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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttgtgttctacttgcctacgttgctctgtaactactttgattgcttgtattgctagttgatgaatggccttgtgatggtagaaaggataatat...

Basic information

species Arabidopsis thaliana
transcript AT5G48760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 5'ss of exon 3
GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgtt-gtgttctacttgcctacgttgctctgtaactactttgattgcttgta-ttgctagttgatgaatggccttgtgatggtagaaaggataatat
||| ||||||||||||||||| ||||| |||||  | |||||| | ||||| || || || || |||||||| || || |||||||||||  | ||| |      | || | || |||  | | ||  |  ||||| |    ||| ||| |  |    | ||  |  |||  |       |   ||  | 
GGTTTTGAGGCTTCAAGCTGGGCACAAGTACTGCTTGTTGGGCAGGCTTTCATCAGAGGTGGGATGGAACCACTATGAAACCATCAAGgtcagagtttgccgcacaatttcttatgttattgtcta-ttgttttgaattaaagtagttgtttctattcggatatctatgtttttaagcctatagtatca-

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 5'ss of exon 3
GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttgtgttctacttgcctacgttgctctgtaactactttgattgcttgtattgctagttgatgaatggccttgtgatggtagaaaggataatat--
||| ||||||||||| ||||| ||||| |||||  |  | ||||| ||||| || || ||||| |||||||||||||| |||||||  ||| |  ||   |||  | | |||       ||  |     || |   |          | |    |   |    |   ||     |   |    ||||   
GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGAgtaagatttcacttc--cctacctcttggaatcaatttgagctctctctctcccctccccaaacaaacacacactcacatgcatagatgcacatcaatactc
















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|86017893|gb|DR313639.1|DR313639
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|124787934|gb|EH877613.1|EH877613
EST:     GGGCCGTCTTTCTTCTGAAGTTGGGTGGTAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: GGGCCGTCTTTCTTCTGAAGTTGGGTGG-AACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|164032270|gb|ES155175.1|ES155175
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCAC
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCAC
EST: gi|47831264|gb|CK120948.1|CK120948
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|164058767|gb|ES172921.1|ES172921
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTG
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTG
EST: gi|125320020|gb|EL334105.1|EL334105
EST:     GTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: GTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|47827976|gb|CK117660.1|CK117660
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|164007785|gb|ES107325.1|ES107325
EST:     TTTCTTCTGAAGTTGGGTGGAACCATTACGACACCTATTCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAA
genomic: TTTCTTCTGAAGTTGGGTGGAACCATTACGACACC-A-TCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAA
EST: gi|164014557|gb|ES157551.1|ES157551
EST:     TTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: TTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
EST: gi|86017892|gb|DR313638.1|DR313638
EST:     TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG                         GAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG
genomic: TGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttg ... caataagcagGAGCTGGAGACAAAGAGGAAGGAGAGAGCCCACGTGGTTTACGAGCGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAGgtatgtgttgtgttctacttgcctacgttgctctgtaactactttgattgcttgtattgctagttgatgaatggccttgtgatggtagaaaggataatat

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA