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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAGAGTTTACTGAACTTGTGAAGAGGGGTTCGACAGCAGAGGACTTAGGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctttttctttcgtaaaaaactctaatttttaactatgttaatgtttttggtggctttatggtttattggtagtttacctttgtcccttgtctcacatgtctttctccaactctgtacag

Basic information

species Arabidopsis thaliana
transcript AT3G52220.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52220.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G06270.1 (Glycine max), 5'ss of exon 3
AGCAAGAGTTTACTGAACTTGTGAAGAGGGGTTCGACAGCAGAGGACTTAGGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctttttctttcgtaaaaaactctaatttttaactatgttaatgtttttggtggctttatggtttattggtagtttacctttgtcccttgtctcacatgtctttctccaactctgtacag
| || |||||| | ||||| || ||| |||| || |||||||||||||||||||||||  ||||||| ||||   ||||||| |||||||| | ||| | ||||  |   |          ||| |   || ||| |  | ||      | |||   |  ||||||  ||  ||  || |||   | | |    ||| |||  ||| |                  
AACATGAGTTTTCAGAACTGGTAAAGCGGGGGTCTACAGCAGAGGACTTAGGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgact-------aggaaagaacatattttatggcaataaagtagatttgattttctttatatttactt--taatttttttctattttctgtttcagttgtttc-----------------

upper sequence: AT3G52220.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 3
AGCAAGAGTTTACTGAACTTGTGAAGAGGGGTTCGACAGCAGAGGACTTAGGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctttttctttcgtaaaaaactctaatttttaactatgttaatgtttttggtggctttatggtttattggtagtttacctttgtcccttgtctcacatgtctttctccaactctgtacag
| || |||||| | ||||| || |||||||| || |||||||||||| ||||||||||  ||||||| || |   ||||||| |||||||| | ||| | ||||  |   |       | | || | |||    |  ||  | ||  || |  ||      |||||  ||  ||  ||||||   | |||    ||| |||  |||                    
AACATGAGTTTTCAGAACTGGTAAAGAGGGGGTCTACAGCAGAGGACGTAGGTGCAGGTCATGCTGAAGCAGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgactaggaaa-gcagaacattcttcaatgcaataaagtagatttgctttta---tttatatttactt--tagttt-tttctgttttctgtttcagttgtt-------------------
















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|125073288|gb|EL137677.1|EL137677
EST:     TGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAA                         AGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTCAGAAAGA
genomic: TGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctt ... ctctgtacagAGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTCAGAAAGA
EST: gi|301503170|gb|HO208710.1|HO208710
EST:     GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAA                         AGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTCAGAAAGA
genomic: GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctt ... ctctgtacagAGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTCAGAAAGA
EST: gi|125143016|gb|EL179930.1|EL179930
EST:     TTCACGGTCTTGGATATGCTAA                         AGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTC
genomic: TTCACGGTCTTGGATATGCTAAgtaagttctt ... ctctgtacagAGCACCACGACCTTGGGAAGATCCGAGCACCCTTGCATCCTCTC
EST: gi|124950204|gb|EL025685.1|EL025685
EST:     GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAA                         AGCACCACGACCTTGGGAAGATCCGAGCACCCTTG
genomic: GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctt ... ctctgtacagAGCACCACGACCTTGGGAAGATCCGAGCACCCTTG
EST: gi|164157632|gb|ES164652.1|ES164652
EST:     GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAA                         AGCACCACGACCTTGGGAAGATCCGAGC
genomic: GGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctt ... ctctgtacagAGCACCACGACCTTGGGAAGATCCGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAGAGTTTACTGAACTTGTGAAGAGGGGTTCGACAGCAGAGGACTTAGGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctttttctttcgtaaaaaactctaatttttaactatgttaatgtttttggtggctttatggtttattggtagtttacctttgtcccttgtctcacatgtctttctccaactctgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG