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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagatatacctcaacggaaatcgacaatctcattattcgaagaatctactgttacgtcaagatgggattacgtatatcagaaagtggtttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGTTGCTGCCGAAGGAATTCACCACAGTTATTGATGTGGCTGGATTCTTGTC

Basic information

species Physcomitrella patens
transcript PP1S5_248V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_248V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g34950.1 (Oryza sativa), 3'ss of exon 1
tttaagatatacc-tcaacggaaatcgacaatctcat-tattcgaagaatctactgttac-gtcaagatgggattacgtatatcagaaagtggtttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGTTGCTGCCGAAGGAATTCACCACAGTTATTGATGTGGCTGGATTCTTGTC-----
|   | |||||   |   | |||||  | | | |  | ||||      |  ||      | |||||  ||| |  |  |    |||||  | |    | |||| ||| |  || |   | || ||||  ||    || || |||||||| || ||||| || |||||||||||||| || |||||||| ||||| ||  | ||     
tggcacatatagagttctctgaaatatatagttttttgtatttttgttaagtaaaaaagctgtcaa--tggaaaaatctcatgcagaatctcgcacat-gcagTTGTTGGTATAGTTAATGCAAAGA--CT----GGGGTCAACAAACCCGAATTGCTTCCCAAGGAATTCACCACCGTCATTGATGTTGCTGGTTTTCTCTCCCCAG
















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|22132594|gb|BQ827244.1|BQ827244
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|162229579|gb|FC404860.1|FC404860
EST:     ACAGAAGGCNGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|67696673|gb|BJ956906.1|BJ956906
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|162229580|gb|FC404861.1|FC404861
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|162224698|gb|FC401946.1|FC401946
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|162224697|gb|FC401945.1|FC401945
EST:     ACAGAAGGCNGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|67701119|gb|BJ961352.1|BJ961352
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
EST: gi|67692877|gb|BJ953110.1|BJ953110
EST:     ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAG                         GTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT
genomic: ACAGAAGGCTGGCGTCGCTTTGGCGCTTGGTCTCTCGCTCTCGTTAGGAGgtcagttaat ... tttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctactgttacgtcaagatgggattacgtatatcagaaagtggtttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGTTGCTGCCGAAGGAATTCACCACAGTTATTGATGTGGCTGGATTCTTGTC
                              tatatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagatatacctcaacggaaatcgacaatctcattattcgaagaatctactgttacgtcaagatgggattacgtatatcagaaagtggtttgtagcagGTGTCGACATGGCGGAGGCCAAGAGGCTCGAAGGCGTGAACAAACCGGAGTTGCTGCCGAAGGAATTCACCACAGTTATTGATGTGGCTGGATTCTTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA