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

gtaagttcaatgaatgttttttaaaccataagaatccgatcaggtttttgtgtcctctgcacattttcacaagtagcatattctttgtttgtctcggtacagtcttattgttttgttagtttctacagtttttgggggtattgaagcagcgacatgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATGAAGCGAGCAGTCTCTTCACACCAAGTTGTAGACCTTGAACGACCAGCAG

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.2
intron # 7
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|162269549|gb|FC445105.1|FC445105
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|37836542|gb|BJ594550.1|BJ594550
EST:     TCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208354680|gb|DC918706.1|DC918706
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208347734|gb|DC925607.1|DC925607
EST:     ATCATNGGGATATAAGCAGCAGCGNATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: ATCAT-GGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208366175|gb|DC955276.1|DC955276
EST:     TATCAT-GGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162238634|gb|FC418997.1|FC418997
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|37850186|gb|BJ608194.1|BJ608194
EST:     ATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGAATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: ATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAG-ATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208381754|gb|DC928417.1|DC928417
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTNTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162192771|gb|FC369622.1|FC369622
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|67699119|gb|BJ959352.1|BJ959352
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|18340062|gb|BJ172090.1|BJ172090
EST:     TATCATGGGATATAAGCAGCAGCGAATCNTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208380520|gb|DC915422.1|DC915422
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208348822|gb|DC925894.1|DC925894
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162191817|gb|FC367966.1|FC367966
EST:     CATGGGATATAAGCAGCAGCGAATCCTTCTCNCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: CATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|208382347|gb|DC919335.1|DC919335
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162164830|gb|FC341345.1|FC341345
EST:     CATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: CATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162162092|gb|FC338883.1|FC338883
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
EST: gi|162195496|gb|FC369353.1|FC369353
EST:     TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAG                         AGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG
genomic: TATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATG

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: 34 (upstream exon), 10 (downstream exon)
Score: 5

TATGAGCGCATCCTACGACTTGAACGAGGACTCTAAAACAGTGGCTACCATATCATGGGATATAAGCAGCAGCGAATCCTTCTCCCTAGATATGTCTAAGgtaagttcaa ... atgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATGAAGCGAGCAGTCTCTTCACACCAAGTTGTAGACCTTGAACGACCAGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttagtttctacagtttttgggggtattgaagcagcgacatgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATGAAGCGAGCAGTCTCTTCACACCAAGTTGTAGACCTTGAACGACCAGCAG
       ttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcaatgaatgttttttaaaccataagaatccgatcaggtttttgtgtcctctgcacattttcacaagtagcatattctttgtttgtctcggtacagtcttattgttttgttagtttctacagtttttgggggtattgaagcagcgacatgtgtgcagAGTGCCGACCGACTTTTCTTCAAAGAGTTGATGGGCTTATTCAGAAATATGAAGCGAGCAGTCTCTTCACACCAAGTTGTAGACCTTGAACGACCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG