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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAGCTGCAGATCAAAGTCGATGAAAAGACCGGGGAAATTATAGATGCCTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggctacaccattcaaccatacgatagggtattctgcctaggtcggaaggatctgaatctgtccttggaaatgaaagcttatcactggatattc...

Basic information

species Physcomitrella patens
transcript PP1S76_212V6.2
intron # 3
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|162224580|gb|FC400476.1|FC400476
EST:     TTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: TTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|67508569|gb|BJ941432.1|BJ941432
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|162250386|gb|FC426248.1|FC426248
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|37824297|gb|BJ582363.1|BJ582363
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|162250385|gb|FC426247.1|FC426247
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|162177237|gb|FC353394.1|FC353394
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|162177238|gb|FC353395.1|FC353395
EST:     CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: CTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|67691788|gb|BJ952021.1|BJ952021
EST:     TCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: TCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
EST: gi|162224579|gb|FC400475.1|FC400475
EST:     TTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTG                         CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA
genomic: TTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGA

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), 33 (downstream exon)
Score: 16

ATGAAGCTGCAGATCAAAGTCGATGAAAAGACCGGGGAAATTATAGATGCCTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggc ... gtgctcgtagCTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAGCTGCAGATCAAAGTCGATGAAAAGACCGGGGAAATTATAGATGCCTGTTTCAAGACCTTCGGATGTGGTTCGGCTATTGCTTCGTCGTCTGTTGgtatgttggctacaccattcaaccatacgatagggtattctgcctaggtcggaaggatctgaatctgtccttggaaatgaaagcttatcactggatattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaaa