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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgcgagatcgccactaaatgtcaggcggcactattgtaatggagatcaacctgctgggttcatacatgtttgctctgacattttgctcatatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCGAAGGTCGATAGGCCAGCGGGAGTGGTCTGTTTCATCAGCAAGATGGATA

Basic information

species Physcomitrella patens
transcript PP1S257_89V6.2
intron # 10
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|18334443|gb|BJ166460.1|BJ166460
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|208395944|gb|DC915704.1|DC915704
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|18334715|gb|BJ166732.1|BJ166732
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|162278918|gb|FC454969.1|FC454969
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|162160422|gb|FC337423.1|FC337423
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|162261867|gb|FC438391.1|FC438391
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|37848402|gb|BJ606410.1|BJ606410
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
EST: gi|37848391|gb|BJ606399.1|BJ606399
EST:     CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAG                         GAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG
genomic: CGAGAATCACCTTGACGAGGCTTTCAGAACTGTTGTGCCTCAGCCTCCAGgtactaattc ... catatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcaacctgctgggttcatacatgtttgctctgacattttgctcatatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCGAAGGTCGATAGGCCAGCGGGAGTGGTCTGTTTCATCAGCAAGATGGATA
                              ctctgac  putative branch site (score: 3)
                                      ttttgctc  CT-rich tract
                                   acatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcgagatcgccactaaatgtcaggcggcactattgtaatggagatcaacctgctgggttcatacatgtttgctctgacattttgctcatatgacagGAAACGGAGAAGCATCTCTCAGAGATGGTGGTTTCGAAGGCCTTGATTGCGAAGGTCGATAGGCCAGCGGGAGTGGTCTGTTTCATCAGCAAGATGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA