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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggactatacgattacagtcaaatatgtttatttgatatagcttttggtttctcattgattgatgctattttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA

Basic information

species Arabidopsis thaliana
transcript AT5G48030.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G36820.1 (Glycine max), 3'ss of exon 4
--------gtagggactatacgattacagtcaa-atatg-----tttatttgatatagcttttggtttctcattgattgatgctattttgtat---acagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA
        | ||  |  | || |     | ||  |||||     | | | | | ||    | |  ||| |   |  |  ||     ||  | |    |||||||| || || |||||||| ||||  || ||||||||||| || ||||| | |||||| || ||||| |||| ||||||||| 
tttgacatgaagtcatcaaacaaggttggccagcatatgaattatctttctaaaatgatatgtatttttttccttctcaatttctcttcatgttctgcagCTTGCAAAAAAGCTCCATCCAGATACAAACAAAGATGATCCTGAGGCTGAAAAGAAGTTTCAAGAAGTTTCAATAGCATATGAG

upper sequence: AT5G48030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G00580.1 (Glycine max), 3'ss of exon 4
-----------gtagggactatacgatta-cagtcaaata---tgtttatttgatatagcttttggtttctcattgattgatgctatt--ttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA
              |  |  | | ||||  |   || ||    | | | |   | ||    | |  ||| ||  |      | || ||  | || | |||||||| || || |||||||| ||||  || |||||||||||  ||||||| | |||||| || ||||| |||| ||||||||| 
ctttgacatgaactgataaaacaggattggccagcatatgaattatctttccaaaatgatatgtattttttccctctcaatttctcttaatggtctgcagCTTGCAAAAAAGCTCCATCCAGATACAAACAAAGATGATCCTCAAGCTGAAAAGAAGTTTCAAGAAGTTTCAATAGCATATGAG

upper sequence: AT5G48030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ23329 (Selaginella moellendorffii), 3'ss of exon 1
gtagggactatacgattacagtcaaatatgtttatttgatatagcttttggtttctcattgattgatgctattttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA----------------
                             || |        |   |||| || |    |||||     ||  ||| |   |||||||| ||||||| ||||||||||||||| || || ||||| || ||||| | ||||||||||||| ||    | |||||||||                
-----------------------------gtatgcaaagggtgattttttgtatagttttgat-----cttctttcttcgcagCTTGCCAAGAAACACCATCCTGATATGAACAAGGACGATCCTGAGGCTGATAAGAAGTTCCAGGAAATCCAGCAGGCATATGAAGTTTTGAAAGACGATC

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|164197509|gb|ES033629.1|ES033629
EST:     GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGG                         CTTGCTAAGAAACTCCATCCTGATATGAATAAAG
genomic: GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGGgtagggacta ... ttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAG
EST: gi|125235687|gb|EL249772.1|EL249772
EST:     GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGG                         CTTGCTAAGAAACTCCATCCTGATATGA
genomic: GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGGgtagggacta ... ttgtatacagCTTGCTAAGAAACTCCATCCTGATATGA
EST: gi|19878626|gb|AU239457.1|AU239457
EST:     GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGG                         CTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAG
genomic: GAGTGAGTAAGAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGGgtagggacta ... ttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAG
EST: gi|164159046|gb|ES024899.1|ES024899
EST:     AGTGAGTAAGTAATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGG                         CTTGCTAAGAAACTCCATCCTGATATGAATAAAG
genomic: AGTGAGTAAG-AATGCTCAAGAAGGTGAAATCAAGAAGGCTTATTATGGGgtagggacta ... ttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatttgatatagcttttggtttctcattgattgatgctattttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA
                                gattgat  putative branch site (score: 4)
                                        ctatttt  CT-rich tract
                                         tattttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggactatacgattacagtcaaatatgtttatttgatatagcttttggtttctcattgattgatgctattttgtatacagCTTGCTAAGAAACTCCATCCTGATATGAATAAAGATGATCCAGAAGCTGAGACGAAGTTCCAGGAAGTCTCAAAAGCATATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA