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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtacctttttacgaatgtgcttaatattgatgtagtttgaggtctttgattgcacctattattgttcgtacggggacaacgaaaaccctactcaatggat...

Basic information

species Physcomitrella patens
transcript PP1S64_220V6.1
intron # 10
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|162160586|gb|FC336355.1|FC336355
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162191335|gb|FC368144.1|FC368144
EST:     ACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: ACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162170440|gb|FC347625.1|FC347625
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162244597|gb|FC424603.1|FC424603
EST:     ACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: ACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|208396587|gb|DC915899.1|DC915899
EST:     CTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: CTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162189526|gb|FC365748.1|FC365748
EST:     CTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: CTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162166217|gb|FC343434.1|FC343434
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162155390|gb|FC332004.1|FC332004
EST:     CGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: CGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162191242|gb|FC367920.1|FC367920
EST:     ACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: ACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162181881|gb|FC357688.1|FC357688
EST:     TACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: TACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162154421|gb|FC330423.1|FC330423
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162156210|gb|FC332585.1|FC332585
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGA
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGA
EST: gi|162165158|gb|FC341153.1|FC341153
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162197023|gb|FC373363.1|FC373363
EST:     TCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: TCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162170441|gb|FC347626.1|FC347626
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162182492|gb|FC357467.1|FC357467
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|161978655|gb|EE296353.1|EE296353
EST:     AACCTCCAAGACCAGGCGACGTCTCGNTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AACCTCCAAGACCAGGCGACGTCTCG-TTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162165339|gb|FC340827.1|FC340827
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162223428|gb|FC400319.1|FC400319
EST:     GCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: GCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|37852182|gb|BJ610190.1|BJ610190
EST:     GCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: GCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162199478|gb|FC373780.1|FC373780
EST:     ATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: ATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162252057|gb|FC428296.1|FC428296
EST:     TCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: TCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162244637|gb|FC424604.1|FC424604
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162188744|gb|FC364030.1|FC364030
EST:     AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: AAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
EST: gi|162174741|gb|FC352157.1|FC352157
EST:     GCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG                         CGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG
genomic: GCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGG

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: 32

ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtaccttttt ... gtcattacagCGCAGCTATCATGCAATCATTGAGAAAAAGAGCGCATATTATGACGGATGGCTTCAATGCATGCGAGAACGTTGTCTGCAACTTTACTGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAGgtacctttttacgaatgtgcttaatattgatgtagtttgaggtctttgattgcacctattattgttcgtacggggacaacgaaaaccctactcaatggat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaaa