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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagcgaagaggggcgccaagattgcatgggccgcaggcactgatttgcctgcagaaacgcgcactcgctcgcacgtgcacctcatgtctccgtcgccctcacccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATGCTGGCCCGCCTGTACACGGGCAACTGGGACATGCTGTGCCTGCGCAACG

Basic information

species Chlamydomonas reinhardtii
transcript EDO96807
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96807 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacagcgaagaggggcgccaagattgcatgggccgcaggcactgatttgcctgcagaaacgcgcactcgctcgcacgtgcacctcatgtctccgtcgccctcacccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATGCTGGCCCGCCTGTACACGGGCAACTGGGACATGCTGTGCCTGCGCAACG
       | |  |  | || || ||| | | |       |   |   || |  |   | ||  |  || |   |   |||    |  ||  |   |  |            ||||| || ||||||||||||  |||   |||||| |||||||||||||| ||| |||| |||||||||||||| | ||  |||||  | |  || || || |
------tggaatgcagtgc-aaaattactttga------gtgtttccttcctagtttacac-tgtgctggtgagattgtgttggttttgattttctttctggttattggagcagGTTGTTTACTTTGTCAACTCTGGATCTGAGGCGAACGACATGGCCATGATGATGGCTCGCCTGTACACGGGAACCTTCGACATTGTTTCTCTTCGAAATG
















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|14231258|gb|BG850074.1|BG850074
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
EST: gi|14231259|gb|BG850075.1|BG850075
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
EST: gi|14231512|gb|BG850328.1|BG850328
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
EST: gi|14231513|gb|BG850329.1|BG850329
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
EST: gi|14231257|gb|BG850073.1|BG850073
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTCTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
EST: gi|10789369|gb|AV645098.1|AV645098
EST:     TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAG                         GTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG
genomic: TTGCGGAGTACGCCAAGGAGCTCACGGACCGCATGCCCGGAAACCTCAAGgtacagcgaa ... cccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcgcactcgctcgcacgtgcacctcatgtctccgtcgccctcacccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATGCTGGCCCGCCTGTACACGGGCAACTGGGACATGCTGTGCCTGCGCAACG
                                       ccctcac  putative branch site (score: 3)
                              tctccgtcgccctcac  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagcgaagaggggcgccaagattgcatgggccgcaggcactgatttgcctgcagaaacgcgcactcgctcgcacgtgcacctcatgtctccgtcgccctcacccccctcagGTGGTGTACTTTGTCAACAGTGGCAGTGAGGCCAACGACATGGCCATCATGCTGGCCCGCCTGTACACGGGCAACTGGGACATGCTGTGCCTGCGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG