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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggaccttactccagcttccgtaactggtgccttcattttgctttctcttcctgatgtgaatactgctatttctgatgcgactggtttaagtgtcatagtcatcatttgaataggagggcttcgtggaagtgtttagttttgtaccttacattgttcagtcgaattgtgttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG

Basic information

species Physcomitrella patens
transcript PP1S62_94V6.7
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|162251336|gb|FC427978.1|FC427978
EST:     TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAG                         GTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
genomic: TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAGgtacggacct ... gttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
EST: gi|162150866|gb|FC327346.1|FC327346
EST:     TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAG                         GTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
genomic: TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAGgtacggacct ... gttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
EST: gi|162179908|gb|FC355979.1|FC355979
EST:     TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAG                         GTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
genomic: TTTGTTCTGATAGTTATCCTAACCACGTCTCATTCACCACCTACGAAAAGgtacggacct ... gttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
EST: gi|162268968|gb|FC445460.1|FC445460
EST:     CTCATTCACCACCTACGAAAAG                         GTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
genomic: CTCATTCACCACCTACGAAAAGgtacggacct ... gttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggaagtgtttagttttgtaccttacattgttcagtcgaattgtgttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG
                    accttac  putative branch site (score: 3)
                                            tgttttc  putative PPT
         tttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggaccttactccagcttccgtaactggtgccttcattttgctttctcttcctgatgtgaatactgctatttctgatgcgactggtttaagtgtcatagtcatcatttgaataggagggcttcgtggaagtgtttagttttgtaccttacattgttcagtcgaattgtgttttcacagGTGAACTGGTTGAACTCTATGTTGGAGAAGTTCTGGCCGTCAATATTAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT