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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtcgggtctaatgtagctaaagacctgaattgtgttagactttccttttatgctttttatcaccgggactctctgctgattgtcattcgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGTGCCCTGAAGGAGAATCACTGGTTGGACGATGGTGCATATTTGATG

Basic information

species Physcomitrella patens
transcript PP1S152_87V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
taggtcgggtctaatgtagctaaagacctgaattgtgttagactttccttttatgctttttatcaccgggactctctgctgattgtcattcgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGTGCCCTGAAGGAGAATCACTGGTTGGACGATGGTGCATATTTGATG
   ||  | |   |   |    |  |     ||||| ||  | |||  | |  | |   |          | | |  |    |  |  |   |    ||||| ||  |||| || ||| | ||||| ||||| ||||| ||||| ||||| || ||||| |||||||||||| | || |||||||||||| | |||
---gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
















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|162166154|gb|FC342591.1|FC342591
EST:     AGAGGGGTTATAAGAATGTCACTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: AGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162170485|gb|FC347644.1|FC347644
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162198122|gb|FC373072.1|FC373072
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162193748|gb|FC371275.1|FC371275
EST:     AAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: AAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162196621|gb|FC374911.1|FC374911
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162159475|gb|FC336264.1|FC336264
EST:     GCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGNTG                         AACACGGTTGGAGAAGAGATTCATTTGGCTATCGAAACCNAGTCAACATGG
genomic: GCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACC-AGTGGACATGG
EST: gi|37850442|gb|BJ608450.1|BJ608450
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162193749|gb|FC371276.1|FC371276
EST:     AAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: AAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162215686|gb|FC391414.1|FC391414
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|18332811|gb|BJ164824.1|BJ164824
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162192137|gb|FC368286.1|FC368286
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162192138|gb|FC368287.1|FC368287
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162196875|gb|FC375152.1|FC375152
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162166155|gb|FC342592.1|FC342592
EST:     AGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: AGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162196876|gb|FC375153.1|FC375153
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162244980|gb|FC424938.1|FC424938
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162170471|gb|FC347643.1|FC347643
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|162215700|gb|FC391415.1|FC391415
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
EST: gi|208381985|gb|DC923844.1|DC923844
EST:     ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTG                         AACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT
genomic: ATCGCTTCAAGAGGGGTTATAAGAATGTCATTGATGAAGGCATTCGGCTGgttagtttac ... cgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttatgctttttatcaccgggactctctgctgattgtcattcgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGTGCCCTGAAGGAGAATCACTGGTTGGACGATGGTGCATATTTGATG
                               tgctgat  putative branch site (score: 3)
           tttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtcgggtctaatgtagctaaagacctgaattgtgttagactttccttttatgctttttatcaccgggactctctgctgattgtcattcgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGTGCCCTGAAGGAGAATCACTGGTTGGACGATGGTGCATATTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA