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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccagggatgaaagaaccacgttctcctaattatagccatacatatgcttacatcttttgattgcagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G79440.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79440.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G128114_T04 (Zea mays), 3'ss of exon 1
---------------------gtaagaccagggatgaaagaaccacgttctcctaatt-atagcca-tacat-atgcttacatct---tttgattg--cagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG
                      |  ||   |   |   || |  |   |  |||| ||  | || | ||||| |   ||| ||||   ||  | ||  |||||||| ||||| || ||||| ||||||||||||||||| || |||||||| ||||| ||  | ||||||||| | |||
aaaaaataaaatgacatacatttttgaatggttgtagtagtat-ataatagcctatttcgtggctagtacatcaatattaaatctggcttaaaatgttcagGTGGCACCATTTGGCGGAGTAAAGCAGTCTGGTCTTGGGAGAGAAGGATCGAAGTACGGCGTCGACGAATACTTGGAG

upper sequence: AT1G79440.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 18
-----------------------gtaagaccagggatgaaagaaccacgttctcctaattatagccatacatat---gcttacatcttttgattg--cagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG
                       |   ||  ||     |     | || || |    | || | | |||   ||   || | |   |||  | ||  |||||||| ||||| || ||||| |||||||||||||| || || |||||||| ||||| || || ||||| ||| | |||
aaaacaacatacatttttgaatggctggagtagtatacagtagcctactttgtggctagtacatcaatattaatctggcattctggtttaaaatgctcagGTGGCGCCATTTGGCGGAGTAAAGCAGTCTGGTCTAGGGAGAGAAGGATCGAAGTACGGCATTGACGAGTACTTGGAG

upper sequence: AT1G79440.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv19s0085g00860.t01 (Vitis vinifera), 3'ss of exon 17
------gtaagaccagggatgaaagaaccacgttctcctaattatagccatacatatgcttacatcttttgattgcagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG
       | | | |  | ||  |  ||| | |        ||||     |      ||   |  |   || |||||||   |||||||| || ||  | |||||||||||||||||| | |||||||||||||||||  |||| || |  || || 
gtgagtcttatatcctgaatcgataaacaaggaa----agattaagattagctgagtgaccatgtgccttcattgcagAGTGCTCCATTTGGTGGGTTTAAGCAGTCTGGTCTTGGACGTGAAGGATCCAAGTATGGGTTGGATGATTTTCTAGAA

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|116482451|gb|EG525043.1|EG525043
EST:     CACTTGAATATGGACTTGTAGGGGTGAACGAAGGACTCATATCAACAGAG                         GTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCC
genomic: CACTTGAATATGGACTTGTAGGGGTGAACGAAGGACTCATATCAACAGAGgtaagaccag ... ttgattgcagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaccacgttctcctaattatagccatacatatgcttacatcttttgattgcagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG
                                       catctttt  CT-rich tract
               taattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccagggatgaaagaaccacgttctcctaattatagccatacatatgcttacatcttttgattgcagGTGGCTCCATTCGGGGGAGTGAAGCAGTCTGGTCTTGGAAGGGAAGGATCCAAGTATGGTATGGACGAATACCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG