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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg...

Basic information

species Glycine max
transcript GLYMA16G01230.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgttttt---ttcatgattgtgattgtgtgcaaaccagcttagg
|| || ||||| |  | |||||||||||||||||| |||||| | ||||| |||||||||||||||||     |   ||   ||||| |   ||||| |    |||  ||      ||     |   |   |||||| ||  || | |  |  | |         
ATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGTgtgagtcccattagggattctttttattttttttattttcttttcttcgtatgcttgaaaatgcataagttcatgctttggactttagggcatcttttcc---

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctatttta-tctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg--
|| || || |||   ||||| || ||||||||||| |||||| ||||||| ||||| ||||||| ||| ||||||   || | ||||   |  ||||  || |    | | |   | | || | |   |    || || |  ||     ||   |    |||   
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtc---acctgttttgccctgtttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg
|| || || ||    |||||||| ||||||||||| |||||| ||||||| |||||||| |||| |||||| |         ||| | ||   ||    ||||     |     | || |   || || |  | |       |   |  ||    ||||   
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttctaaattcttcttttaagaacatctacataaaatatggcttttc

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 3
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg-
|| || || ||    |||||||| ||||||||||| |||||| ||||||| |||||||| |||| |||||| |         ||| | ||   ||    ||||     |     | ||     || || |  | |       |   |  ||    ||||    
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttccaaattcttctt-taagaacatctccataaaatatggcttttct

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg
|| || ||  | ||||||||||| || ||||||||||||||||||| ||||||||| ||||||||||| |||      |  |  |||||   | || ||      ||   |   ||       ||   ||  | |||||  || | ||     |||      
ATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGTgtgagttttttatttcaattggtttttctttctttctttcgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttttgcag------

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg
 | || ||  ||||||||||||| || ||||||||||||||||| ||||||||||| || |||||||||  | |    |   |   |||| ||   |     | ||        || ||||   || |   || ||| | ||  || |||            
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgcagttccgagtttatgttttaacttctccaattattctaatattg-gcag-----------

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttg-tccagacattttttttgcc--ttttactcctattttatctcccatttttttgtttttttcatgattgtgattgt-gtgcaaaccagcttagg
|| |||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||| | |   |   ||| |||||    ||||  ||   |||||| |    ||||  ||||||     | |  ||    || ||| |  | || ||   
ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttaggtttcgttttttcttttggtatttttgttcactttttatgtat-gttttggtgttttggctttaaaagtttcagtagtgaactcaagttt---

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtg-tgcaaaccagcttagg
|| || ||||| |||||||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||  |||||||||||| | |||   |  | | ||   |     ||  || |  |       | |   |  |   |   |     ||||  
ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtttgtctggacatttttttttcttttgttttttttgttgcatgtttgttgcttctcatgcatgcaactagaagagcacttttatttttcttaa-

upper sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ13606 (Selaginella moellendorffii), 5'ss of exon 2
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttact---cctattttatctcccatttttttgttt---------ttttcatgattgtgattgtgtgcaaaccagcttagg-------------------------------------------------------------------------------
||||| ||||||||||||||||||||||| || || |||||| ||| | |||| ||||||||||||||| || ||      | ||||||   ||||  |   || |||       |  |||| || |||         ||||| |  ||    |||  ||   |  | ||||                                                                                 
ATTGAGCCAATTCCAAGTGGAAATCTGCCACCAGGGTTTGATGCAACTTCTTGTCGCAGTGTgtgagtgcttttctttttttcttttttcttttttgttgtaccaattcaggtatctgttttcttttttcaatttcctttttcttttttccttttggttgtttattaacttaaaaactatgctgagcttgggccgtcattgctttggttgcggaatgattttgtttctagtctgatgttcattcctgctgcag

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|5606316|gb|AI900414.1|AI900414
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|209725663|gb|BW663152.1|BW663152
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|4313794|gb|AI460913.1|AI460913
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|298165726|gb|HO008697.1|HO008697
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|5058332|gb|AI736808.1|AI736808
EST:     CCAAGTGGAAATCTGCCTTCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|5342734|gb|AI795018.1|AI795018
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
EST: gi|4282741|gb|AI440569.1|AI440569
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgttt ... gaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg

- - - - - - -  AGTGGA