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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcctctaatttgtagttttgttgtcgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG

Basic information

species Physcomitrella patens
transcript PP1S234_26V6.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 5
agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcc---------tctaatttgtagttttgttgt-cgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG
      | ||| | ||     |  || | | || |  | ||  |||   |||    |  | ||              ||| | ||| ||||||||| | |  | ||| |||||||    ||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||| ||||||||||| |||||  | ||  | ||| | |
gtttggactcttggatcactaaccaaatat-atttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttg-agttttgttttgcttggtta-agTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 5
agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcc---------tctaatttgtagttttgttgtcgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG
      | ||| | ||     |  || | | || |  | ||   ||   |||   |   | ||              ||| | |||   |||  || ||  | ||| |||||||    ||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||| ||||||||||| |||||  | ||  | ||| | |
gtttggactcttggatcactaaccaaatat-atttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggtta-agTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 8
agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcc--tctaatttgtagttttgttgtcgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG
            || |  |  ||||||    || |   |         |||||   |  ||||   ||   |     |   ||| | || ||  | |   ||||||||   ||||| || |||||||||||||| || |||||||| || ||||||||||||||||| ||||||||||| |||||  | ||  | ||| | |
------------gtttgaatcatgaatagaaattttcttgacaatgaatatatattgaaccaaaacccaagcccgagtacggttattttttcatgatc-cagTTTGTCAGCGATGTAACAAAATACATTAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 6
agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcctctaatttgtagttttgttgtcgggct-tatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG
            || |  |  |||||| |  || |   | |        ||||   |  ||||   ||     |  |||  |||||| |       |  ||||||||   ||||| || |||||||| ||||| || |||||||| || ||||||||||||||||| ||||||||||| |||||  | ||  | ||| | |
------------gtttgaatcatgaatataaattttcttgtcaatgaagatatattgaaccaaaaaccaagcctgagtacgtttgttttttcatgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG

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|67695764|gb|BJ955997.1|BJ955997
EST:     GGACTTCAATGTTTGTGCTG-TTACATGACTGATTCACAG                         TTTGTTTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
genomic: GGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAGgtctgcagac ... gggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
EST: gi|100430653|gb|BY978328.1|BY978328
EST:     TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAG                         TTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
genomic: TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAGgtctgcagac ... gggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
EST: gi|67572391|gb|BJ945215.1|BJ945215
EST:     TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAG                         TTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
genomic: TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAGgtctgcagac ... gggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
EST: gi|100399107|gb|BY954203.1|BY954203
EST:     TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAG                         TTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
genomic: TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAGgtctgcagac ... gggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCT
EST: gi|18350386|gb|BJ182437.1|BJ182437
EST:     TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAG                         TTTGTCTCAGATGT
genomic: TGAAGAGATGGGACTTCAATGTTTGTGCTGTTTACATGACTGATTCACAGgtctgcagac ... gggcttatagTTTGTCTCAGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatatgcggtgccaatgtcctctaatttgtagttttgttgtcgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG
                      ctctaat  putative branch site (score: 3)
                         taatttgtagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcctctaatttgtagttttgttgtcgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT