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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttggtactttgtattgtattaattgaaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG

Basic information

species Arabidopsis thaliana
transcript AT4G13020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 6
gtatgttttggtactttgtattgtattaattg-aaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
||||   ||   ||| | |  |||   | ||  |    || |     |  |  | ||    ||  |   || | |  |   |||  ||| ||| || |||||||  |    |   | ||||||||||||||||||||||| ||||||||  | || |  |||||||| ||||| ||||| |||||  |
gtatacctttcgactatattctgttgaagttataggctgtctatataccctagaagttaattagcc---ttctctctttcctctttagAAAATCTGTTGGTGACAGATGGCACTGTTAAAATTGCTGACTTTGGGTTGGCAAGAGAAGTATCTTCCAGTCCTCCTTATACTGACTATGTTTCCACCAG

upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 2
gtatgttttggtactttgtattgtatta-attgaaatggttttcgctctttgaatgtcttataaacaagttttgttc----tgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
    ||  || |   |||| |  ||||| |||| |||  | ||  || | |   ||||  |  ||  |||||| |||    | ||| || |||||||||| ||||||| ||   |||  | ||||||||||||||||||||||| |||||| |  | || |  |||||||||||||| ||||| |||||  |
----gtaatg-tgtcttgt-tgatattacattggaattatcttatctttctttctgtcaaaataattagtttttttccttctatttgtgcagAGAATTTGTTGGTGACAAATGGTATTATTAAAATTGCTGACTTTGGGTTGGCAAGAGAAATATCTTCCAATCCTCCTTACACTGATTATGTTTCCACCAG

upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G21610.2 (Glycine max), 3'ss of exon 6
----------------------------------------gtatgttttg---gtactttgtattgta-ttaattgaaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
                                         |||||| ||    ||||||  | |  | |   |  ||| |||  |     | |  || | ||   ||    || || | |        ||||||| ||||||| || ||  || |  ||||||||||||| |||||  |||||||||||||  |||| |||||||| || ||| ||||||| ||||||||
gtgaggcatatatatgatttcatttagcgaatttatgatgttatgttgtgtttatactttccagtccagtctgtctaaaaggtcatgtggatcttgatcttttgggaatgttttctgctatac------agAGAATATGCTGGTAACAAATGATGTTTTGAAAATTGCTGATTTTGGACTGGCTAGAGAAGTATCATCGATGCCTCCATATACTCAATATGTTTCCACACG

upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G10820.2 (Glycine max), 3'ss of exon 7
----------------------------------------gtatgttttg---gtactttgta-ttgtattaattgaaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
                                        |||| || ||    ||||||  | ||  ||   |  |||  ||  |     |||  || | ||   ||    || || | |        ||||||||||||||| ||  |  || |  ||||||||||||| |||||  |||||||||||||  |||| |||||||| || ||| | ||||| ||||||||
gttaggcatatatatgatttcatttagcaaatttctgatggtatattgtgtttatactttccagttcaatctgtctaaaaagtcatatggattttgatcttttgggaatgttttctgctatac------agAGAATTTGCTGGTAACAGATGATGTTTTGAAAATTGCTGATTTTGGACTGGCTAGAGAAGTATCATCGATGCCTCCATATACTCAGTATGTTTCCACACG

upper sequence: AT4G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0151g00350.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------gtatgttttggtactttgtat-tgtattaattga-aatggttttcgctct-ttgaatgtcttata--aacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
                                         |||| ||||| | ||| | |   | || ||  | ||| || |  ||| | |  |||    ||||  | |||      ||    |  | ||||||||||||||||||| |||||| |  | |||||||||||||| ||  |||||||||||||  |||||||||||||||| ||||| ||||||||||||||
gtatgaagttgacttctacaaaattatgcacttgtgcagtctatgatttggaattttatttgcatcttcatgaagaattgtgtaggctttatctaatagtgtatattatcaaacaccatttctgtcttcaagAGAATTTGCTGGTGACAAACAATGTGATTAAAATTGCTGACTTCGGACTGGCTAGAGAAGTATCATCTATGCCTCCTTATACTGACTATGTGTCCACACG

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|124958306|gb|EL033059.1|EL033059
EST:     GCTCGCACACATGCATAAAAACGGTTATTTCCATCGAGACCTGAAACCTG                         AGAATTTGCTGGTGACCAACAATATCCTCGAAAATTG
genomic: GCTCGCACACATGCATAAAAACGGTTATTTCCATCGAGACCTGAAACCTGgtatgttttg ... gtttctgaagAGAATTTGCTGGTGACCAACAATATCCT-GAAAATTG
EST: gi|116427860|gb|EG470452.1|EG470452
EST:     GCTCGCACACATGCATAAAAACGGTTATTTCCATCGAGACCTGAAACCTG                         AGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGG
genomic: GCTCGCACACATGCATAAAAACGGTTATTTCCATCGAGACCTGAAACCTGgtatgttttg ... gtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG
                                    ttttgttctgtttct  CT-rich tract
                         ttataaacaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttggtactttgtattgtattaattgaaatggttttcgctctttgaatgtcttataaacaagttttgttctgtttctgaagAGAATTTGCTGGTGACCAACAATATCCTGAAAATTGCTGACTTTGGGTTGGCTAGAGAAGTTGCATCTATGCCTCCTTACACTGAATATGTGTCCACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT