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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcctcgtatttgtgtggaaatgaattgtttctgaaggtattttgtccgaatacctgcgatgtatgttttgacgcttaatgtgttcgtggaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGACCAGCGCTACTCCCAGGGATCCACGAAGTACTACGGCTATCCACAGAGCT

Basic information

species Physcomitrella patens
transcript PP1S77_55V6.1
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|18344302|gb|BJ176342.1|BJ176342
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162195079|gb|FC371367.1|FC371367
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162180646|gb|FC357003.1|FC357003
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18372024|gb|BJ203626.1|BJ203626
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18347240|gb|BJ179286.1|BJ179286
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162191928|gb|FC366933.1|FC366933
EST:     GCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: GCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18367522|gb|BJ199605.1|BJ199605
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18344035|gb|BJ176074.1|BJ176074
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18373989|gb|BJ205567.1|BJ205567
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18369557|gb|BJ201645.1|BJ201645
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18366602|gb|BJ198681.1|BJ198681
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162172714|gb|FC348095.1|FC348095
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162152272|gb|FC328251.1|FC328251
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18345769|gb|BJ177812.1|BJ177812
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18346945|gb|BJ178990.1|BJ178990
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18345078|gb|BJ177119.1|BJ177119
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18329153|gb|BJ161159.1|BJ161159
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162187327|gb|FC363485.1|FC363485
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162223806|gb|FC400060.1|FC400060
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACAAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18373494|gb|BJ205072.1|BJ205072
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|162151842|gb|FC328088.1|FC328088
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
EST: gi|18360689|gb|BJ192752.1|BJ192752
EST:     CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAG                         TTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC
genomic: CTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGAC

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: 61

ATCCAGGGATTAGTGTTTGCTGACGGTTTAGCACACACCAGAGTCCCAAACTCAGAGCCAGGTTTTAACTATGTCTCGCCTCGTGGAGGGCATCAAGGAGgtatgttatc ... gaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGACCAGCGCTACTCCCAGGGATCCACGAAGTACTACGGCTATCCACAGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccgaatacctgcgatgtatgttttgacgcttaatgtgttcgtggaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGACCAGCGCTACTCCCAGGGATCCACGAAGTACTACGGCTATCCACAGAGCT
                  tatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcctcgtatttgtgtggaaatgaattgtttctgaaggtattttgtccgaatacctgcgatgtatgttttgacgcttaatgtgttcgtggaccttgcagTTGTTGAAAGGGAAGGACGAGCCAGAGTATCGTTACCGCTCTGGGTACGACCAGCGCTACTCCCAGGGATCCACGAAGTACTACGGCTATCCACAGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT