413760 19413800
chr_2 g6869 g6869.t1 cds g6869.t1.CDS2 19413760 19413800
chr_2 g6869 g6869.t1 exon g6869.t1.exon3 19421813 19421894
chr_2 g6869 g6869.t1 cds g6869.t1.CDS3 19421813 19421894
chr_2 g6869 g6869.t1 exon g6869.t1.exon4 19428504 19428557
chr_2 g6869 g6869.t1 cds g6869.t1.CDS4 19428504 19428557
chr_2 g6869 g6869.t1 exon g6869.t1.exon5 19430030 19430114
chr_2 g6869 g6869.t1 cds g6869.t1.CDS5 19430030 19430114
chr_2 g6869 g6869.t1 exon g6869.t1.exon6 19431197 19431238
chr_2 g6869 g6869.t1 cds g6869.t1.CDS6 19431197 19431238
chr_2 g6869 g6869.t1 exon g6869.t1.exon7 19459674 19459766
chr_2 g6869 g6869.t1 cds g6869.t1.CDS7 19459674 19459766
chr_2 g6869 g6869.t1 exon g6869.t1.exon8 19459948 19460118
chr_2 g6869 g6869.t1 cds g6869.t1.CDS8 19459948 19460118
chr_2 g6869 g6869.t1 TSS g6869.t1 NA NA
chr_2 g6869 g6869.t1 TTS g6869.t1 NA NA

Sequences

>g6869.t1 Gene=g6869 Length=633
ATGGAGCAACAACAGCATCAAGATATGGCATCAGGATCTCCAGCTGAGATTAAAAATGAT
CCAGGAAAAATGTTCATAGGAGGACTAAGTTGGCAAACAAGCCCAGAGAGCCTAAGAGAC
TATTTTAGTAAATTTGGAGAAATTTCAGAAGTCATGGTCATGAAAGATCCTACAACAAGA
AGACCGAGTTCAACTGGAATGGGAATCAATGACACAACAGGACCACTCTTTTCAAGACCA
AGGGGGTTTGGTTTCATCACTTTTGCAGATCCATCTAGCGTAGACAAAGTCTTATCACAT
GGTACACATGAATTAGATGGTAAAAAGATTGATCCAAAAGTCGCATTTCCAAGAAGAGCA
CATCCAAAAATGGTGACTAGAACGAAAAAAATTTTTGTGGGCGGTCTCTCAGCACCCACA
ACATTAGAAGATGTTAAAAGTTACTTTGAGCAATTTGGAACGTCCAAAAATTCATATCAA
TTTCTTATACATATTTATATTTTGCGTGGCGCAATAATGTTGCCTTTTATGAAGGCTAAT
GAAATTCCAAGCAGCATAAAAGGCACGATTATTGGCTTCTTACTGACGACGACTTGCGAG
CAACTTGGGCCTTGCCGAAATCGCACCGAGTGA

>g6869.t1 Gene=g6869 Length=210
MEQQQHQDMASGSPAEIKNDPGKMFIGGLSWQTSPESLRDYFSKFGEISEVMVMKDPTTR
RPSSTGMGINDTTGPLFSRPRGFGFITFADPSSVDKVLSHGTHELDGKKIDPKVAFPRRA
HPKMVTRTKKIFVGGLSAPTTLEDVKSYFEQFGTSKNSYQFLIHIYILRGAIMLPFMKAN
EIPSSIKGTIIGFLLTTTCEQLGPCRNRTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6869.t1 Gene3D G3DSA:3.30.70.330 - 13 125 6.8E-23
8 g6869.t1 Gene3D G3DSA:3.30.70.330 - 126 170 5.2E-5
6 g6869.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
2 g6869.t1 PANTHER PTHR48032:SF10 RNA-BINDING PROTEIN MUSASHI HOMOLOG 2 6 157 6.5E-58
3 g6869.t1 PANTHER PTHR48032 RNA-BINDING PROTEIN MUSASHI HOMOLOG RBP6 6 157 6.5E-58
1 g6869.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 25 63 8.0E-8
9 g6869.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 22 119 16.159
5 g6869.t1 SMART SM00360 rrm1_1 23 113 1.4E-16
4 g6869.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 21 158 5.7E-30

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

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.

Raw TPM values