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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccaagtttgcggcggcatgcaccgaatccctccagctggacagctttactcaccgccattcattacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTTCCCGACCTGCGTCTCTGCCAACAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO98981
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98981 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ35350 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggccaagtttgcggcggcatgcaccgaatccctccag-ctggacagctttactcaccgccattcattacgtacagGGAGTGCGCTAACATCTACAAGGGC------AAGGAGATCGAGAAGGGCGTGGCCTTCCCGACCTGCGTCTCTGCCAACAG-------------------
                |   |  |        | | |  || | ||| | |||    |   |   ||  |     ||||  |    || | | ||||||||  |      ||| ||||||| |||||||| ||||||||||| ||||||||    ||||                    
----------------gtaagtgtttttttttttcattgagacgggagaacttagaactttggtgttt-tgtttcacagCCAAACGGCCAGCGTCTACAAGAACGCAAAGAAGAAGATCGACAAGGGCGTCGCCTTCCCGACTTGCGTCTCGCTAAACAACACAGTATGCCATTTCTCT

upper sequence: EDO98981 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ10608 (Selaginella moellendorffii), 3'ss of exon 2
gtaagg---ccaagtttgcggcggcatgcaccgaatccctccagctggacagctttact-caccgccattcattacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTTCCCGACCTGCGTCTCTGCCAACAG-------------------
|||||         ||    | | |  | |  ||   | |  | ||     | |||  | ||| ||||      |||  ||| |  | |   ||    | ||| |  ||| ||||||| |||||||| ||||||||||| ||||||||    ||||                    
gtaagtgttttttcttcattgagacggggaaggagaacttagaactttggtgttttgtttcacagCCAA-----ACGGCCAGCGTCTACAAGAA----TGCAAAG--AAGAAGATCGACAAGGGCGTCGCCTTCCCGACTTGCGTCTCGCTAAACAACACAGTATGCCATTTCTCT
















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|161808568|gb|FC094884.1|FC094884
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|8514103|gb|BE121998.1|BE121998
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|6546929|gb|AV392713.1|AV392713
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14242417|gb|BG861233.1|BG861233
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14237056|gb|BG855872.1|BG855872
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|161797931|gb|FC087420.1|FC087420
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10794296|gb|AV631662.1|AV631662
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14238089|gb|BG856905.1|BG856905
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|15370986|gb|BI530412.1|BI530412
EST:     GCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|22053864|gb|BQ811001.1|BQ811001
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10780917|gb|AV637597.1|AV637597
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14240342|gb|BG859158.1|BG859158
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|15369196|gb|BI528622.1|BI528622
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|6542859|gb|AV388643.1|AV388643
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGT
EST: gi|10787302|gb|AV643974.1|AV643974
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|22076196|gb|BQ824972.1|BQ824972
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14242051|gb|BG860867.1|BG860867
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10791112|gb|AV628478.1|AV628478
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|16431135|gb|BI996361.1|BI996361
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|15370984|gb|BI530410.1|BI530410
EST:     GCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|22071303|gb|BQ820641.1|BQ820641
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10773522|gb|AV624345.1|AV624345
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|161795972|gb|FC085317.1|FC085317
EST:     GGCGCTAAGGTGGTGGACCTGTGCCACATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|6544166|gb|AV389950.1|AV389950
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10790999|gb|AV628365.1|AV628365
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10784987|gb|AV641659.1|AV641659
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|7687062|gb|AW757710.1|AW757710
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|10779996|gb|AV636676.1|AV636676
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14240161|gb|BG858977.1|BG858977
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|15367764|gb|BI527190.1|BI527190
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|6545280|gb|AV391064.1|AV391064
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|6545353|gb|AV391137.1|AV391137
EST:     GGCGCTAATGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         TGAGTGCGCTAACATCTACAATGGCAACGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|22071304|gb|BQ820642.1|BQ820642
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
EST: gi|14240115|gb|BG858931.1|BG858931
EST:     GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAA                         GGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT
genomic: GGCGCTAAGGTGGTGGACCTGTGCCGCATGGGCGACCAGTTCATCAACAAgtaaggccaa ... ttacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaccgaatccctccagctggacagctttactcaccgccattcattacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTTCCCGACCTGCGTCTCTGCCAACAG
                             tactcac  putative branch site (score: 1)
                                        attcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggccaagtttgcggcggcatgcaccgaatccctccagctggacagctttactcaccgccattcattacgtacagGGAGTGCGCTAACATCTACAAGGGCAAGGAGATCGAGAAGGGCGTGGCCTTCCCGACCTGCGTCTCTGCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC