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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctttccccaacatctcatttttttgagattgctggatctgcttggagtagcagattacttccaaagtcggtcctctacttcctgatattcctttttctctggtattatatgactagcgaagctgaaagtgatgagttttttctgattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAGAGAGCGGGACACCTACAAACAGTCACGA

Basic information

species Physcomitrella patens
transcript PP1S46_281V6.1
intron # 4
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|162229227|gb|FC405314.1|FC405314
EST:     ATTGCAATGGCACTGCCAAACATC                         AACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAG
genomic: ATTGCAATGGCACTGCCAAACATCgtatgatgct ... gattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAG
EST: gi|162191790|gb|FC367939.1|FC367939
EST:     TCGGCAGTTCGGCTGCATCTACCCATTNGCA-TGGCACTGCCAAAACATC                         A-CTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTC
genomic: TCGGCAGTTCGGCTGCATCTACCCATT-GCAATGGCACTGCCAAA-CATCgtatgatgct ... gattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTC
EST: gi|162178629|gb|FC353924.1|FC353924
EST:     TCTCGGCAGTTCGGCTGCATCTACCCATTGCAATGGCACTGCCAAACATC                         AACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAG
genomic: TCTCGGCAGTTCGGCTGCATCTACCCATTGCAATGGCACTGCCAAACATCgtatgatgct ... gattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAG

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: 32 (upstream exon), 30 (downstream exon)
Score: 6

GTCTTGCTAGGTCTCGGCAGTTCGGCTGCATCTACCCATTGCAATGGCACTGCCAAACATCgtatgatgct ... gattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAGAGAGCGGGACACCTACAAACAGTCACGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtattatatgactagcgaagctgaaagtgatgagttttttctgattgtgcagAACTAAATGGGGTGCAAGCGACTTTGTCAAATGGATGTATACTCCTGTCAGAGAGCGGGACACCTACAAACAGTCACGA
                                         ttctgat  putative branch site (score: 6)
                                     ttttttctg  CT-rich tract
     attatatga  TA-rich tract