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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTGTCGTTTTTACTTCGATCTTGGGTCAGTCCGTTGCTGTTCGGGTTTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacgcttacaaacttgctttgttttggaaacttatgtagcgtgtcgcattttcaatttggtctttctcgacttgtgggttcagtcttgtgattg...

Basic information

species Physcomitrella patens
transcript PP1S49_242V6.4
intron # 1
splice site 5'
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|100436441|gb|BY961219.1|BY961219
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100438705|gb|BY961760.1|BY961760
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100416828|gb|BY993109.1|BY993109
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|208383578|gb|DC903535.1|DC903535
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|67570622|gb|BJ943446.1|BJ943446
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18327864|gb|BJ159868.1|BJ159868
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|208400191|gb|DC908852.1|DC908852
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100443529|gb|BY981956.1|BY981956
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|162213606|gb|FC389686.1|FC389686
EST:     CAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: CAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18371195|gb|BJ202797.1|BJ202797
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100398885|gb|BY990564.1|BY990564
EST:     AGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: AGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|67572941|gb|BJ945765.1|BJ945765
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100385646|gb|BY987711.1|BY987711
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18355332|gb|BJ187391.1|BJ187391
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|162205337|gb|FC382046.1|FC382046
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100391786|gb|BY989552.1|BY989552
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100436316|gb|BY961156.1|BY961156
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18327075|gb|BJ159076.1|BJ159076
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100429286|gb|BY978034.1|BY978034
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18364005|gb|BJ196078.1|BJ196078
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|208384750|gb|DC915283.1|DC915283
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100366216|gb|BY967337.1|BY967337
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100428415|gb|BY977794.1|BY977794
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100424686|gb|BY976764.1|BY976764
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|67574720|gb|BJ947544.1|BJ947544
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100382784|gb|BY986928.1|BY986928
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGGGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|208378626|gb|DC903657.1|DC903657
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|208347007|gb|DC901842.1|DC901842
EST:     AGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: AGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18365731|gb|BJ197808.1|BJ197808
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100397637|gb|BY990326.1|BY990326
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100428972|gb|BY959526.1|BY959526
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100444892|gb|BY982720.1|BY982720
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|18372050|gb|BJ203652.1|BJ203652
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100370396|gb|BY985389.1|BY985389
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
EST: gi|100432373|gb|BY960452.1|BY960452
EST:     GTTGCGGACAGCGNGAGAGGCTTCGNNCGTAGAGGGTCCTTCTCTGCTNG                         GGTGATTTAGNAGAACGAAAACAAGGACTCATGGGCGGACGAAAGAGATC
genomic: GTTGCGGACAGCG-GAGAGGCTTCG--CGTAGAGGGT-CTTCTCTGCT-Ggtgcgcgacg ... tgtgatttagGGTGATTTAG-AGAACGAAAACAAGGACTCAT-GGCGGACGAAAGAGATC
EST: gi|208385161|gb|DC911393.1|DC911393
EST:     TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTG                         GGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG
genomic: TTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 33 (downstream exon)
Score: 4

TTTTGTGTCGTTTTTACTTCGATCTTGGGTCAGTCCGTTGCTGTTCGGGTTTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacg ... tgtgatttagGGTGATTTAGAGAACGAAAACAAGGACTCATGGCGGACGAAAGAGATCGAGAAGTTGCCGAGCTGGAGGAAAATGTTAGAGAAGTGACGATTAATGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTGTCGTTTTTACTTCGATCTTGGGTCAGTCCGTTGCTGTTCGGGTTTGTAGTTGCGGACAGCGGAGAGGCTTCGCGTAGAGGGTCTTCTCTGCTGgtgcgcgacgcttacaaacttgctttgttttggaaacttatgtagcgtgtcgcattttcaatttggtctttctcgacttgtgggttcagtcttgtgattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG