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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagtttagttaaagagaaagaagaatcagagatctcaagattctcaacccattgaatcttctttggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG

Basic information

species Arabidopsis thaliana
transcript AT2G21960.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtagagtttagttaaagagaaagaagaatcagagatctcaagattctcaacc--cattgaatcttctttggtt-tttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG
                     | |  ||  |    ||  ||   | | | || ||  |   | |   || |   ||||  | |||     ||| || ||||||||| | ||| ||||||||||||||||| || || || ||| | |||||||||||  |||| |||||||| ||||| ||| ||||||||
acataatcctccatagatagttcggattatggattagttaatttaaattaagggaattgccggtagacagctgacattccacctttaactgttattccagGTTGGCGGTTGTAGCAATGGCTGGACTTGCAGCAGAAGGCCTGCAATATGACAAAGTGGTTGGTCAATCTGCCGATCTTTTCACTCTTCAG

upper sequence: AT2G21960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ34800 (Selaginella moellendorffii), 3'ss of exon 6
gtagagtttagttaaagagaaagaagaatcagagatctcaagattctcaacccattgaatcttcttt--ggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG
                         | ||| ||  ||  |    | ||   |  |||||  ||||||    | | ||||| ||||||  ||| |||||||||| ||||| ||||||| ||| || ||||||||||| |||||||| ||||| ||| | ||||| ||||||
-------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttctattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCCCTTCAG

upper sequence: AT2G21960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ23530 (Selaginella moellendorffii), 3'ss of exon 6
gtagagtttagttaaagagaaagaagaatcagagatctcaagattctcaacccattgaatcttcttt--ggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG
                         | ||| ||  ||  |    | ||   |  |||||  ||||||    | | ||||| ||||||  ||| |||||||||| ||||| ||||||| ||| || ||||||||||| |||||||| ||||| ||| | ||||||||||||
-------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttctattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCTCTTCAG

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|86079351|gb|DR375108.1|DR375108
EST:     CTAGCTAAACTAATATACAGCGGCAAGCTTGACTCAAAGGAGCTCGATAG                         GTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGA
genomic: CTAGCTAAACTAATATACAGCGGCAAGCTTGACTCAAAGGAGCTCGATAGgtagagttta ... ggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGA
EST: gi|124863059|gb|EH947496.1|EH947496
EST:     TATACAGCGGCAAGCTTGACTCAAAGGAGCTCGATAG                         GTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGA
genomic: TATACAGCGGCAAGCTTGACTCAAAGGAGCTCGATAGgtagagttta ... ggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaatcagagatctcaagattctcaacccattgaatcttctttggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG
                                     tcttctttggtttttc  CT-rich tract
                               attgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagtttagttaaagagaaagaagaatcagagatctcaagattctcaacccattgaatcttctttggtttttcagGTTGGCTGCTGTTGCAATGGCTGGACTTGCCGCCGAGGGTCTGAAGTATGACAAAGTAATTGGCCAATCTGCAGATCTCTTCTCTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT