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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttctctgtcaaattatgttgaataactgaaagtccatctctttgttttagcttcttttctttctaaaactctacttttcag

Basic information

species Arabidopsis thaliana
transcript AT3G24170.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G24170.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA16G27210.1 (Glycine max), 5'ss of exon 8
GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttctctgt-caaattatgttgaataactgaaagtccatctctttg---ttttagcttcttttc--tttctaaaactctacttttcag------
 |||||||| || ||||||||||| ||||||||||| |||||| | || || ||| || | ||||| ||||||||||| || ||||   | |||  ||| ||  || |||| ||    | |     |||   |  |   || | |||   | ||  ||||    | | | ||||| ||      
TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAGgtttggcttcggtgtacatcttgtgtttaagttttaagttatcataaatggggccttatggctatgtctccttttcccctagtttgcttttaagttttaa

upper sequence: AT3G24170.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA02G08180.1 (Glycine max), 5'ss of exon 7
GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttctctgt-caaattatgttgaataactgaaagtccatctctttg---ttttagct---tcttttctttctaaaactctacttttcag------
 |||||||| || ||||||||||| ||||||||||| |||||| | || || ||| || | ||||| ||||||||||| || ||||   | |||  ||| ||  || |||| ||    | |     |||   |  |   || | |||   |||||| || |   |  | | ||||| ||      
TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGGATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAGgtttggcttcgatgtacatcttgtgtttaagttttaagttatcataaatggggccttctggctatgtctttttttcccctagtttt-cttttaagttttaa

upper sequence: AT3G24170.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 5'ss of exon 9
GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctg--gttctctgtcaaattatgttgaataactgaaagtccatctctttgttt--tagcttcttttctttctaaaactcta-----cttttcag---
||| |||||||| |||||||| |||||||||  ||| ||||||| | |||||||| |||| ||||| |||||||||||  ||||||  ||  | ||    |   ||    ||   | ||   ||  | ||   | |  |   |      | |    | ||||||| ||     ||| |||    
GTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAGgttatgtagctcatgttttgatcccattttttgaccataatcctattgatctcctgaatgatggttgtgggctttaaaactttattgggcttatcatgtt

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|164116577|gb|ES088726.1|ES088726
EST:     GGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG                         GGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCT
genomic: GGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttc ... tacttttcagGGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCT
EST: gi|116457529|gb|EG500121.1|EG500121
EST:     GGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG                         GGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG
genomic: GGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttc ... tacttttcagGGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG
EST: gi|124854185|gb|EH938622.1|EH938622
EST:     TTTATTNTTCAGGAAGGAACTTCCGCTAAG                         GGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG
genomic: TTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttc ... tacttttcagGGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG
EST: gi|125106361|gb|EL159814.1|EL159814
EST:     TTTATTCTTCAGGAAGGAACTTCCGCTAAG                         GGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG
genomic: TTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttc ... tacttttcagGGGTTTTGATGACGAAATGAGGGCACTAGTTGCTAGAAATCTTGAAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAGgtgctggttctctgtcaaattatgttgaataactgaaagtccatctctttgttttagcttcttttctttctaaaactctacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA