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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatttgagagactgttgaattatatttatgttatgaagttctagactgctcttgtgatggctttattataaaactcgtgtttctgaatgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.2
intron # 16
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|37840929|gb|BJ598937.1|BJ598937
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|162255598|gb|FC431596.1|FC431596
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|162279090|gb|FC455429.1|FC455429
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208386299|gb|DC953012.1|DC953012
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|18339902|gb|BJ171929.1|BJ171929
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208348107|gb|DC916917.1|DC916917
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|67696733|gb|BJ956966.1|BJ956966
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|18341451|gb|BJ173486.1|BJ173486
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGAGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208376570|gb|DC922601.1|DC922601
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|162183659|gb|FC359900.1|FC359900
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208381414|gb|DC927850.1|DC927850
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|162189304|gb|FC366774.1|FC366774
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208394434|gb|DC928486.1|DC928486
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTCGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208354437|gb|DC926614.1|DC926614
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208397506|gb|DC916390.1|DC916390
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|18334107|gb|BJ166123.1|BJ166123
EST:     ACCTCGTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208347298|gb|DC925322.1|DC925322
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208356794|gb|DC926805.1|DC926805
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|18340631|gb|BJ172659.1|BJ172659
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208395040|gb|DC924175.1|DC924175
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208380224|gb|DC919060.1|DC919060
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208355907|gb|DC926668.1|DC926668
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
EST: gi|208354673|gb|DC918699.1|DC918699
EST:     ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAG                         CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG
genomic: ACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGG

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: 26 (upstream exon), 10 (downstream exon)
Score: 8

TGAACCTCTTGTGGATGAGACTTGGGTCTTGGTTGGCTTCTGTGCTTTCACAGgtacggttca ... tgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactgctcttgtgatggctttattataaaactcgtgtttctgaatgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG
                   tttattataaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatttgagagactgttgaattatatttatgttatgaagttctagactgctcttgtgatggctttattataaaactcgtgtttctgaatgacttgcagCTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG

- - - - - - - -tgttgaa