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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcagcaaacgctcagcgcccgaagttgtatgcgcaccaagtgctttgtcattgcggattaccagtcaccgcactgcccagtctaccgccacggcgcttctaaactgtaccactgtccctttggttgatgtatgcgcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTGACAACCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO98397
intron # 3
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|10782963|gb|AV639635.1|AV639635
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10788132|gb|AV644804.1|AV644804
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10784426|gb|AV641098.1|AV641098
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10784113|gb|AV640785.1|AV640785
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10787070|gb|AV643742.1|AV643742
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10787824|gb|AV644496.1|AV644496
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGC
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGC
EST: gi|161813272|gb|FC101441.1|FC101441
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10786131|gb|AV642803.1|AV642803
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGAACACGCTGGTGGACGCT
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCT
EST: gi|10787248|gb|AV643920.1|AV643920
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10786937|gb|AV643609.1|AV643609
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10787542|gb|AV644214.1|AV644214
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10788160|gb|AV644832.1|AV644832
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10789572|gb|AV645301.1|AV645301
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10785772|gb|AV642444.1|AV642444
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|49468183|gb|BP096044.1|BP096044
EST:     CCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: CCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10786776|gb|AV643448.1|AV643448
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10791188|gb|AV628554.1|AV628554
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10786864|gb|AV643536.1|AV643536
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10783914|gb|AV640586.1|AV640586
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|49469202|gb|BP097063.1|BP097063
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACG
EST: gi|10787514|gb|AV644186.1|AV644186
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10787307|gb|AV643979.1|AV643979
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGT
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGT
EST: gi|10785156|gb|AV641828.1|AV641828
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|10787701|gb|AV644373.1|AV644373
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
EST: gi|23360235|gb|BU648055.1|BU648055
EST:     TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACG                         GCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG
genomic: TGTGCGCGAGGACATCCGCAACATTGCCATCATCGCCCACGTCGACCACGgtgcgtgcag ... gcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcgcttctaaactgtaccactgtccctttggttgatgtatgcgcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTGACAACCAG
       ttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcagcaaacgctcagcgcccgaagttgtatgcgcaccaagtgctttgtcattgcggattaccagtcaccgcactgcccagtctaccgccacggcgcttctaaactgtaccactgtccctttggttgatgtatgcgcacattcagGCAAGACCACGCTGGTGGACGCTATGCTCAAGCAGTCCAAGGTGTTCCGTGACAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA