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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggaaattacttttctgagtgcattggggttaagaattatcaacagcgctagtgttcaggaatagaggtctaatattttgattgttgtttctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG

Basic information

species Physcomitrella patens
transcript PP1S37_122V6.1
intron # 10
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|162235794|gb|FC412345.1|FC412345
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|37830933|gb|BJ588945.1|BJ588945
EST:     TGTATCAAAGGGAGTTTCCATGGCTGCNGCCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TGTATCAAAGGGAGTTTCCATGGCTGATG-CAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAAT-
EST: gi|162172093|gb|FC347969.1|FC347969
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|162248390|gb|FC422566.1|FC422566
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|37828610|gb|BJ586622.1|BJ586622
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|162172079|gb|FC347968.1|FC347968
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|162235377|gb|FC412344.1|FC412344
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|37822289|gb|BJ580355.1|BJ580355
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|162266004|gb|FC442689.1|FC442689
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|37839391|gb|BJ597399.1|BJ597399
EST:     TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
EST: gi|37837549|gb|BJ595557.1|BJ595557
EST:     TATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCG                         AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC
genomic: TATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATC

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: 33 (upstream exon), 32 (downstream exon)
Score: 9

ACTTTTCCAGCTGAGGGAGCGGGGATTGTTAGAGCTTCTATCCTCGCAAGTTTCATCTCTTGTATCAAAGGGAGTTTCCATGGCTGATGCAGTCATTTCGgtacgattct ... tctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgctagtgttcaggaatagaggtctaatattttgattgttgtttctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG
                                     ttgttgtttctttccc  CT-rich tract
                          taatattttgattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggaaattacttttctgagtgcattggggttaagaattatcaacagcgctagtgttcaggaatagaggtctaatattttgattgttgtttctttcccagAGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA