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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaccttcatcgggtgtctgcagccatcggcgatactgtgtcacaagttggaaggctacgatgtttcagattttttaaatttgatttttggacttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAAG

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 6
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|67574237|gb|BJ947061.1|BJ947061
EST:     CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAG                         GTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
genomic: CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaattagct ... acttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
EST: gi|208363504|gb|DC935269.1|DC935269
EST:     CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAG                         GTTCGACCTATTATTGAANCTTTTCTGAAGGGCTCATTCNCTGTCTTTGAA
genomic: CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaattagct ... acttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
EST: gi|100401167|gb|BY990864.1|BY990864
EST:     CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAG                         GTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
genomic: CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaattagct ... acttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
EST: gi|162235868|gb|FC412419.1|FC412419
EST:     CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAG                         GTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
genomic: CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaattagct ... acttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
EST: gi|162219070|gb|FC394653.1|FC394653
EST:     CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAG                         GTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA
genomic: CTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaattagct ... acttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggaaggctacgatgtttcagattttttaaatttgatttttggacttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAAG
                                atttgat  putative branch site (score: 5)
                                              cttttcc  putative PPT
              atgtttcagatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccttcatcgggtgtctgcagccatcggcgatactgtgtcacaagttggaaggctacgatgtttcagattttttaaatttgatttttggacttttccagGTTCGACCTATTATTGAAGCTTTTCTGAAGGGCTCATTCGCTGTCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG