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

...tgttctttgtataggcagagtcttagcagtttatgtttaagtccagtatatttgagcatgagctgaaatatgtagttgatgtctttgagcatgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA

Basic information

species Physcomitrella patens
transcript PP1S77_252V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_252V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
tgttctttgtataggcagagtcttagcagtttatgtttaagtccagtatatttgagcatgagctg-aaatatgtagttgatgtctttgagcatgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA
       ||   || |    |    | ||     |   |  |    | |    ||  |||   ||  ||||   | ||   |||||      |  |  |||||||||||||||| | |||||| ||||| || || |||||||| ||||| ||||||||| | || ||    || ||  | || ||  |    || |||||
------gtgagcagcctcgattgctg-agaaggagagaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttct--tgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA

upper sequence: PP1S77_252V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G55870.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------tgttctttgtataggcagagtcttagcagtttatgtttaagtccagtata--tttgagcatgagctgaaatatgtagttgatgtc-tttgagcatg--attgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA
                   | |||||  | ||   | | | ||    ||| ||  || |   || ||  |||||| |     ||| | ||   ||  |  ||   ||| | |   ||   |||||||||||||||||||||||| ||||| || ||    ||||  || ||    |||||| |  | |||   || ||    |||||||||  | |||| ||
gtgagtggattttgctaactactttggtttggtt-actttgagacaattaggtcaaaatttggtttagttttgagaacataatgaca-attaggtcaaaatcacatgatcttcttataacagGTGGATGGGTTGGTTACTTTTCTTATGATACTGTTCCCTATGCCGAAAAGCGAAAGCTACCTCTCTCAAAGGCTCCGGTTGATGACCGAAATTTACCAGA
















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|162171713|gb|FC348174.1|FC348174
EST:     ATCAAAGTGGAATCCGGTTAAAATTGATAGTATTCCGGATATTTTCTGTG                         GTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAA
genomic: ATCAAAGTGGAATCCGGTTAAAATTGATAGTATTCCGGATATTTTCTGTGgtatgtatta ... atgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAA
EST: gi|100383453|gb|BY950237.1|BY950237
EST:     ATCAAAGTGGAATCCGGNTAAA-TTGATAGTATTCCGGATATTTTCTGTG                         GTGGNATGGGT-GGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAA
genomic: ATCAAAGTGGAATCCGGTTAAAATTGATAGTATTCCGGATATTTTCTGTGgtatgtatta ... atgattgtagGTGG-ATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAA
EST: gi|162167077|gb|FC342539.1|FC342539
EST:     ATCAAAGTGGAATCCGGTTAAAATTGATAGTATTCCGGATATTTTCTGTG                         GTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAA
genomic: ATCAAAGTGGAATCCGGTTAAAATTGATAGTATTCCGGATATTTTCTGTGgtatgtatta ... atgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatatttgagcatgagctgaaatatgtagttgatgtctttgagcatgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA
                            agttgat  putative branch site (score: 5)
                    aaatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttctttgtataggcagagtcttagcagtttatgtttaagtccagtatatttgagcatgagctgaaatatgtagttgatgtctttgagcatgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG