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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcataattctttatcctctccacactcactttgatcattgtcgaagtcgacaaggttttgtcatgaagagttactgacgtgcagctgttcctttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAAGCAGATTACGGCAAGCACGCCACTAACTTGCAAGGTGTCTTCGCCGCTG

Basic information

species Physcomitrella patens
transcript PP1S79_140V6.1
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|162197518|gb|FC375691.1|FC375691
EST:     GGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: GGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162249230|gb|FC421248.1|FC421248
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162198168|gb|FC373092.1|FC373092
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162172195|gb|FC348760.1|FC348760
EST:     TGGCCATGGGTTTTTTGGGTCCCGAGCAA                         ATCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAATTTCAAA
genomic: TGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162181454|gb|FC358484.1|FC358484
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162162619|gb|FC338921.1|FC338921
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|22132620|gb|BQ827257.1|BQ827257
EST:     TTGAAACGGCCCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162198167|gb|FC373091.1|FC373091
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162186531|gb|FC363295.1|FC363295
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162172124|gb|FC347987.1|FC347987
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162198870|gb|FC372897.1|FC372897
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162188617|gb|FC364527.1|FC364527
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162151792|gb|FC328649.1|FC328649
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162198869|gb|FC372896.1|FC372896
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162187383|gb|FC363541.1|FC363541
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162172196|gb|FC348761.1|FC348761
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162181453|gb|FC358483.1|FC358483
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|37853204|gb|BJ611212.1|BJ611212
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162192162|gb|FC368311.1|FC368311
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|67569424|gb|BJ942248.1|BJ942248
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|19776823|gb|BQ039119.1|BQ039119
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAACTTGGACTCGAGACCGATGCCCGATCCAACTTCA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCA
EST: gi|162166747|gb|FC342716.1|FC342716
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162173943|gb|FC349743.1|FC349743
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162161936|gb|FC338519.1|FC338519
EST:     TGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162188618|gb|FC364528.1|FC364528
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|162192163|gb|FC368312.1|FC368312
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
EST: gi|67692687|gb|BJ952920.1|BJ952920
EST:     TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAA                         CTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA
genomic: TTGAAACGGACCTTGTTCTTCTGGCCATGGGTTTCTTGGGTCCCGAGCAAgtgagttcat ... ttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacaaggttttgtcatgaagagttactgacgtgcagctgttcctttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAAGCAGATTACGGCAAGCACGCCACTAACTTGCAAGGTGTCTTCGCCGCTG
                        tactgac  putative branch site (score: 1)
                                     ctgttcctttttttgc  putative PPT
                                            ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcataattctttatcctctccacactcactttgatcattgtcgaagtcgacaaggttttgtcatgaagagttactgacgtgcagctgttcctttttttgcagCTCATTTCGGAGAAGCTTGGACTCGAGACCGATGCCCGATCCAACTTCAAAGCAGATTACGGCAAGCACGCCACTAACTTGCAAGGTGTCTTCGCCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT