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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttgatgctacactgttttgtctctgaagttcgtgtatttgtgtaatttaccattccacatcaaacattttcgtttaataatgcgaatggataatctcttacaaactcaaataaatattaattatcaagattatgttataatagcggctgggtggttcctgatattttag

Basic information

species Physcomitrella patens
transcript PP1S47_175V6.1
intron # 2
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|100446572|gb|CJ970871.1|CJ970871
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100448859|gb|CJ973158.1|CJ973158
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCNGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100375388|gb|BY948854.1|BY948854
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100416395|gb|BY975367.1|BY975367
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100448868|gb|CJ973167.1|CJ973167
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208353342|gb|DC946290.1|DC946290
EST:     TACGACTNG-AAGGAAC-AANTATCGAGAGTGCAGAAGCGGCAA-TTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100379831|gb|BY949966.1|BY949966
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCGGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|67724008|gb|BJ974267.1|BJ974267
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208355833|gb|DC930196.1|DC930196
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGGTTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100427879|gb|BY959171.1|BY959171
EST:     ACGACTCGAAAGGAACAAATTTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: ACGACTCGAAAGGAACAAATT-ATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|67569178|gb|BJ942002.1|BJ942002
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|18356169|gb|BJ188228.1|BJ188228
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208384047|gb|DC911225.1|DC911225
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208366345|gb|DC943863.1|DC943863
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208370373|gb|DC931785.1|DC931785
EST:     TACGACTCGAAAGGAACAAATTATCGAGAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100381026|gb|BY986852.1|BY986852
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208394403|gb|DC942563.1|DC942563
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208389723|gb|DC938299.1|DC938299
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208391012|gb|DC929331.1|DC929331
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|67716920|gb|BJ967179.1|BJ967179
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|67709929|gb|BJ965745.1|BJ965745
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100442587|gb|BY963281.1|BY963281
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|100364611|gb|BY947820.1|BY947820
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208385596|gb|DC937141.1|DC937141
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208380443|gb|DC914867.1|DC914867
EST:     TACGACTCGAAAGGAACAAATTACCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208354200|gb|DC957420.1|DC957420
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|67725438|gb|BJ975697.1|BJ975697
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208389767|gb|DC933641.1|DC933641
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208361102|gb|DC957553.1|DC957553
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|162272918|gb|FC448854.1|FC448854
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|162272917|gb|FC448853.1|FC448853
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208368823|gb|DC951347.1|DC951347
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
EST: gi|208387707|gb|DC937272.1|DC937272
EST:     TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG                         GAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG
genomic: TACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTG

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: 28 (upstream exon), 35 (downstream exon)
Score: 10

GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttga ... gatattttagGAACTGGTGAGAAATGATGGGTTCTACACTATCCGGCTGCCCGCAGATTTGATCAAACCCCGGCACAAGTTTGTCTTGGCCTCAGTGAAGGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAGgtgattttgatgctacactgttttgtctctgaagttcgtgtatttgtgtaatttaccattccacatcaaacattttcgtttaataatgcgaatggataatctcttacaaactcaaataaatattaattatcaagattatgttataatagcggctgggtggttcctgatattttag

- - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - AGAAGC