Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacttcgatgtaattgtgaattcgctgatcaagggcgggggtctccgtttttacattgcacagcaacctcatgtttagggtgttctctttgtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCATGCGACATTCGTACCCCACACCGCCGGACGATACTCCGTCAAGCGCTTCA

Basic information

species Physcomitrella patens
transcript PP1S400_33V6.1
intron # 1
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|162204682|gb|FC380896.1|FC380896
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67575030|gb|BJ947854.1|BJ947854
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162226409|gb|FC402402.1|FC402402
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162224908|gb|FC401116.1|FC401116
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162246678|gb|FC425271.1|FC425271
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|208357916|gb|DC934835.1|DC934835
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162224019|gb|FC400377.1|FC400377
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67712612|gb|BJ966061.1|BJ966061
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67724322|gb|BJ974581.1|BJ974581
EST:     GACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: GACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67698472|gb|BJ958705.1|BJ958705
EST:     TTCGGGCGCTNGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: TTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67728065|gb|BJ978324.1|BJ978324
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67712655|gb|BJ966104.1|BJ966104
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67719803|gb|BJ970062.1|BJ970062
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18372645|gb|BJ204247.1|BJ204247
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162204683|gb|FC380897.1|FC380897
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18344654|gb|BJ176695.1|BJ176695
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18358968|gb|BJ191028.1|BJ191028
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67693895|gb|BJ954128.1|BJ954128
EST:     TCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: TCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67717985|gb|BJ968244.1|BJ968244
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162237857|gb|FC412497.1|FC412497
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162224018|gb|FC400376.1|FC400376
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18362407|gb|BJ194477.1|BJ194477
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162246677|gb|FC425270.1|FC425270
EST:     GGGCGCT-GTCTTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: GGGCGCTGGTC-TTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18365457|gb|BJ197533.1|BJ197533
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|162258530|gb|FC434745.1|FC434745
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67570610|gb|BJ943434.1|BJ943434
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67702118|gb|BJ962351.1|BJ962351
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|67576601|gb|BJ949425.1|BJ949425
EST:     CTCAGCNGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|208373799|gb|DC936584.1|DC936584
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
EST: gi|18370250|gb|BJ201852.1|BJ201852
EST:     CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAG                         ATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT
genomic: CTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCAT

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: 35 (upstream exon), 34 (downstream exon)
Score: 33

TCCCCCTCCCTTTCCCTCCCTGCATCTGTGCTGTGTCGCCATGGCCGTCGCTCAGCCGGAGGTTAAGCTCTTCGGGCGCTGGTCTTTCGACGACATCGAGgtttgattct ... gtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCATGCGACATTCGTACCCCACACCGCCGGACGATACTCCGTCAAGCGCTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttttacattgcacagcaacctcatgtttagggtgttctctttgtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCATGCGACATTCGTACCCCACACCGCCGGACGATACTCCGTCAAGCGCTTCA
                                   tgttctctttgtcctt  CT-rich tract
     ttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacttcgatgtaattgtgaattcgctgatcaagggcgggggtctccgtttttacattgcacagcaacctcatgtttagggtgttctctttgtccttgcagATTAATGACATCTCGTTGGCCGATTATATTGCTGTATCCGTAGACAAGCATGCGACATTCGTACCCCACACCGCCGGACGATACTCCGTCAAGCGCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcaca