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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcctcttgaaagtgtttcgatgcctgcaagacatctactacctcttagcgaacccgaaggcttaatttccaattggtccattggtttgtgtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAAGTTGAAGCTGCCAGTGTGAATCCGGTAGACTGGAAAGTCATTCAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S45_86V6.1
intron # 1
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|100362458|gb|BY947367.1|BY947367
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100425613|gb|BY958683.1|BY958683
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100437465|gb|BY979665.1|BY979665
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGTGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100422238|gb|BY957925.1|BY957925
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CGTGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100418702|gb|BY975699.1|BY975699
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100386765|gb|BY970306.1|BY970306
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|208391431|gb|DC937579.1|DC937579
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|208374474|gb|DC941203.1|DC941203
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100397599|gb|BY990307.1|BY990307
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|208390052|gb|DC938107.1|DC938107
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCANCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100392348|gb|BY953318.1|BY953318
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100360635|gb|BY984217.1|BY984217
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100356582|gb|BY965177.1|BY965177
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100430157|gb|BY978275.1|BY978275
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100441285|gb|BY962574.1|BY962574
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|18328811|gb|BJ160817.1|BJ160817
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
EST: gi|100443033|gb|BY981659.1|BY981659
EST:     TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAG                         CATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA
genomic: TGCGTGCTGTTCAATATTCGACGTTCGGAGGGGGCGCTGCTGCGCTTCAGgtactcggtg ... gtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcgaacccgaaggcttaatttccaattggtccattggtttgtgtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAAGTTGAAGCTGCCAGTGTGAATCCGGTAGACTGGAAAGTCATTCAAGCAG
               gcttaat  putative branch site (score: 4)
                 ttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcctcttgaaagtgtttcgatgcctgcaagacatctactacctcttagcgaacccgaaggcttaatttccaattggtccattggtttgtgtaaatgcagCATGTGGAGATACCCATGCCCGTGCCAGCTAAGGACCAGTTGTTGATTAAAGTTGAAGCTGCCAGTGTGAATCCGGTAGACTGGAAAGTCATTCAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC