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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG

Basic information

species Physcomitrella patens
transcript PP1S371_31V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG
     |||| |  | |  |  || | |  | |      || |||||  | |  ||    |   |||    ||| |   |   || | |    || ||          || ||||||||||||||||||||||||||||||  | | ||||     || ||||| |||||||| |  |||||||    |
--gtatatttatgtctgcaaagaatgtaaatt----gtctattgttactaagcaca---tatattttgtattgctaactccttgcccacatcttcta----------gCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG

upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG
                   ||  |   | | | |    ||||||||||    |    |  | || |  || || ||  || | | |      || |  |  |||  ||||||||| ||||| ||||||||||||||||||  | | || |   | ||  ||||  | |||||||  || || |    |
-------------------gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgc-tagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG
















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|208382974|gb|DC927724.1|DC927724
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|67577808|gb|BJ949975.1|BJ949975
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|208373862|gb|DC956336.1|DC956336
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|67508343|gb|BJ941211.1|BJ941211
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|18338022|gb|BJ170046.1|BJ170046
EST:     CTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: CTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|67573313|gb|BJ946137.1|BJ946137
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
EST: gi|67696699|gb|BJ956932.1|BJ956932
EST:     TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTG                         CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT
genomic: TGAGCTCCCTCGGTATGGTCTGAAGGGCGGTCTGACTAATTATGCTGCTGgtacgtattc ... tggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG
                       gtttgat  putative branch site (score: 5)
                                      tttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG

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