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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGGCTGACTCCTGAAGAAGTGGTAGCAAAGATCATGGCAAATCCAGAAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtggtcgcactcataaatgacgagattgtgcattaaaatggtcttgctcgagacgagattatggcaaatgtcattatgaatgaatggtgggtc...

Basic information

species Physcomitrella patens
transcript PP1S110_13V6.1
intron # 12
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|37835216|gb|BJ593228.1|BJ593228
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162193091|gb|FC369929.1|FC369929
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|37850772|gb|BJ608780.1|BJ608780
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162193090|gb|FC369928.1|FC369928
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGGTGCTATCATGGAT                         TGTTCCACAAATCCTTTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162248204|gb|FC423667.1|FC423667
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162179084|gb|FC356485.1|FC356485
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162179083|gb|FC356484.1|FC356484
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|37824986|gb|BJ583052.1|BJ583052
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|37853301|gb|BJ611309.1|BJ611309
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         NGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|208395403|gb|DC924471.1|DC924471
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162176402|gb|FC353587.1|FC353587
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162184457|gb|FC359203.1|FC359203
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162166027|gb|FC340423.1|FC340423
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|37836231|gb|BJ594239.1|BJ594239
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|208349470|gb|DC921944.1|DC921944
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162169704|gb|FC345241.1|FC345241
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162183778|gb|FC360695.1|FC360695
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162183777|gb|FC360694.1|FC360694
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|162244160|gb|FC419811.1|FC419811
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
EST: gi|208396401|gb|DC920067.1|DC920067
EST:     AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGAT                         TGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG
genomic: AAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG

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: 27 (upstream exon), 34 (downstream exon)
Score: 7

AATTGGGCTGACTCCTGAAGAAGTGGTAGCAAAGATCATGGCAAATCCAGAAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtg ... attgttacagTGTTCCACAAATCCATTAAATATTACTAAGTACCAGAATGACAAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGGCTGACTCCTGAAGAAGTGGTAGCAAAGATCATGGCAAATCCAGAAGTTGCAGTAGCCTTCCAGAACCCGAAAGTCCAGGCTGCTATCATGGATgtaagttgtggtcgcactcataaatgacgagattgtgcattaaaatggtcttgctcgagacgagattatggcaaatgtcattatgaatgaatggtgggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA