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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttttgatgagaatcgtgatataagttggtgtgtatatagtattcatgacctgtctctgatacattctttcataacttaaatattggctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTGAGGCCGCCGTGGACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAG

Basic information

species Physcomitrella patens
transcript PP1S98_136V6.2
intron # 1
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|67578873|gb|BJ951040.1|BJ951040
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162210330|gb|FC386210.1|FC386210
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67574583|gb|BJ947407.1|BJ947407
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67701028|gb|BJ961261.1|BJ961261
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162250085|gb|FC427394.1|FC427394
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67571413|gb|BJ944237.1|BJ944237
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162250084|gb|FC427393.1|FC427393
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162276312|gb|FC452419.1|FC452419
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162223989|gb|FC400347.1|FC400347
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162226371|gb|FC403287.1|FC403287
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162236290|gb|FC411409.1|FC411409
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTGTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|19790227|gb|BQ041763.1|BQ041763
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162261462|gb|FC438298.1|FC438298
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162226370|gb|FC403286.1|FC403286
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|37847166|gb|BJ605174.1|BJ605174
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67695443|gb|BJ955676.1|BJ955676
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162216551|gb|FC392448.1|FC392448
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162246712|gb|FC424694.1|FC424694
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162269839|gb|FC445889.1|FC445889
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67694743|gb|BJ954976.1|BJ954976
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|162210329|gb|FC386209.1|FC386209
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAATGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
EST: gi|67701356|gb|BJ961589.1|BJ961589
EST:     GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAG                         ATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG
genomic: GATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTG

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), 35 (downstream exon)
Score: 153

CATTGCGCGCTGGGCCAGAGCGTGCTTCTGTCTTCGCGTCGCGCTTCTGTGATGTCTGGCGTCTCTCTTCCTTCCCTCGCCAGCTCTAGTTACCGAACAGgtcagttatg ... ctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTGAGGCCGCCGTGGACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgacctgtctctgatacattctttcataacttaaatattggctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTGAGGCCGCCGTGGACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAG
                           tcataac  putative branch site (score: 153)
                     attctttcataactta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttttgatgagaatcgtgatataagttggtgtgtatatagtattcatgacctgtctctgatacattctttcataacttaaatattggctactagcagATGCGAAAAGGTCTTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTGAGGCCGCCGTGGACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT