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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattc------tgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||||     |          | | ||| ||   |    |    || |  | |   |  |||||| | | ||  ||       | |   ||||||||||||| |||||||| |||||||| || ||| | ||||||||||| |||||||||||||| || || ||  | ||||| ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatc--attctcatgtgctatgtatttaaatgcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtataaggtttcctgggactacttttaatgcgttggagtt-cagtttttttttatgaa---atatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||||     |          | | ||| ||   |    |     |  | |  |||| |   | |||  ||  ||   || | |   ||||||||||||| |||||||| |||||||| || ||| | ||||||||||| |||||||||||||| || || ||  | ||||| ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
---------gta-taaggtttcctgggactactt-ttaatgcgttggagttca-----gtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
         ||| |   || |   |   ||  |  ||  ||||| |    |||     | ||   | |  |||   || || | |||   |   |   ||||||| || ||||||||||| || || || ||||| || ||||||||||||||||||||||||||||| || ||  | || ||||||||||||||  | |
gttcagaaggtagttgtgtgtttcgactctgttaattcgtgcgtcgttcctcataataggttgagtatgagaatggttaattcttttttcttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
gta-taaggtttcctgggactactt-ttaatgcgttggagtt-----cagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||| |   || |   |   ||  |  ||  ||||  |    |      || ||   | |  |||  ||| || | |||   |   |   ||||||| || ||||||||||| || || || ||||| || |||||||||||||||||| |||||||||| || ||  | || || | |||||||||  | |
gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 19
gtataaggtttcctgggactacttttaat----gcgttggagttcagtt--tttttttatgaaatatttatacgtttgattctgtc------aaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||||     | | ||     ||| ||| |    ||||     ||||  |  | |||  |  |  | |||    ||||  || ||||        |||| || ||||| ||||||||||| || || |||||  | || |||||||||||||| |||||||| || || ||  | |||||||||||||||||  |||
gtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 20
------------gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttata-cgtt-tgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
            | || |    | |||  |      ||| | |        | |  |  ||| | ||    | | ||| | || ||  |   | | |||||||||| ||||||||||| ||||| || |||||| |  | |||||||||||||| ||||||||||| |||||| | ||||||||||||||||| || |
gtattatagtttgcattaataatgctgtaatcttgcttattacacaaatact-atctactttctctgccccactcataacattgtgccttctttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGCCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 21
gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||||||   |  |   |  ||  |     | | |         |||| | |    |  ||    | |||    |||| | | |||||||||| |||||||| || |||||||| |||||| |||| |||||||||||| | ||||||||||| |||||| | || || |||||||||||||| |
gtataatagtagccttgcttatctcatgagtgctatctactctttttctctgcctatgtaaaacttcgtgcctttctat-acagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 20
------------gtataaggtttcctgggac--tacttttaatgcgt-tggagttcagttttt---ttttatgaaatatttatacgtttga---ttctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
            | || |    | |||  ||  | ||||| |   |  |    |  ||| | |   || | ||    | | |||  ||||    || | | | |||||||||| ||||||||||| ||||| || |||||| |  | ||||||||||| || ||||||||||| |||||| | ||||||||||||||||| || |
gtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGTCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtc---aaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
||||||   |  ||  |  ||  |   |||  |||   |  | | ||||| | ||   ||| || |  ||||   || ||   | |||||||||| |||||||| || |||||||| |||||| |||| |||||||| ||| | ||||||||||| |||||| | || || |||||||||||||| |
gtataatagtagctttgcttatctc--atg-attgctatctactctttttctctgcc-tatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------gtataa-ggtttcctgggactacttttaatgcgttgg---agttcagtttttttttatgaaat--attta--tacgtttgattctgtcaa-agGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
                                               || | |   ||||| |  | |||  |||||  |     | || ||| ||   ||||   ||  | |||  | | |||| |||| |  | ||||||||||| | ||||| || |||||||| |||||| |||| ||||||||||| || |||||||| || ||||| || ||||| ||||| || ||  |||
gtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttc-aatgccctaattaattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatagGTGAACCCTAGTAATGCACCTTTAGTTGTGGGGCAGCTGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 21
gtataaggtttcctgggactacttttaatgcgttggagttcagttttttt-ttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
                               ||  |  |||| |   ||| ||     ||| |  |   |||||   | |||  ||| || ||||  || || |   | || || || ||  |  | ||||||||||| ||||| ||||||||||||   ||||| ||||||||||| || || |
-------------------------------gtacggattcaatgcatttgttgctctataatcgt---tttgaaattttca--gGTCAATCCTGCAAACGCACATCTGGTCGTGGGCCAACTTTTAGATGATGAATGTCCTGAGGATTTTATAAAAAATCTCATCCTCTCTGTTCGATCGTTAC

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|124936463|gb|EL013354.1|EL013354
EST:     ACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAG                         GTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGA
genomic: ACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtt ... tctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
                                      gtttgat  putative branch site (score: 5)
                                            ttctgtc  CT-rich tract
            agtttttttttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA