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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctctctctctctatatatatatatatatatatatatatatatatatacatatttaatattcaaatttacaactactttgtcatcttctacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG

Basic information

species Physcomitrella patens
transcript PP1S340_38V6.1
intron # 3
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|18337179|gb|BJ169203.1|BJ169203
EST:     TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAG                         ACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
genomic: TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAGgtatgtttcc ... tacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
EST: gi|67691703|gb|BJ951936.1|BJ951936
EST:     TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAG                         ACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
genomic: TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAGgtatgtttcc ... tacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
EST: gi|67508482|gb|BJ941348.1|BJ941348
EST:     TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAG                         ACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
genomic: TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAGgtatgtttcc ... tacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
EST: gi|67695048|gb|BJ955281.1|BJ955281
EST:     TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAG                         ACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
genomic: TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAGgtatgtttcc ... tacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
EST: gi|162217820|gb|FC394120.1|FC394120
EST:     TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAG                         ACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
genomic: TAAAATCGAAGCAAATCGGAAAATCGGGTTGCACACATTATGTCTCTTAGgtatgtttcc ... tacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatacatatttaatattcaaatttacaactactttgtcatcttctacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG
        atttaat  putative branch site (score: 4)
                                ctttgtcatcttct  putative PPT
      atatttaatattcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctctctctctctatatatatatatatatatatatatatatatatatacatatttaatattcaaatttacaactactttgtcatcttctacattacagACATCCGAGTGAAGGAGCAATCAGTTGAAGCTTTGTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC