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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagcgccactcttctcactcaaaagcaacgtccttgtatcatcacagcttctgctatctgctcgcagctaatgtttcaattctgagaataccaccatcagtgcccagttttgaggtatgcagatgtctaaaagctaattgtgtgagtcgaatgttgtgctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCATTTCAACTGGGCTGGAGCTTTTGAATAAGTGAGGTCAAGAGATTTTTGTA

Basic information

species Physcomitrella patens
transcript PP1S292_39V6.2
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|208398843|gb|DC920791.1|DC920791
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67695892|gb|BJ956125.1|BJ956125
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67696190|gb|BJ956423.1|BJ956423
EST:     AATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: AATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67692929|gb|BJ953162.1|BJ953162
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208356563|gb|DC922353.1|DC922353
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGNTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|37827016|gb|BJ585028.1|BJ585028
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162175139|gb|FC351181.1|FC351181
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67699516|gb|BJ959749.1|BJ959749
EST:     AACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: AACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208384383|gb|DC928134.1|DC928134
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162255228|gb|FC431538.1|FC431538
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67579180|gb|BJ951325.1|BJ951325
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208375198|gb|DC945348.1|DC945348
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162261073|gb|FC437454.1|FC437454
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|37852856|gb|BJ610864.1|BJ610864
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162250706|gb|FC426555.1|FC426555
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67700692|gb|BJ960925.1|BJ960925
EST:     CCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: CCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162250705|gb|FC426554.1|FC426554
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67695026|gb|BJ955259.1|BJ955259
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208396408|gb|DC920074.1|DC920074
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|67692416|gb|BJ952649.1|BJ952649
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162205854|gb|FC381092.1|FC381092
EST:     GCCCTCACGAGTACCCAATTTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|162205855|gb|FC381093.1|FC381093
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208399367|gb|DC924797.1|DC924797
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
EST: gi|208399137|gb|DC916534.1|DC916534
EST:     GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAG                         GGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT
genomic: GCCCTCACGAGTACCCAATCTGCAACCTGGATGCAGGACTTTGCCTCAAGgtgcagcgcc ... gctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtatgcagatgtctaaaagctaattgtgtgagtcgaatgttgtgctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCATTTCAACTGGGCTGGAGCTTTTGAATAAGTGAGGTCAAGAGATTTTTGTA
                   agctaat  putative branch site (score: 3)
             tctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagcgccactcttctcactcaaaagcaacgtccttgtatcatcacagcttctgctatctgctcgcagctaatgtttcaattctgagaataccaccatcagtgcccagttttgaggtatgcagatgtctaaaagctaattgtgtgagtcgaatgttgtgctactgcagGGATCACACGACAAGGAGGGTGTTGCGCTGATGAAGCGTACACTAGCTCATTTCAACTGGGCTGGAGCTTTTGAATAAGTGAGGTCAAGAGATTTTTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA