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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAATCGGAGAAAGTATTAATCAAAGAGGGCGTCAGTAAGCAAGTCATCAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgtggctctcatcttgagatttctctcgactttgaagcctgatatttcgatgtgattccaatttgtcttgtagatctttactgtgtgctgacaggggcctatatatgtaattttccccacag

Basic information

species Physcomitrella patens
transcript PP1S364_48V6.1
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|162153625|gb|FC330174.1|FC330174
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|162203750|gb|FC378625.1|FC378625
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|18356837|gb|BJ188896.1|BJ188896
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGC
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGC
EST: gi|208374277|gb|DC940662.1|DC940662
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTANGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGANACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|162219329|gb|FC395325.1|FC395325
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|100443139|gb|BY981765.1|BY981765
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|100443175|gb|BY981801.1|BY981801
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|208376795|gb|DC902962.1|DC902962
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTANGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
EST: gi|18329902|gb|BJ161908.1|BJ161908
EST:     CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTG                         TGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT
genomic: CAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTT

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: 19 (upstream exon), 35 (downstream exon)
Score: 6

GTGAAATCGGAGAAAGTATTAATCAAAGAGGGCGTCAGTAAGCAAGTCATCAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgt ... ttccccacagTGCACTATCGAGCATGGACAGCGAGCACAATGCACAAGTTTGATGATACTTGGAATGAGCAACAACCCCAAGAGCTTAGGCTTGGTCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAATCGGAGAAAGTATTAATCAAAGAGGGCGTCAGTAAGCAAGTCATCAAAGAAGGGCAGGGTGACGGGCCGCCTCCTAGGCATTCAAGCTGCTTTGgtatgctcgtggctctcatcttgagatttctctcgactttgaagcctgatatttcgatgtgattccaatttgtcttgtagatctttactgtgtgctgacaggggcctatatatgtaattttccccacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT