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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatatccacattgagattctctggcagtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC

Basic information

species Physcomitrella patens
transcript PP1S340_7V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 3
gtaagttatatccacattgagattctctggc--agtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcattttt-ttgtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC
              |||     || |  |||  |   | |  ||  |  |   |     || |  |||  || | || |  |||   |    | |  ||  | ||  |  | ||||| || ||| | ||||| ||||| ||||| || || ||||   | ||||| ||||||||||||||||||||||| ||||||||||| || ||||| ||||
--------------cataatattttttaggcttaagcatgacttatagttcaaaaaaaaaagagaaatcaaactcatttt-tgtaaaatatcctttgttcctatttcgattgcagACTATATTCCTTCCTGTGGTTGGGCTAGTTGACCCTGATAAACTCAAGCCTGGTGATTTGGTTGGAGTAAACAAAGACAGCTACCTTATACTGGACACAC

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttatatccacattgagattctctggcagtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtg---tacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC
    || | |    ||     ||||| |   ||  | |||||| |||| |     ||  | |        || || ||       |      |  |||  || ||||   | ||||| |||||  | || || ||||| || || ||||| ||||||||||| || ||||| ||||||||||| ||||| || |||||| ||||| |||||||  
----gtgagacttccaaacccattcttt---agatatgttttctacatcttctcttccgttt---cccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCTGGTGACTTGGTTGGAGTTAACAAAGATAGCTACTTGATTTTGGATACCT

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttatatccacattgagattctctggcagtgacgttttc--cacatgtgactgtcaa--tatgaatttaatttatatcatgttgcactgacatcat---ttttttgtg-tgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC
|| |  | | |  ||  | | || | | |  || ||  |||||   ||  |||     |||  | ||| |   | |    |  |  |  | |||  ||||   ||  || |  | | ||||| |||||| | ||||| ||||| || || ||||||||||  |||||||| || || || |||||||| ||||| || || ||| |||||||||||||  
gtgaagttt-tagactcttatat-caccgttagagagattttcagaactagtggggaacaaactctgactactagtgtagtgtttgtataatgatctcatgggttaattatacttttcagACCATCTTCCTCCCTGTTGTTGGACTTGTTGATCCAGATACATTGAAGCCTGGGGACTTAGTTGGAGTTAACAAAGATAGTTACTTGATTCTGGATACTT

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|100446734|gb|CJ971033.1|CJ971033
EST:     ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
genomic: ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttata ... gtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
EST: gi|208366108|gb|DC935869.1|DC935869
EST:     ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
genomic: ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttata ... gtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
EST: gi|208373535|gb|DC941104.1|DC941104
EST:     ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
genomic: ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttata ... gtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
EST: gi|208382087|gb|DC914776.1|DC914776
EST:     ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC
genomic: ACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttata ... gtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC
                           cactgac  putative branch site (score: 2)
                                      tttttttgt  putative PPT
      aatttaatttatatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatatccacattgagattctctggcagtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtgtacagACGATCTTCTTGCCTGTAGTTGGTCTAGTCGATCCAGATAGTTTGAAGCCCGGTGATTTGGTTGGAGTAAACAAGGACAGCTACCTGATTCTGGATACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG