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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcacataagcacttcgctcttcctcttgcagacagtgtgtggtattaagccgtaaatcaagtcaagaatatgatctgatggactgcaatgtttggcttgtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTCTGGTTGCGAATGTTGAAGACCATTGGAGGAGCTAGTGATGGTGCTTGCC

Basic information

species Physcomitrella patens
transcript PP1S398_18V6.1
intron # 5
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|162275204|gb|FC451180.1|FC451180
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTTCCCG
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCG
EST: gi|162275203|gb|FC451179.1|FC451179
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|162224645|gb|FC401893.1|FC401893
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTATACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|37821766|gb|BJ579832.1|BJ579832
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|22491664|gb|BU051587.1|BU051587
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|162278758|gb|FC454868.1|FC454868
EST:     TTTCAGGTTATTGCTAAGAATGCATTGNAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGTACTCCAGTAGACCTCANAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|37826297|gb|BJ584309.1|BJ584309
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|162239904|gb|FC415743.1|FC415743
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|100394822|gb|BY989942.1|BY989942
EST:     TTTCAAGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGAACGTGA-CTCCAGTAGACCTCAAAAAGCTT
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGA-CGTGAACTCCAGTAGACCTCAAAAAGCTT
EST: gi|208365879|gb|DC951136.1|DC951136
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
EST: gi|162278757|gb|FC454867.1|FC454867
EST:     TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAAT                         TTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC
genomic: TTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTC

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), 34 (downstream exon)
Score: 21

TTCCCTACTTCGAGACATCTGCCAAGGAAGATTTCAATGTAGATGTGGCATTTCAGGTTATTGCTAAGAATGCATTGAAGAACGAGACAGAGGAAGAAATgtaagttgca ... gtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTCTGGTTGCGAATGTTGAAGACCATTGGAGGAGCTAGTGATGGTGCTTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcaagtcaagaatatgatctgatggactgcaatgtttggcttgtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTCTGGTTGCGAATGTTGAAGACCATTGGAGGAGCTAGTGATGGTGCTTGCC
                   atctgat  putative branch site (score: 21)
 aagaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgcacataagcacttcgctcttcctcttgcagacagtgtgtggtattaagccgtaaatcaagtcaagaatatgatctgatggactgcaatgtttggcttgtggttgcagTTATGTCCCCGACACAATCGACGTGAACTCCAGTAGACCTCAAAAAGCTTCTGGTTGCGAATGTTGAAGACCATTGGAGGAGCTAGTGATGGTGCTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT