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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacatatatctataggttttatgggttcagaacagagtttcttctctctgtttctaatgttttgtttctcttttgccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTCGGAATCAGCAGTGTCTACTTGGGTTTTGCTGGAGTCTGCGTCCTTGCGG

Basic information

species Arabidopsis thaliana
transcript AT5G16150.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 13
------------gtatatacatatatctataggtttt---atgggttcagaacagagtttcttctctctgtttctaatgttttgtttctcttttgccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTCGGAATCAGCAGTGTCTACTTGGGTTTTGCTGGAGTCTGCGTCCTTGCGG
              | | ||    |  |  | ||||    ||||    |   |||    |   || ||   |  |     ||  |   | |       || ||||| |||||||||||||| || || |||||||| |||||||| |  || ||||| |||||||  || |||||||| ||| | |  |||||  | ||||| |
gaagtactttctaaaaacactgtcaaatggaagtttcttcatggtgctaatgcag----tagactttcatctaatggaacttcatgattttcccattgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTCGGGATCAGCACAGTTTACTTGGGATTTTCAGCCGTCTGTCTTCTTGCTG
















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|116412120|gb|EG454712.1|EG454712
EST:     CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
genomic: CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
EST: gi|125029346|gb|EL101615.1|EL101615
EST:     CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTC
genomic: CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTC
EST: gi|164132213|gb|ES146862.1|ES146862
EST:     AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
genomic: AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
EST: gi|163967359|gb|ES038684.1|ES038684
EST:     AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGTCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTCTTAAGTCGTTGTGACTAAATT
genomic: AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGG-CATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAG-CGTTGTGACTAAATT
EST: gi|164055840|gb|ES203705.1|ES203705
EST:     AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGTCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
genomic: AATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGG-CATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
EST: gi|86081281|gb|DR377038.1|DR377038
EST:     CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGG                         ATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC
genomic: CATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGGgtatatacat ... gccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacagagtttcttctctctgtttctaatgttttgtttctcttttgccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTCGGAATCAGCAGTGTCTACTTGGGTTTTGCTGGAGTCTGCGTCCTTGCGG
                      ttctaat  putative branch site (score: 2)
                            tgttttgtttctcttt  CT-rich tract
                         taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatacatatatctataggttttatgggttcagaacagagtttcttctctctgtttctaatgttttgtttctcttttgccctaacagATATCAAACTTTGTGATCGGACTATACTTCTTAAGCGTTGTGACTAAATTCGGAATCAGCAGTGTCTACTTGGGTTTTGCTGGAGTCTGCGTCCTTGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA