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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagttccgcatatcgggggggggggggggtgtcatcttacaaattttatggttgaaatatgagctgcatagggagacagtgaattgtgagggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCATCTGCGGTTTGAATCTCAGTCGCAG

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 2
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|18342243|gb|BJ174278.1|BJ174278
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|208380031|gb|DC914581.1|DC914581
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|100407853|gb|BY955811.1|BY955811
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|208355357|gb|DC929804.1|DC929804
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|162155579|gb|FC331530.1|FC331530
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|67718012|gb|BJ968271.1|BJ968271
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|18357519|gb|BJ189578.1|BJ189578
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|67578657|gb|BJ950824.1|BJ950824
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|18371944|gb|BJ203546.1|BJ203546
EST:     AGCAGCACAGGTCGTCGTTCGAT-TTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|18344030|gb|BJ176069.1|BJ176069
EST:     AGCAGCACAGGTCGTCGTTCGAT-TTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|18348917|gb|BJ180966.1|BJ180966
EST:     AGCAGCACAGGTCGTCGTTCGAT-TTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|100409673|gb|BY956049.1|BY956049
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|100435291|gb|BY979169.1|BY979169
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|100411979|gb|BY956357.1|BY956357
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
EST: gi|100423150|gb|BY958171.1|BY958171
EST:     AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG                         GAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT
genomic: AGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCAT

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: 34 (upstream exon), 12 (downstream exon)
Score: 4

GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAGgtaaggtttg ... gggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCATCTGCGGTTTGAATCTCAGTCGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatggttgaaatatgagctgcatagggagacagtgaattgtgagggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCATCTGCGGTTTGAATCTCAGTCGCAG
       ttgaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagttccgcatatcgggggggggggggggtgtcatcttacaaattttatggttgaaatatgagctgcatagggagacagtgaattgtgagggtgtgcagGAACCCTTGCAAATGGATCTAGTTCTCAACTTTCCTGAGCATGGTTTTCATCTGCGGTTTGAATCTCAGTCGCAG

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