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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgccttcaagtgcttgtgttgtgtcggccttagagcttactgatctttgttggtacctactatctgacttgtttctgacataatacttggttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGACCAGTATTACCTATCGTCAAGCCTCGACCCACTGTTGATATCGTATCTA

Basic information

species Physcomitrella patens
transcript PP1S126_52V6.1
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|162265032|gb|FC440911.1|FC440911
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162218145|gb|FC394982.1|FC394982
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162243608|gb|FC421807.1|FC421807
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|18338986|gb|BJ171012.1|BJ171012
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67700459|gb|BJ960692.1|BJ960692
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|37831315|gb|BJ589327.1|BJ589327
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67699691|gb|BJ959924.1|BJ959924
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67699716|gb|BJ959949.1|BJ959949
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162252357|gb|FC426165.1|FC426165
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162274823|gb|FC450850.1|FC450850
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67574166|gb|BJ946990.1|BJ946990
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162270108|gb|FC446184.1|FC446184
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67698454|gb|BJ958687.1|BJ958687
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67696535|gb|BJ956768.1|BJ956768
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|18351988|gb|BJ184040.1|BJ184040
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67697564|gb|BJ957797.1|BJ957797
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162243609|gb|FC421808.1|FC421808
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162252356|gb|FC426164.1|FC426164
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67573151|gb|BJ945975.1|BJ945975
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162274992|gb|FC450851.1|FC450851
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67572987|gb|BJ945811.1|BJ945811
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67696367|gb|BJ956600.1|BJ956600
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|67575015|gb|BJ947839.1|BJ947839
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
EST: gi|162218146|gb|FC394983.1|FC394983
EST:     CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAG                         GCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA
genomic: CCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGA

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: 27 (upstream exon), 35 (downstream exon)
Score: 10

TAAGAATCGGTGCTTGGAGAGCCTTCAAGAGAACGTTAACCGTCTTAACACCTACAGGGCTAAGTTGGTTGTGTTCCCTAGACGCTCAAAGAAGACCAAGgtatgcgtga ... gttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGACCAGTATTACCTATCGTCAAGCCTCGACCCACTGTTGATATCGTATCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttggtacctactatctgacttgtttctgacataatacttggttttctaagGCCGGGGACTCGAGTGCTGAGGAGTTATCGAGCTTCACCCAGGTGATCGGACCAGTATTACCTATCGTCAAGCCTCGACCCACTGTTGATATCGTATCTA
                            ttctgac  putative branch site (score: 10)
                                              ttttct  putative PPT
                                   ataatactt  TA-rich tract