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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcttaaacgctgctgttcctgtgtgttattgatactgtcacatggtaggcctgaaatgctaactaagttcaaggatatcatgatcatgttgttttatatacgactggtttggctttgcattgcgatttcatttagggtataagcgaagaacgttgatctagtagctgagtcgtgaaaacccttcatacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATCAGGCAACCAAGAACCTGTTCGGGTTGAGATTACCGAAGCCGCCTTGGAA

Basic information

species Physcomitrella patens
transcript PP1S76_146V6.1
intron # 3
splice site 3'
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|37833535|gb|BJ591547.1|BJ591547
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|162204037|gb|FC379406.1|FC379406
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|162228920|gb|FC404206.1|FC404206
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|67570323|gb|BJ943147.1|BJ943147
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|162226667|gb|FC402738.1|FC402738
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|162204038|gb|FC379407.1|FC379407
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|67693595|gb|BJ953828.1|BJ953828
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|67569434|gb|BJ942258.1|BJ942258
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
EST: gi|67692697|gb|BJ952930.1|BJ952930
EST:     CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGC                         TGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC
genomic: CAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATC

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: 25 (upstream exon), 33 (downstream exon)
Score: 11

GAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTGAGGAAAGCCCAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAGAGCTTGCTGCgtacgttctt ... atacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATCAGGCAACCAAGAACCTGTTCGGGTTGAGATTACCGAAGCCGCCTTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcgaagaacgttgatctagtagctgagtcgtgaaaacccttcatacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATCAGGCAACCAAGAACCTGTTCGGGTTGAGATTACCGAAGCCGCCTTGGAA
           cgttgat  putative branch site (score: 11)
                                       cccttcat  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcttaaacgctgctgttcctgtgtgttattgatactgtcacatggtaggcctgaaatgctaactaagttcaaggatatcatgatcatgttgttttatatacgactggtttggctttgcattgcgatttcatttagggtataagcgaagaacgttgatctagtagctgagtcgtgaaaacccttcatacacgcagTGCGGAGTTCGACGGTTACTGTGACGACGAGCTTGTGAGAGTGACCTTATCAGGCAACCAAGAACCTGTTCGGGTTGAGATTACCGAAGCCGCCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC