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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag

Basic information

species Glycine max
transcript GLYMA17G18200.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| ||||||||| | ||||| || |||||||| ||||| || ||||||||||| | |||||| ||||||||||| | ||| ||||||||||||||        |          |      ||| ||  ||| || |    |   ||       |  |  || ||  | || |      || ||||   |||     || |  ||||
ACCTTCAAGCGCCGCAATGGCGGCCGCAACAAGCACGGTCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgt--------aaggcgaagcgaatccccttttgccctctctcgttgcgcgcgaggcacccactgg--atctctgtgttgatttgggaatcttt---gctttgggtgcgggacag

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g39960.1 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttc--caccttcagatttgtgcgaggcatttcaattttcaac--aactaaccttttg-tgctcgctctgtgaaacag------
|| |||||||||||||| || || |||||||| || ||||| ||||| || || | |||||| ||||||||||| | ||| |||||||||||||||       |||    |  | |      || | | |  |  |||  |   ||   | |  | || |  || |    ||||  |    || |    ||| | || |    ||      |      
ACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgttcgcgg--attcagattctcttgcagatttgttattatcattcagcgtgttattactgttacgcgaaatctgcggtttcggcttggctgattcgttggttcttgggtcgtcgccttgtcgcag

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttc--caccttcagatttgtgcgaggcatttcaattttcaac--aactaac-cttttgtgctcgctctgtgaaacag------------
|| |||||||||||||| || || |||||||| || ||||| ||||| || || | |||||| ||||||||||| | ||| |||||||||||||||       |||    |  | |      || | | |  |  |||  |   ||   | |  | || |  || |    ||||  |    || |  | || || || |    ||      |            
ACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgttcgcgg--attcagattctcttgcagatttgttattatcattcagcgtgttattactgttacgcgaaatctgcggtttcggcttggctgattcgttggttcttgggtcgtcgccttgtcgcaggacaag

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G899149_T01 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgt--ttttttttattttatt-attatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttca-attttcaacaactaaccttttgtgctcgctctgtgaaacag
|| |||||||| |||||||| || |||||||| ||||| || ||||||||||| | |||||| ||||||||||| | ||| ||||||||||||||     ||    |   ||  |      || |||    |   |   ||   |    | |   |||  || |  |   ||| || |      |||| | ||                  
ACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGgtaacacttcccttcccatagagcgcggttgtttgtgatggatgaatcgggccgttgttagctgcagggaaagtggtattctcgagtctagacctctcgt------------------

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G827266_T03 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| ||||||||| | || || || |||||||| || ||||| || |||||||| | |||||| ||||| ||||| | ||| ||||||||||||||       |   |    |   ||    ||    ||   ||| |  |||       | | |      || |  ||  ||   |                               
ACCTTCAAGCGCCGCAACGGCGGCCGCAACAAGCATGGCCGCGGTCACGTCAAGTACATCCGGTGCTCAAACTGCGCCAAGTGCTGCCCCAAGgtgaggagatgcctc--cacagtcgcctttctttttctcttcatttacccgtgtggtggagtccttgatcttgatgctcgttacag----------------------------

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G129015_T02 (Zea mays), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| |||||||| ||||| || || |||||||| ||||| || ||||||||||| | ||| || ||||||||||| | ||| ||||| || |||||     |||  ||   | |   |  |||||   | |  |             |||   | |||| | ||   |  | |||   |    | |   ||  | |  |||  |    
ACGTTCAAGCGGAGGAACGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATACGCTGCTCCAACTGCGCCAAGTGCTGTCCAAAGgtagccgtttccttccctttggaccgtatttgtttgtgat------------ggatgaat-cgagccgttgttagctgcaagggcatggcctcgttggccacattgtttagat-

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgt--ttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaatt-ttcaacaactaaccttttgtgctcgctctgtgaaacag
|| |||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||| |||||||||||||||||||||| |||||||||||  | | ||| |  || |  |    || | |     | |  |  | |   |    ||||      |   ||    |  ||| | ||  |    |||| | | |             
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAGgtactctctttcaccttctcttctcaatcaatcaatctccagtaattcttatgtgtattttgatttgatcttgtggtggttctataataa----tttgggatag-------------

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgt-ttttttttattttattattatc--attatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| |||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||| ||||||||||||| |||||||||||||| |||||  | | ||  |  |  | || ||  || | |     | |  |    |   |   |||||     ||   ||    |  | || |  |||  ||   |                  
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggtggt-aata--taaatttggatag----------------

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 5'ss of exon 2
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| |||||||| |||||||| ||||||||||| |||||||| ||||||||||| ||||| || |||||||||||||||||||||||||| |||||  |||||  |||  ||      |||  |||  ||  |||||| |   |   | |    | ||   ||    |     |  ||  ||   ||||       | |         
ACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAGgtactttttcttttgcttgcctcaatt--ttcctttattttctttcgttt---ggtggccgagaaatatccataaccataggaaagaaaactttgaatctttttt---------

upper sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 5'ss of exon 3
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattt-tattattatc--attatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag
|| ||||||||||| || || || |||||||| ||||||||||| || ||||| |||||||| ||||| ||||| || ||||||||||| ||||| |   |  |||| |||| | ||    |  ||| |  |     | ||     |   ||| ||||| |    ||     ||     |  |                           
ACGTTCAAGCGCAGAAACGGCGGCCGCAACAAGCACGGCCGTGGACATGTCAAGTTCATCCGCTGCTCAAACTGCGGAAAATGCTGCCCAAAGgtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagttgaattggtgcgtg----tttggaattgtgtgatcag--------------------------

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|21285658|gb|BQ473529.1|BQ473529
EST:     CTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: CTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|31307027|gb|CD392230.1|CD392230
EST:     GTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|16346765|gb|BI972360.1|BI972360
EST:     GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|10848274|gb|BF070805.1|BF070805
EST:     GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|22933841|gb|BU550980.1|BU550980
EST:     GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|209723888|gb|BW675234.1|BW675234
EST:     GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|13790582|gb|BG653173.1|BG653173
EST:     GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: GCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
EST: gi|31309293|gb|CD394496.1|CD394496
EST:     CACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG                         GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA
genomic: CACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgttttttttt ... tgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC