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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgttgctctttttcaagtgctcatgttttctctattttttacttctccag

Basic information

species Arabidopsis thaliana
transcript AT2G02560.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 13
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgttgctctttttcaagtgctcatgttttctctattttttacttctccag
||||||||||||||| ||||  || ||||| ||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||| | |||  | |||||| |||   ||   ||||   ||||       | | | |    |||   | ||  || |    |||| |  | || ||| |||  ||         
TGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGTCTTGCTGATCATATTGGGTCACTTGTTCCTGGGATTGAGAAGGCTTTGAATgttggtg---attcccattttgctta------aaatattatgtgcaggacttctacttgt----tgctaacttgttttctttttcatag--------

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G053644_T02 (Zea mays), 5'ss of exon 11
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgt-tgctctttttcaagtgct-catgttttctctattttttacttctccag
|||  |||| || ||  |||  || |||||||||||  | || |||||||||||||||||| |||| |||||||||||||| ||||| | |||  | ||||||||  |  |  |||| | |  || |||  ||||    ||| ||||    |       |||  |||   ||| |||   ||  |  |   ||   |||
TGGGACATTTTCAGTACTGAAGGAGCTTGTGGTTGTATTACCAGACTGTCTTGCTGATCATTTTGGATCACTTGTTCCTGGGATTGAGAAGGCTTTGAATgttagctgtgactttcactcccttttttt--ggacaaaaactttcagcccctaaaaaacttcttgtgaaacatttttgaacttatagtcgatttgacag

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G386614_T01 (Zea mays), 5'ss of exon 2
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacac-ttatttatggactgtcactgtcagtgt-tgctctttttcaagtgct-catgttttctctattttttacttctccag
||| ||||| || ||  |||  || |||||||||||  | || |||||||||||||||||| |||| |||||||||||||| ||||| | |||  | ||||||||  |  |  |||| | |   || ||| |||||    ||| ||||    |       |||  |||   ||| |||   ||  |  |   ||   |||
TGGGGCATTTTCAGTACTGAAGGAGCTTGTGGTTGTATTACCAGACTGTCTTGCTGATCATTTTGGATCACTTGTTCCTGGGATTGAGAAGGCTTTGAATgttagctgtgactttcactccctattttttttggacaaaaactttcagcccctaaaaaacttcttgtgaaacatttttgaacttatagtcgatttgacag

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 13
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtg-ttgctctttttcaagtgctcatgttttctctatttt-ttacttctccag
||| ||||| || ||  |||  || |||||||||||  | || |||||||||||||||||| | || |||||||||||||| ||||| | |||  | ||||||||  |  |  |||| | |   | ||| |||||    ||| ||||   ||       |||  |||      |||| |  | ||  |   ||   |||
TGGGGCATTTTCAGTACTGAAGGAGCTTGTGGTTGTATTACCAGACTGTCTTGCTGATCATTTCGGGTCACTTGTTCCTGGGATTGAGAAGGCTTTGAATgttagctgtgactttcactccctatttttttggacaaaaactttcagcccttaaaaaacttcttgtgaaaccatttttttaacttagtcgatttgacag

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G40230.2 (Glycine max), 5'ss of exon 14
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgttgctctttttcaagtgctcatgttttctctattttttacttctccag
|||||| || |||||||||| |||||||||||||||  ||||  |||||||||| || |||||||| |||||  |||| ||||||||||  ||  |||||||  |      | |  |||||| || | | |  |||  ||            ||  ||| | ||| || ||   ||   | ||  || ||| ||   
TGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTGCCCAACTGTCTTGCAGACCATATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTAAATgtaggcaatattttgaattacaattttgtttaaact--cat-----------ctagtttcccagtactgattgctttgtttttcattgcttgtcag-

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G00570.1 (Glycine max), 5'ss of exon 13
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgttgctctttttcaagtgctcat-gttttctctattttttacttctccag
|||||| || |||||||||| |||||||||||||||  | ||  |||||||||| ||||| ||||| |||||  |||| ||||||||||  ||  | |||||  |         | |||    | | ||||    | |   | | |      ||  ||| | ||| |  || | ||| ||| || ||| ||| ||   
TGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGAATgtaggca-------tgattgttttgaattataa--ttttgtt-taaactcatctagtttcccagtaccgattgctttgtcttttctttgcttgtcag-

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|164229599|gb|ES134854.1|ES134854
EST:     GGAATTGAAAGGGCGCTAAAT                         GATAAATCTTCTACATCAAACTTGAAAATTGAAGCTCTTGTCTTCACCAAA
genomic: GGAATTGAAAGGGCGCTAAATgttagtggat ... acttctccagGATAAATCTTCTACATCAAACTTGAAAATTGAAGCTCTTGTCTTCACCAAA
EST: gi|164083216|gb|ES173012.1|ES173012
EST:     GGAATTGAAAGGGCGCTAAAT                         GATAAATCTTCTACATCAAACTTGTAAAAATTGAAGCTCTTGTCTTCACCA
genomic: GGAATTGAAAGGGCGCTAAATgttagtggat ... acttctccagGATAAATCTTCTACATCAAACTTG--AAAATTGAAGCTCTTGTCTTCACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAAATgttagtggatatattcattacacttatttatggactgtcactgtcagtgttgctctttttcaagtgctcatgttttctctattttttacttctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT