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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggttgatgccctggcggagcagtggggtagccaggggagctgcagtctttgattcgctcacggaacgatcgtgccccttcgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTCTGTGCGGTGGCCTGAACTCCAACATCGCAAAGTACACGCGTGCCCTGCT

Basic information

species Chlamydomonas reinhardtii
transcript EDO97956
intron # 4
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|10793767|gb|AV631133.1|AV631133
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|161806299|gb|FC092278.1|FC092278
EST:     GTCTCGCGGCATTGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|10790688|gb|AV628054.1|AV628054
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|6541786|gb|AV387570.1|AV387570
EST:     GTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|10127224|gb|BE725928.1|BE725928
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|14229626|gb|BG848426.1|BG848426
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|6546060|gb|AV391844.1|AV391844
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGACGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|161807848|gb|FC098961.1|FC098961
EST:     GTCTCGCGGCATTGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|49464988|gb|BP092901.1|BP092901
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|15372595|gb|BI532021.1|BI532021
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|161822022|gb|FC105975.1|FC105975
EST:     GTCTCGCGGCATTGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|7615315|gb|AW720762.1|AW720762
EST:     GTCTCGTGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|15369223|gb|BI528649.1|BI528649
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|239841871|gb|GR283728.1|GR283728
EST:     GTCTCGCGGCTTTGTGAACCCGTTCGTGCGCCTTTTC-GTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCGGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|161809306|gb|FC097065.1|FC097065
EST:     GTCTCGCGGCATTGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|239841870|gb|GR283727.1|GR283727
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
EST: gi|9210378|gb|BE337293.1|BE337293
EST:     GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAG                         CCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC
genomic: GTCTCGCGGCATCGTGAACCCGTTCGTGCGCCTTTTCGGTGACTTCCCAGgtgcggttga ... cgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggagctgcagtctttgattcgctcacggaacgatcgtgccccttcgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTCTGTGCGGTGGCCTGAACTCCAACATCGCAAAGTACACGCGTGCCCTGCT
                    cgctcac  putative branch site (score: 3)
                                       ccccttcgtc  putative PPT
             tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggttgatgccctggcggagcagtggggtagccaggggagctgcagtctttgattcgctcacggaacgatcgtgccccttcgtcgcgcagCCATCGAGGGCAAGCAGAACATCACCGTGGCCGTCTCCTCGGACCGTGGTCTGTGCGGTGGCCTGAACTCCAACATCGCAAAGTACACGCGTGCCCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG