Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCCATTATTAAATCGAGTCGTTGATGGGTTTGTCAAGGTTGGAGGAGTGGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgccaggacctattctgatgcttttatacctaatcacttgcccatatcaccaagagatatcttcctcttgtatcattgcaggccctttctttg...

Basic information

species Physcomitrella patens
transcript PP1S46_326V6.1
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|162278434|gb|FC454520.1|FC454520
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162265952|gb|FC442955.1|FC442955
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162279986|gb|FC456172.1|FC456172
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259016|gb|FC435127.1|FC435127
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208381670|gb|DC915536.1|DC915536
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259138|gb|FC436432.1|FC436432
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208367972|gb|DC950997.1|DC950997
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162269068|gb|FC444936.1|FC444936
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162264590|gb|FC440886.1|FC440886
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|67576061|gb|BJ948885.1|BJ948885
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162229199|gb|FC404558.1|FC404558
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259211|gb|FC436466.1|FC436466
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|67569310|gb|BJ942134.1|BJ942134
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208395552|gb|DC928967.1|DC928967
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162272952|gb|FC449083.1|FC449083
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259139|gb|FC436433.1|FC436433
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162276798|gb|FC452792.1|FC452792
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162226856|gb|FC403044.1|FC403044
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208391705|gb|DC937937.1|DC937937
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|19784287|gb|BQ040153.1|BQ040153
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162271484|gb|FC446433.1|FC446433
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208384616|gb|DC915219.1|DC915219
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162276799|gb|FC452793.1|FC452793
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162229198|gb|FC404557.1|FC404557
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259212|gb|FC436467.1|FC436467
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162276680|gb|FC452258.1|FC452258
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|67692570|gb|BJ952803.1|BJ952803
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162271530|gb|FC446479.1|FC446479
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162245700|gb|FC419600.1|FC419600
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162226857|gb|FC403045.1|FC403045
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259912|gb|FC436047.1|FC436047
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162280258|gb|FC456275.1|FC456275
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162262668|gb|FC438463.1|FC438463
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162262669|gb|FC438464.1|FC438464
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|162259370|gb|FC436235.1|FC436235
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
EST: gi|208352185|gb|DC901706.1|DC901706
EST:     GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAG                         AGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG
genomic: GGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGG

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), 34 (downstream exon)
Score: 129

CACCCATTATTAAATCGAGTCGTTGATGGGTTTGTCAAGGTTGGAGGAGTGGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgc ... aaatgtgcagAGGAGACGAACAAGAAGTCTTTGGAAAAGACCGTTCAGCGTATGGGCAAGGAGGCCGTGCAATGGGGCCTTGTCGCTGGAGTTTACACTGGCATGACCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCCATTATTAAATCGAGTCGTTGATGGGTTTGTCAAGGTTGGAGGAGTGGGCGCTCTGCATGCTGCTTCTCAAGATACCTACCTATTTTTGCTCCAAGgtttgtccgccaggacctattctgatgcttttatacctaatcacttgcccatatcaccaagagatatcttcctcttgtatcattgcaggccctttctttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT