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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgtatccttttatctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT

Basic information

species Physcomitrella patens
transcript PP1S9_51V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G08750.1 (Glycine max), 3'ss of exon 2
ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgt--atccttttatctttctcagT---TATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                              ||  |  | | |   ||||   || ||||  |   | ||  ||| |||| |  ||    ||   |     | |   || ||||||||||| || | |||   |||||||||||||||||||||||| ||||||||||| ||   ||  || || |||   |  |||||  |    
-----------------------------gtacttttattctcatttttcaattgctcaattccaacgttcctatttttattaatttaattggatcaacgaatagGTACCATTTCGATGGGACTACTCGCAAATTCTTCGAGGGTTGGTACTTCAAAGTCTCCATTCCCGAACGGAGGCAGAGCTTTTGCTTCATGTATTCCGTC

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G08850.1 (Glycine max), 3'ss of exon 1
ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgt---atccttttatctttct-cagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                                 ||  || |||  || ||   | |     ||  ||||  ||| |||| |    |   || |||   |   || || ||||||||||| || | |||   ||||||||||||||||||||||||  | |||||||||||   ||  || ||||||   |  |||||| |    
-------------------------------gtatttaactttctttcttcaattcatgaattcaatgttcctatttttctcaatttaattgatcaaccaatagCTACCATTTCGATGGGACTACTCGCAAATTCTTCGAGGGTTGGTACTTCAAACTTTCCATTCCGGAACGGAGGCAGAGTTTTTGCTTCATGTACTCCGTC
















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|67712771|gb|BJ966220.1|BJ966220
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100387687|gb|BY951687.1|BY951687
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100402906|gb|BY973411.1|BY973411
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|18372337|gb|BJ203939.1|BJ203939
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|162227522|gb|FC403464.1|FC403464
EST:     GCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100378952|gb|BY986500.1|BY986500
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|22492059|gb|BU051982.1|BU051982
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100374390|gb|BY985771.1|BY985771
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|18367348|gb|BJ199431.1|BJ199431
EST:     AGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACNGCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTT
genomic: AGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACT-CCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttactcatgtttcatgtagctaattttgtatccttttatctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                        agctaat  putative branch site (score: 3)
                              ttttgtatccttttat  CT-rich tract
                           taattttgtat  TA-rich tract