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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG

Basic information

species Arabidopsis thaliana
transcript AT4G29100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G083749_T02 (Zea mays), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                                                                    || |       |||  |   | ||   || |  | | | | |  || ||  |    ||||     | |||||||||||||||| ||||| |||||   |||  ||||||| |||||||||||||| | ||||||||| |||
--------------------------------------------------------------------------------cactgaaaacaagcaagtccctgacatgcatatatgca-tattacttgttgttgttgttgttttttt--ttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G083749_T05 (Zea mays), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                                       ||  |  |   |    |     |||    || |       |||  |   | ||   || |  | | | | |  || ||  |    ||||     | |||||||||||||||| ||||| |||||   |||  ||||||| |||||||||||||| | ||||||||| |||
------------------------------------------------------ttaggaggt--gcgcggagtgacaatcactgaaaacaagcaagtccctgacatgcatatatgca-tattacttgttgttgttgttgttttttt--ttttttgcagACTGACACTGCCTCCGTCCTACAGGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaact-tttaacat-taattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatctt--ttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                                              | | ||    | ||| |||  |  ||    ||||||    ||    |   ||    | |||   | |||   | | | |||| |  |  | ||  | ||||||||||||||| ||||| ||    ||||| ||||| ||||| |||||||| || ||||||||||||
--------------------------------------------------------------ttagctacacatcatgtaaaagaagatccatttttacagacaaagatacaaaaacgagatcctga-catggctaacctctttctctcttttttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 3
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                                            | |  ||     | |     |  |   ||    | | ||  | | || | |||    | |   ||| |   |           ||     ||||||||||||||||| ||||||||| |||  ||||||||||| || || ||||||||||||||||||||||||
-----------------------------------------------------------tattttacagaagaaaaagggttcgtttatagcataaattaaaatattataaataatgagtgggaataacgttgtggtgtggcatatttcacttttgcagACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G35610.1 (Glycine max), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                             || | |   || ||   | | | ||  ||||  |  | | |||  |   | |    ||   ||| | | |    |  || |  || || ||   |||||||     |||||||||||||||| || |||||| | |  ||||||||||| || || ||||||||||||||||||||||||
---------------------------------------------aacaatatgctctctgtttagcatt--acatagaa-gagaagagatgactgggaatatgactgt-agtgtgtggt--aattttttatttat---tttttac-----ttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGCTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG----------------------------------
                                              ||  || |   | | || | | ||  ||||  |  | | |||  |   |      ||   ||| | | |   || ||    ||| |   |   |||||||     |||||||||||||||| || |||||| | |  ||||||||||| || || ||||||||||||||||||||||||                                  
----------------------------------------------atgctctttgtttatat-agcatt--acatagaa-gagaagagatgactgagaatatgactgt-agtgtgtgatata---tattttgattttttttttac-----ttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                              ||  || |   | | || | | ||  ||||  |  | | |||  |   |      ||   ||| | | |   || ||    ||| |   |   |||||||     |||||||||||||||| || |||||| | |  ||||||||||| || || ||||||||||||||||||||||||
----------------------------------------------atgctctttgtttatat-agcatt--acatagaa-gagaagagatgactgagaatatgactgt-agtgtgtgatata---tattttgattttttttttac-----ttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 4
gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
                                       | ||        ||  | |    |    ||||  ||  |||   | |||                   || ||| | |  |   |    |      |   ||||| |   ||||||||||||||||||||| |||||| |||  ||||||||||| || || |||||||| |||||||||||||||
--------------------------------------atggttcccccccccctttttttttttttttttttcagaaataaagaagac------------------gtgaatatgactttggagggttgtggtgtggtttttttc---tcttttgcagACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAG

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|164211214|gb|ES034168.1|ES034168
EST:     TAGGAGGCCGAATCGCAGCGCTTCATCAGCTAGTATCTCCATTTGGAAAG                         ACTGACACAGCCTCTGTCCTGTCGGAAG
genomic: TAGGAGGCCGAATCGCAGCGCTTCATCAGCTAGTATCTCCATTTGGAAAGgtaaagatcg ... tcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
              atctaaa  putative branch site (score: 3)
                     tcattcttcatccctt  CT-rich tract
     taatctaaaatctaaa  TA-rich tract