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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacccatgactgcaattcgacattttttaaaccataatgttagttaacattgtttctcatctaacagaccggttaaatgtttctctttgaattactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTCCAACTTGCTGTGTTTCTTTATCTTCTTTCTACAATGAAACCATTGTTGG

Basic information

species Arabidopsis thaliana
transcript AT5G60920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
gtaagaacccatgactgcaattcgacattttttaaaccataatgttagttaacattgtttctcatctaacagaccggttaaatgtttctctttgaattactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTCCAACTTGCTGTGTTTCTTTATCTTCTTTCTACAATGAAACCATTGTTGG
                                |||  |||     |  ||    |  |||||    | |||     |  |    ||  || ||   ||  ||||||||| |||||  | || |||||||| ||||||||  ||||||||||| |||||||||| ||||||||  | || || || |||||||| || || |||  
-------------------------------gtaagtcatttcagtgttttttgtc-tttctggcgtcacaattatgacaccctttcttcctt---tttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G167520_T02 (Zea mays), 3'ss of exon 4
gtaagaacccatgactgcaattcgacattttttaaaccataatgttagttaacattgtttctcatctaacagaccggttaaatgtttctctttgaattactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTCCAACTTGCTGTGTTTCTTTATCTTCTTTCTACAATGAAACCATTGTTGG
                    | ||  |  |  | ||||  ||   ||   ||  |  |   |   | | |     | ||||     | |||| |       |||||||| |||||| | |||||||| ||||| ||||||||||| || ||| ||||||| |||||||| ||  | || || |||||||| || ||||||||| |
-------------------gtacgtaagatgattaacctcaagcctaccaaat-tcatgcattgacgatcgacttgtttaa-----tttcttcg------cgcagTGACCTGGAACGTGACGTGCACGTACTCCCAGTTCCTTGCCCAGAGATCTCCAACCTGCTGTGTCTCGCTCTCGTCGTTCTACAACGACACCATTGTTAG
















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|125232627|gb|EL246712.1|EL246712
EST:     CCACTCAAGCTATGA                         TGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTC
genomic: CCACTCAAGCTATGAgtaagaaccc ... attactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTC
EST: gi|116480429|gb|EG523021.1|EG523021
EST:     ACCAACAAAATTTGTCACGACTGACACACGCAGAACCACTCAAGCTATGA                         TGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTC
genomic: ACCAACAAAATTTGTCACGACTGACACACGCAGAACCACTCAAGCTATGAgtaagaaccc ... attactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTC
EST: gi|124744695|gb|EH835857.1|EH835857
EST:     ACCAACAAAATTTGTCACGACTGACACACGCAGAACCACTCAAGCTATGA                         TGACATGGAACATTACGTGCA
genomic: ACCAACAAAATTTGTCACGACTGACACACGCAGAACCACTCAAGCTATGAgtaagaaccc ... attactgcagTGACATGGAACATTACGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattgtttctcatctaacagaccggttaaatgtttctctttgaattactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTCCAACTTGCTGTGTTTCTTTATCTTCTTTCTACAATGAAACCATTGTTGG
             atctaac  putative branch site (score: 2)
                           ttaaatgttt  TA-rich tract