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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgcctgtcatttggagatcctcctctgtgttcaaaagtgttgcatccatttacatattgatacccatggtttctaatcagtgcaattttttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGGTGTCCTTGTGGGCACTCCTGAGGAAGGCGTGGCTCATTTTTTTGACACT

Basic information

species Physcomitrella patens
transcript PP1S3_96V6.2
intron # 4
splice site 3'
intron type U2

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|162196437|gb|FC375429.1|FC375429
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162215135|gb|FC390760.1|FC390760
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162219753|gb|FC395957.1|FC395957
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162265473|gb|FC440799.1|FC440799
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|37847318|gb|BJ605326.1|BJ605326
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|37841761|gb|BJ599769.1|BJ599769
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162193871|gb|FC368733.1|FC368733
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|18335025|gb|BJ167043.1|BJ167043
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162239162|gb|FC416262.1|FC416262
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162219754|gb|FC395958.1|FC395958
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162269779|gb|FC444932.1|FC444932
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|37824254|gb|BJ582320.1|BJ582320
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|37839889|gb|BJ597897.1|BJ597897
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162206181|gb|FC382251.1|FC382251
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|7067026|gb|AW496881.1|AW496881
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAATGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACNG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162160000|gb|FC335662.1|FC335662
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
EST: gi|162197016|gb|FC375228.1|FC375228
EST:     CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAG                         TGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG
genomic: CCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 31 (downstream exon)
Score: 22

ACGGGCGAAGACGACTCGGGGACTCGATAGCAGTGCAAGGCAATGTGGACCCAGCTGTTCTCTTTGCCCCATTACCTGCAATTACTGAAGCGATTGAAAGgttccttatg ... ttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGGTGTCCTTGTGGGCACTCCTGAGGAAGGCGTGGCTCATTTTTTTGACACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatttacatattgatacccatggtttctaatcagtgcaattttttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGGTGTCCTTGTGGGCACTCCTGAGGAAGGCGTGGCTCATTTTTTTGACACT
                          ttctaat  putative branch site (score: 22)
                                         ttttttgtcc  putative PPT
                                       aattttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgcctgtcatttggagatcctcctctgtgttcaaaagtgttgcatccatttacatattgatacccatggtttctaatcagtgcaattttttgtccgcagTGTGGTGAGCAAGGCGGGAACTAATGGTCATATTCTTAACCTAGGTCACGGTGTCCTTGTGGGCACTCCTGAGGAAGGCGTGGCTCATTTTTTTGACACT

- - - - - - - - - - - - - - - - - - - tgttgca