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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCAAAGAAGGAGAGATGTGGATGCCTTGTGGGCCCCGAGAACCAGGTGCTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattctcgctagacgtgatttattctattcatttcttgtgttccctttccttcaggaagtcgagaaaaacgatatggccaatttattgttgcttg...

Basic information

species Physcomitrella patens
transcript PP1S76_197V6.1
intron # 7
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|162261190|gb|FC437207.1|FC437207
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162192379|gb|FC369087.1|FC369087
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162268434|gb|FC444203.1|FC444203
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162189691|gb|FC366329.1|FC366329
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162181630|gb|FC357932.1|FC357932
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162176272|gb|FC352729.1|FC352729
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162268433|gb|FC444202.1|FC444202
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162196818|gb|FC373886.1|FC373886
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162229089|gb|FC404773.1|FC404773
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162243141|gb|FC416741.1|FC416741
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37846864|gb|BJ604872.1|BJ604872
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37853252|gb|BJ611260.1|BJ611260
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37830846|gb|BJ588858.1|BJ588858
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162187241|gb|FC363191.1|FC363191
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37850914|gb|BJ608922.1|BJ608922
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162149983|gb|FC326514.1|FC326514
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37825618|gb|BJ583684.1|BJ583684
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37824718|gb|BJ582784.1|BJ582784
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162269734|gb|FC445628.1|FC445628
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162169206|gb|FC345173.1|FC345173
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|37837980|gb|BJ595988.1|BJ595988
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|208350314|gb|DC925762.1|DC925762
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
EST: gi|162154849|gb|FC331891.1|FC331891
EST:     CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCAAAG                         ATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG
genomic: CTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAG

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: 16 (upstream exon), 26 (downstream exon)
Score: 7

TACCAAAGAAGGAGAGATGTGGATGCCTTGTGGGCCCCGAGAACCAGGTGCTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattc ... tcgagaacagATTTTACCACCTCCAATCACAAAATCAGATTTCGACAAAGTCCTCGCAAAGCAGAGGCCCACTGTCAGCAAAGGCGACCTTATTATTCAAGAGAAATTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCAAAGAAGGAGAGATGTGGATGCCTTGTGGGCCCCGAGAACCAGGTGCTAGGCAAACCACTATGACGGAGCTTGCCGCTGAAGGGCAGGCATCGAAGgtacgaattctcgctagacgtgatttattctattcatttcttgtgttccctttccttcaggaagtcgagaaaaacgatatggccaatttattgttgcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaac