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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaactcctctcaccctcacagcaaaactgactgcggtgaaatcccttgccgagaaccggcacccttctgacattgattgggtgtattcctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCCTCCTACATGGGCACCATACACGTCACCAGAAGCGCCCACTCCTTACGTT

Basic information

species Physcomitrella patens
transcript PP1S4_236V6.2
intron # 3
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|208384529|gb|DC915001.1|DC915001
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|67719718|gb|BJ969977.1|BJ969977
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208371913|gb|DC951877.1|DC951877
EST:     CGATT-GTATGG                         TCT-ATCACAGNTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: CGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|100371102|gb|BY985939.1|BY985939
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208399209|gb|DC912438.1|DC912438
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208361476|gb|DC935135.1|DC935135
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208351536|gb|DC905713.1|DC905713
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGGGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|100372516|gb|BY985636.1|BY985636
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACCCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208382079|gb|DC903095.1|DC903095
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208355779|gb|DC910545.1|DC910545
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208393216|gb|DC908039.1|DC908039
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|100441086|gb|BY980707.1|BY980707
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|100373759|gb|BY967797.1|BY967797
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208380400|gb|DC907725.1|DC907725
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCGCCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208395995|gb|DC915755.1|DC915755
EST:     ATGCNGATTGGTATGG                         T-TAATCACAGNTCCAGTATACTCGCNTCAGGCGGCACCGGAGACTATCCC
genomic: ATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208349434|gb|DC901770.1|DC901770
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208349438|gb|DC921926.1|DC921926
EST:     ATGCCGATTGGTATNG                         TTTAATCACAGCTCCAGTATACTCGNCTCAGGCGGCACCGGAGACTATCCC
genomic: ATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|67716674|gb|BJ966934.1|BJ966934
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|208356249|gb|DC902243.1|DC902243
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|100411013|gb|BY956285.1|BY956285
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|67719626|gb|BJ969885.1|BJ969885
EST:     TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: TTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
EST: gi|67703243|gb|BJ963476.1|BJ963476
EST:     CTCGGCCAATGCCGATTGGTATGG                         TCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC
genomic: CTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCC

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: 21 (upstream exon), 35 (downstream exon)
Score: 6

TGGCAGCTAAAGGAGGGCATGGCTTCCAGTATCTCAACATCATAACAGTGTTGTTAAGCTCACTACTGATCTTCGACTCGGCCAATGCCGATTGGTATGGgtgagtaact ... cctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCCTCCTACATGGGCACCATACACGTCACCAGAAGCGCCCACTCCTTACGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttgccgagaaccggcacccttctgacattgattgggtgtattcctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCCTCCTACATGGGCACCATACACGTCACCAGAAGCGCCCACTCCTTACGTT
                                           ttcctgct  CT-rich tract
                             attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaactcctctcaccctcacagcaaaactgactgcggtgaaatcccttgccgagaaccggcacccttctgacattgattgggtgtattcctgctgcagTCTAATCACAGCTCCAGTATACTCGCCTCAGGCGGCACCGGAGACTATCCCTCCTACATGGGCACCATACACGTCACCAGAAGCGCCCACTCCTTACGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC