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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G54080.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
                                            || |    |  |  | |   |    |  |    | | |   | |  | ||    | | | | ||||| |   | |  ||   |||   |||     ||  |||     |  ||  ||    || | || || || ||  || || || || ||||||||||| |||||||||||||| || ||||| |||||||||||||| ||| | |||||||||
-------------------------------------------gta-agtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtat-tttaccagttgttcaagattatgcattttctttcttacccatatgtatttttt-ttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
                                                   | | |   | ||   | || ||    |  |   |  | ||| | |   | |||        ||||        ||||  |   ||   ||||  || | |  ||| || | |   |     | ||   | ||  || || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||
-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
                                                   | | |   | ||   | || ||    |  |   |  | ||| | |   | |||        ||||        ||||  |   ||   ||||  || | |  ||| || |     |     | ||   | ||  || || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||
-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
                                                                                    || | | ||| | |   |  | | ||          ||      | |||| |    |   || |        | ||||  ||| | |  |      |  || || || || || |||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||||||||| |||
----------------------------------------------------------------------------------atatttgt-actgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattt--tattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

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|124811855|gb|EH896721.1|EH896721
EST:     GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC                         GGACGCAAGAGTAATGTGGGACCAAGAAAACTGGACGCTCAAGAGGCTTT
genomic: GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttctt ... cttattatagGGACGCAAGAGTAATGTGGGACCA-GAAAACTGGACGCTCAAGAGGCTTT
EST: gi|86052517|gb|DR348274.1|DR348274
EST:     GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC                         GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAAGGNNTTT
genomic: GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttctt ... cttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGA-GGC-TTT
EST: gi|124900435|gb|EH975053.1|EH975053
EST:     GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC                         GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAA
genomic: GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttctt ... cttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAA
EST: gi|86052513|gb|DR348270.1|DR348270
EST:     GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC                         GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGG
genomic: GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttctt ... cttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGG
EST: gi|86052514|gb|DR348271.1|DR348271
EST:     GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC                         GGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGG
genomic: GTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTCgtaagttctt ... cttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
                            atttaat  putative branch site (score: 4)
                                           ttcttatt  putative PPT
                    aatctttgatttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagttcttattatagGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG