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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgttatcgtattgacaagcgttttggaggggataaggagagggtgattttaggcagaagggataatggtggatgtcgggcttttttggggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAGATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG

Basic information

species Physcomitrella patens
transcript PP1S58_258V6.1
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|162270598|gb|FC446523.1|FC446523
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|18329931|gb|BJ161937.1|BJ161937
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|18359856|gb|BJ191917.1|BJ191917
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|67570099|gb|BJ942923.1|BJ942923
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|162278520|gb|FC453982.1|FC453982
EST:     CTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: CTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|18343994|gb|BJ176033.1|BJ176033
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|37853257|gb|BJ611265.1|BJ611265
EST:     TTTGTATGGTNNGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|67698429|gb|BJ958662.1|BJ958662
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|37847801|gb|BJ605809.1|BJ605809
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|208362046|gb|DC943487.1|DC943487
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|19790467|gb|BQ041885.1|BQ041885
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|67574994|gb|BJ947818.1|BJ947818
EST:     TTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
EST: gi|162244647|gb|FC424614.1|FC424614
EST:     TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAG                         GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG
genomic: TTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAG

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: 34 (upstream exon), 30 (downstream exon)
Score: 19

ATATCTCTCCTTAAAGAGTTTCTCGTCGAGTCGTGTGCTTTTGTGCTTCATTCGGTTCCTCTCGTAACCCACTGCTCCTGGTCTTTTGTATGGTTTGGAGgtacgttggg ... ggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAGATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttaggcagaagggataatggtggatgtcgggcttttttggggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAGATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG
                                     tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgttatcgtattgacaagcgttttggaggggataaggagagggtgattttaggcagaagggataatggtggatgtcgggcttttttggggtcttgaagGGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAGATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG