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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagaattttgttgctgaatcctgtgattttctaaagaatgagaattttttcctggtcctgtgaattctaaagtagtactatttggtcttcattttgtagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCTCGTCACGACTACTATCCTCTAACACTCGAAGCGCAGGAGCAGGTCCCTA

Basic information

species Arabidopsis thaliana
transcript AT5G22350.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 3
gaagaattttgttgctgaatcctgtgattttctaaagaatgagaattttttcctggtcctg--tgaattctaaagtagtactatttggtcttcattttg-tagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCTCGTCACGACTACTATCCTCTAACACTCGAAGCGCAGGAGCAGGTCCCTA
| || |||| | | || | || | | | | || || | | | |||| || | ||||||| | | | ||| | ||||||||||||| || || ||||| ||||||||||||||||| || || |||| ||| || || |||||| | || | |||| ||| ||||||| ||||
-tggtgacttattgc--acttctatacttctgtggtgtttattgcttcatttaagcattggcttcaatttgtaactttgactattttttttccttttggacagATACAACATCCAAGGTCTCATTTGAATAGGTTTGACATGGTAATTACACCTCATCATGATTATTATCCTTTGACTCCAGAAGGACAGAAGCAGGTTCCTA

upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G31170.1 (Glycine max), 3'ss of exon 3
gaagaattttgttgctgaatcctgtgattttctaaagaatgagaattttttcctggtcctg--tgaattctaaagtagtactatttggtcttcattttg--tagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCTCGTCACGACTACTATCCTCTAACACTCGAAGCGCAGGAGCAGGTCCCTA
| | || |||| | | || | | | | | | || || | | | |||| || | |||||| | | || || ||||||||||||| || || ||||| ||||||||||||||||| || || |||| ||| || || |||||| | || | |||| ||| ||||||| ||||
--ggtaacttattgc--atttctatactactgtggtgtttattgcttcatttaagcattggcttcaatttgtaactttgactattattttccccttctggacagATACAACATCCAAGGTCTCATTTGAATAGGTTTGACATGGTAATTACACCTCATCATGATTATTATCCTTTGACTCCAGAAGGACAGAAGCAGGTTCCTA
















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|116460254|gb|EG502846.1|EG502846
EST:     TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAG                         ATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCT
genomic: TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAGgtctattata ... cattttgtagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCT
EST: gi|116460255|gb|EG502847.1|EG502847
EST:     TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAG                         ATACAACATCCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCC
genomic: TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAGgtctattata ... cattttgtagATACAACAT-CCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCC
EST: gi|116472246|gb|EG514838.1|EG514838
EST:     TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAG                         ATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCT
genomic: TTGCTAGCTCGATAAGACGTTTGGCTTCTGAAAACGTCTTCGTTGTTCAGgtctattata ... cattttgtagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcctggtcctgtgaattctaaagtagtactatttggtcttcattttgtagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCTCGTCACGACTACTATCCTCTAACACTCGAAGCGCAGGAGCAGGTCCCTA
                    ttctaaa  putative branch site (score: 2)
 tcttcatttt  putative PPT
 aattctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagaattttgttgctgaatcctgtgattttctaaagaatgagaattttttcctggtcctgtgaattctaaagtagtactatttggtcttcattttgtagATACAACATCCTAGATCACATTTAAATAGGTTTGACATGGTGATCACGCCTCGTCACGACTACTATCCTCTAACACTCGAAGCGCAGGAGCAGGTCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
gaagaat
- - - - - - - ctgaatc
- - - - - - - - - - - - - - - - taaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatttgg