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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatgtcttccatgaatcttttgcattctagacttgtataaaatcattttcacattcctttatgtggtatactgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCCAAAGCTAAGTCATTCAAAGCACGAATGACG

Basic information

species Arabidopsis thaliana
transcript AT2G30200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g07380.t01 (Vitis vinifera), 3'ss of exon 6
gtatatatgtcttccatgaatcttttgcattc-tagacttgtataaa--atcattttcacattcctt---------tatgtggta-----tactgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCCAAAGCTAAGTCATTCAAAGCACGAATGACG
|||    | | ||  ||   ||| |||  |   || || |  | |    |||| ||    |||| ||          |||   |      |||| |   |||| ||||| ||||| ||||||||  | |||||| | ||||  |||||||| || |||||||||||||| || |||||||||
gtaaggttcttttagatccttctattggttcagtaaacctagacagcttatcaattcttgattctttagaccatagcatgaaatgcttgttactttggtagGGGAATTATGCAGTCTCTGGAGGAGTGAAAGGAGTGGAAGCGGTTGAAGCTAAGGCTAAGTCATTCAAGGCCCGAATGACG
















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|116380444|gb|EG423036.1|EG423036
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|116380443|gb|EG423035.1|EG423035
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|86080301|gb|DR376058.1|DR376058
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|116401255|gb|EG443847.1|EG443847
EST:     AATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|116380445|gb|EG423037.1|EG423037
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTC
EST: gi|86074247|gb|DR370004.1|DR370004
EST:     AAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|116380442|gb|EG423034.1|EG423034
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
EST: gi|116377112|gb|EG419704.1|EG419704
EST:     AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCG                         GGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC
genomic: AAGAAGTAGATGAAGCTGACAAAGTTCAGATCGCAAATTACTTATGTCCGgtatatatgt ... actgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctagacttgtataaaatcattttcacattcctttatgtggtatactgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCCAAAGCTAAGTCATTCAAAGCACGAATGACG
        ttgtataaaatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatgtcttccatgaatcttttgcattctagacttgtataaaatcattttcacattcctttatgtggtatactgttacagGGTAATTACGCAGTATCTGGAGGTCTTAAAGGAATCGAAGTTGTTGAAGCCAAAGCTAAGTCATTCAAAGCACGAATGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC