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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccctgtgtagatgttgggttgtcgtcgttggtgtttttgagacgttgtgtgactcgtagggttttgacgttcgtttggttttcgaggggctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCGCATGCAAGTGGGAGTGGCTGCGTCATGGGTGCAGGGTCCTGCTTTCGCT

Basic information

species Physcomitrella patens
transcript PP1S49_175V6.2
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|18349948|gb|BJ181999.1|BJ181999
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|37828919|gb|BJ586931.1|BJ586931
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|162260497|gb|FC435084.1|FC435084
EST:     CCACAGCCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGC
genomic: CCACAG-CTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAAC-AATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGC
EST: gi|67508429|gb|BJ941296.1|BJ941296
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|67692636|gb|BJ952869.1|BJ952869
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|162260496|gb|FC435083.1|FC435083
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGC
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAAC-AATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGC
EST: gi|162233088|gb|FC408495.1|FC408495
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|15262130|gb|BI437440.1|BI437440
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|67691648|gb|BJ951881.1|BJ951881
EST:     TTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
EST: gi|67569375|gb|BJ942199.1|BJ942199
EST:     TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAG                         CGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG
genomic: TCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCG

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: 8 (upstream exon), 28 (downstream exon)
Score: 1

CCTAGCACTGCTTGAAGGACTCTGAAGGACTCTCCATCTCGATTCGTGCATCCACAGCTTGATTAAAGCACTTGGGTTAACTTCGTGGGGTTGTTTGGAGgtattcaatg ... ctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCGCATGCAAGTGGGAGTGGCTGCGTCATGGGTGCAGGGTCCTGCTTTCGCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgactcgtagggttttgacgttcgtttggttttcgaggggctggtttcagCGACAGGAAGGAGAACAATATGCAGGCTGTGCGGGCTGCCGTGCTGAAGCGCATGCAAGTGGGAGTGGCTGCGTCATGGGTGCAGGGTCCTGCTTTCGCT
                 ttttgac  putative branch site (score: 1)