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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagtgttctcaacttagttctggtttttgcatgtttgatttggaaatggtggattttgaaagctgcatctttttaagtatctaatgtttctgtgaggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCATACACGCTGCTTGTGCTGTTCTGGGCAGAGATATATCACCAG

Basic information

species Arabidopsis thaliana
transcript AT4G21790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g36790.3 (Oryza sativa), 3'ss of exon 2
gtgagagtgttctcaacttagttctggtttttgcatgtttgatttggaaatggtggattttgaaagctgcatctt--tttaagtatcta--atgtttctgtgaggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCATACACGCTGCTTGTGCTGTTCTGGGCAGAGATATATCACCAG
           |   || ||| | || || | |  | ||  ||  |||  |  |   |||| |    ||  |  |   |  | |    |  |    ||| |  | | |   |||    |   | |||  |||||||||||||||| ||||| ||||||||| |||||||||| |||||||||||||||||||| ||||| || |||
-----------cgacacctagctttgtttgtggacttttcaat--ggatttcctaatttttaatgtttgtgttctagctggattgctcatcagaactctttatgtttaaatagGTGTATACTTTGGTGTTATTGGATCTTCCTGGTCTTCTATTTTTCTCGACATACACGCTACTTGTGCTGTTCTGGGCAGAAATATACCATCAG

upper sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 3
gtgagagtgttctcaacttagttctggtttttgcatgtttgatttggaaatggtggattttgaaagctgcatctttttaagtatctaatgtttctgtgaggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCATACACGCTGCTTGTGCTGTTCTGGGCAGAGATATATCACCAG-------
     | ||   |  |           | ||| | ||  |  | | | |      |   |  || ||     || |||    |    |||  | ||     | |  ||||  ||    | |||| | |||||||||||||| ||||| ||||||||  ||||||| || |||||||| || |||||||||||||||||||||       
----cactggaatagatggtaccacactgttttcctgcatcttgtagcatctacagtgctcaaaggc-----ctgtttgctgacagcatgcatttgcatcttgaatcagGTACTGATTTTGGTATTGTTGGATCTTCCTGGACTTCTGTTTTTCTCTACATACACACTTCTTGTGCTATTTTGGGCAGAGATATATCACCAGGCAAGTA
















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|86038980|gb|DR334735.1|DR334735
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTAGGTACTATYGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|164219991|gb|ES190089.1|ES190089
EST:     TGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: TGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|301502535|gb|HO208075.1|HO208075
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|86038985|gb|DR334740.1|DR334740
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTT
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTT
EST: gi|86038987|gb|DR334742.1|DR334742
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|86038988|gb|DR334743.1|DR334743
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGNTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|125206042|gb|EL220996.1|EL220996
EST:     ATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGCACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: ATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|124909554|gb|EH983634.1|EH983634
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTT
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTT
EST: gi|86038984|gb|DR334739.1|DR334739
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|116408117|gb|EG450709.1|EG450709
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|86038989|gb|DR334744.1|DR334744
EST:     GGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCT
genomic: G-CGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTG-TTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCT
EST: gi|125311321|gb|EL325406.1|EL325406
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCT
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCT
EST: gi|86038983|gb|DR334738.1|DR334738
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCA
EST: gi|116479083|gb|EG521675.1|EG521675
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCT
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCT
EST: gi|86038986|gb|DR334741.1|DR334741
EST:     GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAG                         GCTCTTTGCTG
genomic: GTGCGGTTCTGTTTGGATTTCACATGCAAGTATTTCTTGTTCATCCCAAGgtgagagtgt ... ggtaatgcagGCTCTTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattttgaaagctgcatctttttaagtatctaatgtttctgtgaggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCATACACGCTGCTTGTGCTGTTCTGGGCAGAGATATATCACCAG
                            atctaat  putative branch site (score: 3)
                   tttttaagtatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagtgttctcaacttagttctggtttttgcatgtttgatttggaaatggtggattttgaaagctgcatctttttaagtatctaatgtttctgtgaggtaatgcagGCTCTTTGCTGGGTACTATTGGATCTTCCTGGCCTTCTCTTTTTCTCGGCATACACGCTGCTTGTGCTGTTCTGGGCAGAGATATATCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT