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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagattcttctaattcccctctcaatcaacaccctaaatattctcgatttccttcttccattgttccctttacattgttttttgttcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGACCTACCAGCTTCAGGTCGATTTTCCTGAGAATTACCCGATGGAAGCTCCT

Basic information

species Glycine max
transcript GLYMA01G37480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaccagattcttctaattcccctctcaatcaacaccctaaatattctcgatttccttcttccattgttccctttacattgttttttgttcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGACCTACCAGCTTCAGGTCGATTTTCCTGAGAATTACCCGATGGAAGCTCCT
                       | |||| |   |       | |  | ||  |   | ||   || || |  | |  ||| |||   | | | | |||||| | |      ||| |||    | || || || |||||||| ||||||||||||||||| ||||| || ||||||||||| || ||||||||  ||||||| |||||||| || 
----------------------gtatcaacctttatgtctc-tgtctttgaaatgagtttttt-ttctttctgtgattttgatttgaatgcgtat-ctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
















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|209697785|gb|BW663924.1|BW663924
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|15664810|gb|BI702173.1|BI702173
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|10844680|gb|BF067906.1|BF067906
EST:     CACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTCTGAAGTCANCTGGAGCTCCTGGGACACTTTACGCTAACGAG
genomic: CACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGT-TGAAGTCA-CTGGAGCTCCTGGGACACTTTACGCTAACGAG
EST: gi|9204241|gb|BE330465.1|BE330465
EST:     GTCAATCCCCCCACTGGTTTCAAGCACAAAGTCACAGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAATGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|209703743|gb|BW656876.1|BW656876
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|20813177|gb|BQ297655.1|BQ297655
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|27445947|gb|CA953070.1|CA953070
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
EST: gi|37996938|gb|CF808527.1|CF808527
EST:     GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAG                         GTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC
genomic: GTCAATCCCCCAACTGGTTTCAAGCACAAAGTCACCGACAATCTCCAGAGgtaccagatt ... tctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccattgttccctttacattgttttttgttcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGACCTACCAGCTTCAGGTCGATTTTCCTGAGAATTACCCGATGGAAGCTCCT
                cattgttttttgttcc  CT-rich tract
            tttacattgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccagattcttctaattcccctctcaatcaacaccctaaatattctcgatttccttcttccattgttccctttacattgttttttgttcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGACCTACCAGCTTCAGGTCGATTTTCCTGAGAATTACCCGATGGAAGCTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG