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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttataggacatcggttctgatttcgaatcaaatagtaactctcttgtccaatctatttctttcttaacatttccttgaagaaaatattctttagttgtagattgtgtctatttaagacgagagggatacgtcgttggaaatgctacgctctcaattgcaacattgttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGCATGGACATTCAGGGACCATCGAATATCTCTGATGGTTTTCGGGTGAAGG

Basic information

species Physcomitrella patens
transcript PP1S32_182V6.1
intron # 4
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|162246708|gb|FC424690.1|FC424690
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162158818|gb|FC335341.1|FC335341
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162152941|gb|FC329243.1|FC329243
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162172189|gb|FC348754.1|FC348754
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162156021|gb|FC332188.1|FC332188
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162197334|gb|FC372296.1|FC372296
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162159618|gb|FC335796.1|FC335796
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162162061|gb|FC338852.1|FC338852
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162151213|gb|FC327693.1|FC327693
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162164955|gb|FC342146.1|FC342146
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162173783|gb|FC349959.1|FC349959
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162151358|gb|FC327487.1|FC327487
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
EST: gi|162161280|gb|FC337343.1|FC337343
EST:     TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAG                         GTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC
genomic: TGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGC

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: 33 (upstream exon), 29 (downstream exon)
Score: 54

ATGCGAGCTACTGTCAAAGAAGTGGCGTCTTGCTTTCCAACTGCGGTGATTAGTGGAAGATCACGACCGAAGgtatttatag ... gttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGCATGGACATTCAGGGACCATCGAATATCTCTGATGGTTTTCGGGTGAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttataggacatcggttctgatttcgaatcaaatagtaactctcttgtccaatctatttctttcttaacatttccttgaagaaaatattctttagttgtagattgtgtctatttaagacgagagggatacgtcgttggaaatgctacgctctcaattgcaacattgttggtgcagGTGTACGATTTTGTGCGATTATCAGAATTGTATTATGCTGGGAGTCATGGCATGGACATTCAGGGACCATCGAATATCTCTGATGGTTTTCGGGTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA