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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgattggaagtggtttctactgcgagcttactgattttggggatgtgagtgaagttgggcagggagtgtgttgacagaaggtgttgatgttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCAGAGGACGAATGATATCAACCAGGTTGGGATTTGACAAACTTCTCCAGAG

Basic information

species Physcomitrella patens
transcript PP1S47_18V6.2
intron # 12
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|162190447|gb|FC365669.1|FC365669
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162167335|gb|FC342323.1|FC342323
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162159093|gb|FC334888.1|FC334888
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37832387|gb|BJ590399.1|BJ590399
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37835979|gb|BJ593991.1|BJ593991
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162158872|gb|FC335395.1|FC335395
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37821841|gb|BJ579907.1|BJ579907
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162190446|gb|FC365668.1|FC365668
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162169730|gb|FC345267.1|FC345267
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37833928|gb|BJ591940.1|BJ591940
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37832682|gb|BJ590694.1|BJ590694
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37843775|gb|BJ601783.1|BJ601783
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162167336|gb|FC342324.1|FC342324
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|18336041|gb|BJ168063.1|BJ168063
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|162172645|gb|FC348026.1|FC348026
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
EST: gi|37823211|gb|BJ581277.1|BJ581277
EST:     AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG                         GAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA
genomic: AGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCA

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: 35 (upstream exon), 29 (downstream exon)
Score: 6

CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAGgttgacacaa ... ttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCAGAGGACGAATGATATCAACCAGGTTGGGATTTGACAAACTTCTCCAGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtgaagttgggcagggagtgtgttgacagaaggtgttgatgttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCAGAGGACGAATGATATCAACCAGGTTGGGATTTGACAAACTTCTCCAGAG
                                           tgttttcttc  CT-rich tract
                                          atgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgattggaagtggtttctactgcgagcttactgattttggggatgtgagtgaagttgggcagggagtgtgttgacagaaggtgttgatgttttcttcagGAAAATTGCGTGCCCCTGTGTCTGCTCAATGTTCTATTGGTACTTACAGCAGAGGACGAATGATATCAACCAGGTTGGGATTTGACAAACTTCTCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA