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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacctcttgttagcttggtccttgctctcgcctttcaaagttccgtaggagatgaaagcctaaattgcggagcagtgatgttgggagcgtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAACGTATGTGCCATCGAGGCAATCCATCATGTCTTTCTCCGTCATGATCGGA

Basic information

species Physcomitrella patens
transcript PP1S9_382V6.1
intron # 1
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|100431683|gb|BY960321.1|BY960321
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|208363996|gb|DC939589.1|DC939589
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|100415807|gb|BY993012.1|BY993012
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|208371599|gb|DC952241.1|DC952241
EST:     TGCTGGCAGCACGCTCGGTGGTGC-TTTAGCTC                         AGGTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: TGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|100425905|gb|BY977179.1|BY977179
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|100418226|gb|BY993395.1|BY993395
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
EST: gi|162153768|gb|FC329171.1|FC329171
EST:     GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTC                         AGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC
genomic: GAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAAC

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: 25 (upstream exon), 14 (downstream exon)
Score: 3

CCGATGAGGGCAGCTTGAGCAGCGTAGCCTCGGCCGCAGCGATGGATCTAGAGGCCGGCCTCTCTTCTGCTGGCAGCACGCTCGTTGGTGCTTTTAGCTCgtatgttttt ... gtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAACGTATGTGCCATCGAGGCAATCCATCATGTCTTTCTCCGTCATGATCGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaggagatgaaagcctaaattgcggagcagtgatgttgggagcgtgtgggcagAGTTACAAAGGGAATGCGTGATCTACCTTCAAGTGTTTCATCCGCGGCAACGTATGTGCCATCGAGGCAATCCATCATGTCTTTCTCCGTCATGATCGGA
              gcctaaa  putative branch site (score: 3)
                 taaatt  TA-rich tract