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'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTGTCGATGGCGGTGTGGGGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtccaaattttcagattttagcatatttttgtcagcgccgtttgtattacgaatcttgtcctatgaaaattcagtctgtgataaaggatttttc...

Basic information

species Physcomitrella patens
transcript PP1S96_201V6.1
intron # 2
splice site 5'
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|208351033|gb|DC910496.1|DC910496
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208354666|gb|DC934310.1|DC934310
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|100354883|gb|BY983614.1|BY983614
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208374274|gb|DC940659.1|DC940659
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208372484|gb|DC940773.1|DC940773
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208400210|gb|DC908871.1|DC908871
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|18342663|gb|BJ174698.1|BJ174698
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|18361295|gb|BJ193361.1|BJ193361
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|100355017|gb|BY964959.1|BY964959
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208360577|gb|DC930849.1|DC930849
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|208376260|gb|DC902655.1|DC902655
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGNATTATTCTGANAANGNG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
EST: gi|100374133|gb|BY985678.1|BY985678
EST:     GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAG                         CCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG
genomic: GGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG

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: 28 (upstream exon), 20 (downstream exon)
Score: 3

GCAGTGTCGATGGCGGTGTGGGGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtcc ... catctttcagCCACGCAGCGGTGTGCCCACGTTCGGATTATTCTGAGAATGGG




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTGTCGATGGCGGTGTGGGGTTCCCTTTATGTGAGCAAATATTTGCGGGAGTTCGACCTAGCTGCCAGgtgcgtgtccaaattttcagattttagcatatttttgtcagcgccgtttgtattacgaatcttgtcctatgaaaattcagtctgtgataaaggatttttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC