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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGACTGCAAAAGAGCTCGCAGCCTATGATGGTACTGATCCGAGCAAGCCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaacttttatattttaaatgggtttcaataatctctgtgaagaagaggcgtgtcaaatagaaataaatttcataaacagcacattgaaggcaaa...

Basic information

species Physcomitrella patens
transcript PP1S97_92V6.1
intron # 2
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|162268785|gb|FC444710.1|FC444710
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|162170536|gb|FC346863.1|FC346863
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208385441|gb|DC953074.1|DC953074
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208387063|gb|DC941235.1|DC941235
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|67693759|gb|BJ953992.1|BJ953992
EST:     TATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: TATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|67570478|gb|BJ943302.1|BJ943302
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208359380|gb|DC954233.1|DC954233
EST:     AAGGACNAATTTATGATGT-TCTCAATCAAG                         GGCA-TTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: AAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208355810|gb|DC929991.1|DC929991
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|162271313|gb|FC446691.1|FC446691
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37837193|gb|BJ595201.1|BJ595201
EST:     CCTTTGCTGATGGTTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|162268786|gb|FC444711.1|FC444711
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|18328263|gb|BJ160267.1|BJ160267
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37838677|gb|BJ596685.1|BJ596685
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|100433736|gb|BY960681.1|BY960681
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTTGGAG-ACCTTATGCCCTCTT
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACT-GGAGGACCTTATGCCCTCTT

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: 30 (upstream exon), 26 (downstream exon)
Score: 3

AGCTGACTGCAAAAGAGCTCGCAGCCTATGATGGTACTGATCCGAGCAAGCCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGACTGCAAAAGAGCTCGCAGCCTATGATGGTACTGATCCGAGCAAGCCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaacttttatattttaaatgggtttcaataatctctgtgaagaagaggcgtgtcaaatagaaataaatttcataaacagcacattgaaggcaaa

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