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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtatacaatgaacttgttattctttttaccaagtattgcgtagtatggtttcagtattctgtcgccttcatgtacttttccgtgtagcaagttgggggaatattgattatgagacgagccaacggtattgttttcttttttccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTTTACAGCTCCGTTGATCCCTCATTGGCTCCCGCCCTGCTTGCG

Basic information

species Physcomitrella patens
transcript PP1S206_101V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S206_101V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtatacaatgaacttgttattctttttaccaagtattgcgtagtatggtttcagtattctgtcgccttcatgtacttttccgtgtagcaagttgggggaatattgattatgagacgagccaacggtattgttttcttttttccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTTTACAGCTCCGTTGATCCCTCATTGGCTCCCGCCCTGCTTGCG
                                              |||  |  |||||  ||  ||   |   | | |||| || | |    |  |      ||||  ||| |      ||       | || || |  |  || | | | ||||||    |    |||||||| || || || |||||||| || ||||||||||||| ||| ||||| || |||||||| ||  | || ||   |
----------------------------------------------gta-agcatcagtgctccttcaattctct-tgctttccccttttcacatatatatatatatatattttatttatagttcttaatgtttttgttgtaatttcatgtgtagAAAAGTTCCCAGAAGCAGCTAGTGCATCATGTGTTTCCAAAACTTGCCGTTTACAACTCGGTTGACCCTTCATTGGCACCTTCTCTTCTCATG
















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|18356166|gb|BJ188225.1|BJ188225
EST:     ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAG                         AAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
genomic: ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAGgtctgtatac ... ccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
EST: gi|18347530|gb|BJ179577.1|BJ179577
EST:     ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAG                         AAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
genomic: ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAGgtctgtatac ... ccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
EST: gi|18342175|gb|BJ174210.1|BJ174210
EST:     ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAG                         AAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
genomic: ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAGgtctgtatac ... ccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
EST: gi|18356309|gb|BJ188368.1|BJ188368
EST:     ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAG                         AAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
genomic: ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAGgtctgtatac ... ccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTT
EST: gi|67571270|gb|BJ944094.1|BJ944094
EST:     ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAG                         AAAGCCGCTGCAAAGCAGCTCGTTCA
genomic: ACTCTCATCTTGCCAGGTCTCTCCAAGAACTTTCTACTTCCGCTGATCAGgtctgtatac ... ccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatattgattatgagacgagccaacggtattgttttcttttttccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTTTACAGCTCCGTTGATCCCTCATTGGCTCCCGCCCTGCTTGCG
    tattgat  putative branch site (score: 3)
                          cggtattgttttcttt  putative PPT
                             tattgttttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtatacaatgaacttgttattctttttaccaagtattgcgtagtatggtttcagtattctgtcgccttcatgtacttttccgtgtagcaagttgggggaatattgattatgagacgagccaacggtattgttttcttttttccttttttagAAAGCCGCTGCAAAGCAGCTCGTTCACCAAGTGTTTCCCAAGCTTGCCGTTTACAGCTCCGTTGATCCCTCATTGGCTCCCGCCCTGCTTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC