Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttatttggggatgaacttgttttagaactgcgctctgtgctgttaattttgacgacgccaattattaaggtgcgatttctgattctttcaaagaactttcttgctctgatgtgcttcgtctgataacaaactaactcattgtgctgtacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAAATGAAAAAGGTGGTTCAGAGCGCATTCTCGAATTTGCCAGCCGTGCTGA

Basic information

species Physcomitrella patens
transcript PP1S93_138V6.1
intron # 5
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37852290|gb|BJ610298.1|BJ610298
EST:     TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAG                         GTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
genomic: TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
EST: gi|162228914|gb|FC404200.1|FC404200
EST:     TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAG                         GTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
genomic: TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
EST: gi|100391012|gb|BY953022.1|BY953022
EST:     TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTAAAGAG                         GTTCGCAGAATGGAGCTCTCCCCAATACATCTGACGATGAAGATTTCGTAA
genomic: TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
EST: gi|162228915|gb|FC404201.1|FC404201
EST:     TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAG                         GTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
genomic: TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAA
EST: gi|100411709|gb|BY992302.1|BY992302
EST:     TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAG                         GTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGGATTTCGTA
genomic: TTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGG-ATTTCGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 29 (upstream exon), 35 (downstream exon)
Score: 4

ATACTCGGATACGGTCATATTGGAAAAGAGTTGGCACTACGCTTGAGATATTTTGGTGTACATTTACTTGCTGTCCGACGATCTTGGACTAGTTTAAGAGgtatttttta ... tacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAAATGAAAAAGGTGGTTCAGAGCGCATTCTCGAATTTGCCAGCCGTGCTGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgatgtgcttcgtctgataacaaactaactcattgtgctgtacattgtagGTTCGCAGAATGGAGCTCTTCCCAATACATCTGACGATGAGGATTTCGTAAATGAAAAAGGTGGTTCAGAGCGCATTCTCGAATTTGCCAGCCGTGCTGA
                           aactaac  putative branch site (score: 4)
                     ataacaaa  TA-rich tract