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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctcccacctatgttagtttttcaaattatgaatttatgagtttgatgcttggtttacatattaccatgcgagctgatggcccatgaaaaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTGCAGCCTTCACGCTGCCGGGAAGAGTTCCTCGAGCGGCGCAAGAGCAATG

Basic information

species Physcomitrella patens
transcript PP1S298_23V6.1
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|37851256|gb|BJ609264.1|BJ609264
EST:     TCGTNTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCAAGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|37837655|gb|BJ595663.1|BJ595663
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67718218|gb|BJ968477.1|BJ968477
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162219415|gb|FC396425.1|FC396425
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162214101|gb|FC389939.1|FC389939
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162242146|gb|FC414485.1|FC414485
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|22491786|gb|BU051709.1|BU051709
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|18367407|gb|BJ199490.1|BJ199490
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|37841903|gb|BJ599911.1|BJ599911
EST:     TCGTNTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162274664|gb|FC450769.1|FC450769
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162274665|gb|FC450770.1|FC450770
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162273710|gb|FC449433.1|FC449433
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67726705|gb|BJ976964.1|BJ976964
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162273014|gb|FC449145.1|FC449145
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|100445578|gb|CJ975727.1|CJ975727
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|7207720|gb|AW561717.1|AW561717
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67704309|gb|BJ964542.1|BJ964542
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162155191|gb|FC331687.1|FC331687
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67703858|gb|BJ964091.1|BJ964091
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162219414|gb|FC396424.1|FC396424
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|18370425|gb|BJ202027.1|BJ202027
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67722371|gb|BJ972630.1|BJ972630
EST:     GTCGTGATGAACAAGCAG                         GTC-GGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: GTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162205086|gb|FC381795.1|FC381795
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|67722824|gb|BJ973083.1|BJ973083
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|18358552|gb|BJ190611.1|BJ190611
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|18364627|gb|BJ196700.1|BJ196700
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
EST: gi|162218347|gb|FC394521.1|FC394521
EST:     TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAG                         GTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG
genomic: TCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgtt ... aaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgcttggtttacatattaccatgcgagctgatggcccatgaaaaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTGCAGCCTTCACGCTGCCGGGAAGAGTTCCTCGAGCGGCGCAAGAGCAATG
                            agctgat  putative branch site (score: 4)
          tttacatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctcccacctatgttagtttttcaaattatgaatttatgagtttgatgcttggtttacatattaccatgcgagctgatggcccatgaaaaattcgtagGTCGGGAACAGGATCATCCAGAAGCGTCTTCATGTGCGCATTGAGCACGTGCAGCCTTCACGCTGCCGGGAAGAGTTCCTCGAGCGGCGCAAGAGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA