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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGACAGATGAAGCTACAACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtacttcccctcttttcccatcctttcccgccgagttcttgtgctctaaaactcgtgttttgaatagtcgagaggaatcgtggaagttaagagtg...

Basic information

species Physcomitrella patens
transcript PP1S39_120V6.1
intron # 14
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|162181521|gb|FC358135.1|FC358135
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|67700770|gb|BJ961003.1|BJ961003
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|100379082|gb|BY986565.1|BY986565
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAA-CGTTCTGTGCGAGT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGT
EST: gi|37851029|gb|BJ609037.1|BJ609037
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162166326|gb|FC342919.1|FC342919
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162181520|gb|FC358134.1|FC358134
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162177126|gb|FC353179.1|FC353179
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|208368827|gb|DC951351.1|DC951351
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162153392|gb|FC329902.1|FC329902
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162253080|gb|FC428912.1|FC428912
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162196480|gb|FC374406.1|FC374406
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162196479|gb|FC374405.1|FC374405
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|162166327|gb|FC342920.1|FC342920
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
EST: gi|67724030|gb|BJ974289.1|BJ974289
EST:     AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAG                         TTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT
genomic: AACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTAT

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: 32 (upstream exon), 31 (downstream exon)
Score: 8

ACTGGACAGATGAAGCTACAACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtact ... atgtttttagTTTGTGGAAGATGCTGCTTCGGACCTTCTTCCAAACGTTCTGTGCGAGTATCTCTACACTCTTTCGGGAATGTTCACAGATTTTTACACCAACTGCAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGACAGATGAAGCTACAACATCCAAGTGAGAGAGCATTGGGTTTGCAGTTGATTCGTTTTGGCGAGgtacagtacttcccctcttttcccatcctttcccgccgagttcttgtgctctaaaactcgtgttttgaatagtcgagaggaatcgtggaagttaagagtg

- - - - - - - - - - - - - - - -  AGAGCA