Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatagttctgactagtttttacttttaatgatttgatatcatctagttatggttgggaccttttgttattgttgttggttcgaatattcttttatatatctgaaatagattgatgattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCGGGCATCCAAAACGTCTATCATTATCTTACACTCTGGCACAATAGTACTG

Basic information

species Physcomitrella patens
transcript PP1S92_76V6.3
intron # 4
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|100390301|gb|BY952709.1|BY952709
EST:     -GAGTGCTGCAAAAGA-GTTAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTA
genomic: AGAGTGCTGCAAA-GAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTA
EST: gi|67691358|gb|BJ951591.1|BJ951591
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|67508139|gb|BJ941010.1|BJ941010
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|67693331|gb|BJ953564.1|BJ953564
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|67693227|gb|BJ953460.1|BJ953460
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|37827449|gb|BJ585461.1|BJ585461
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|37829825|gb|BJ587837.1|BJ587837
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|37834771|gb|BJ592783.1|BJ592783
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208378179|gb|DC918800.1|DC918800
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208366899|gb|DC951386.1|DC951386
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208382625|gb|DC919807.1|DC919807
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208397034|gb|DC928877.1|DC928877
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATG-A-                         -AAA-TCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|162271257|gb|FC447194.1|FC447194
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208390888|gb|DC945905.1|DC945905
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208362326|gb|DC954572.1|DC954572
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208371204|gb|DC955996.1|DC955996
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|67700473|gb|BJ960706.1|BJ960706
EST:     AAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
EST: gi|208396867|gb|DC920435.1|DC920435
EST:     AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTAT                         GAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG
genomic: AAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCG

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), 28 (downstream exon)
Score: 19

CCGTTCAGTTGGCCGAGCAGATGAGGGAGAAATATGGGAAGTGGACTGACAAGAGTGCTGCAAAGAAGTAAACTAGGAGTGTTGTAAGCTGCTGATGTATgtaagtcata ... gattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCGGGCATCCAAAACGTCTATCATTATCTTACACTCTGGCACAATAGTACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttggttcgaatattcttttatatatctgaaatagattgatgattgtgcagGAAAATCTTTGCACGAAATGCGTAGAAGTAGTTGTGTGATCGTGGATGGCGGGCATCCAAAACGTCTATCATTATCTTACACTCTGGCACAATAGTACTG
                                      gattgat  putative branch site (score: 19)
             aatattcttttatata  TA-rich tract