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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccatttttttccttcctttattgccctttatgcttatggttcactcactcactgtgttttgcgaag

Basic information

species Glycine max
transcript GLYMA03G02240.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g02960.3 (Oryza sativa), 5'ss of exon 4
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc-aatttgacctaatgtttcgttcttc-------actccatttttttccttcctttattgccctttatgcttatggttcactca-ctcactgtgttttgcgaag----------------------------------------------------------------------------------
 ||    |  ||||| |||||||| ||||| || ||||| ||||| || || ||||| ||||| |||||||| || || |||||||| ||||| ||||||||||||| || ||| |       | ||    ||||        |    |||||      |  | || | |     |  ||     |  ||  |  |      || |   || |                                                                                  
TCACCAAAATGAAGAGTTTGCCGTGAGAGGAAAGGAGCCGAAAGATGAAGTGCAGATATACACGTGGAAGGATGCCACACTCCGAGAGCTCACTGATCTTgtaatttttctaatattgtgctttcttgtcctctttggggaaaatgaaattttacctagttttatactacttaacaaactagaaatcaacaaaatttgactagtctgatgatgataagtggggtttggcactacgtttgactaaatgttgtttttagatggagatctgatcagcacagttttggttatgtttcag

upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G060669_T01 (Zea mays), 5'ss of exon 4
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccat--------------ttttttccttccttta------ttgccctttatgcttatggttcactcactcactgtgttttgcgaag--------------------------------------------------
|||    |  ||||| ||| | || ||||| ||||| || || || || |||||||||||||| |||||||| || |||||||| || || || |||||||||| | ||  |||    || |  || |      ||||  |               ||| ||  | |||| |      | |   || |||  |     |  |  || ||||| ||||    | |                                                  
CCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGCTTACTGATCTTgtaagtcctttattcagacttaacttgctcgggccactttaaggaaaaaagagatgtttatttataccttgaggaaagtagggtttcatgtcttataatagcatac-cactgggtttgagcatgcatgtcaataacacatcaatcttatcagtgcatatgattgaatttttcag

upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G064988_T03 (Zea mays), 5'ss of exon 3
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccatttttttccttcctttattgcc--ctttatgcttatggttcactcactcactgtgttttgcgaag------------------------------------------------------------------------------
|||    |  ||||| ||||| || ||||| || || || || || || |||||||||||||| |||||||| || || ||||| || ||||| |||||||||  | ||   |     || |  ||   |    |||| ||         |   | ||||  |  ||| | |    | |    |    | |     |    |   |                                                                              
CCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGCTCACTGATCTTgtatgtcctttctacagacttaacttgtttgtgccacttcaaggaaaaaatatgtctatttacaccttgaggaacgtagggtgccttataataacataccactgggtttgagcaatagctattgagtcctgagcctgcatgtcaataacactttaaatcttatcagttatgattattttttcag

upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0048g01290.t01 (Vitis vinifera), 5'ss of exon 3
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaattt--gacctaat--gtttcgttcttcactccatttttttccttcctttattgccctttatgcttatg-gttcactcactcactgtgttttgcgaag
 || |||| |||||||||||| || ||||| || |||||||| || ||||| || |||||||| |||||||| |||||||| || ||  | || ||||| |||  |    | |||  || || |    | | ||   |   | | ||||       |   |   |    ||      ||| ||| | || || |||    |        
TCACTCCAAGGAAGACTTTGCAGTGAGAGGGAAGGAGCCCAAGGATGAGGTCCAAATTTACACATGGAAGGATGCTACTCTTCGTGAGTTAACTGATCTGgtatgtagctactttttgagctgactgatctagtgtattgttactttttgagttgactgatccagtatgttgaaacaatgtgtttattc-cttactactct--------

upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ15544 (Selaginella moellendorffii), 5'ss of exon 3
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccatttttttccttcctttattgccctttatgcttatggttcactcactcactgtgttttgcgaag
 ||     ||||||| ||||| ||  |||| ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||| || || || |   ||   ||   | |  |    |||  ||| ||  | ||||||| ||  ||| |                                             
TCACAGTGTGGAAGATTTTGCAGTGCGAGGGAAAGAGCCCAAGGAGGAAGTCCAAATCTATACCTGGAAGGACGCTACTCTCCGGGAGCTCACAGAGCTGgttagaccttggttc--cttcgttgcgcgtatttctctg-aattttttcattgttttgtccag-----------------------------------------

upper sequence: GLYMA03G02240.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ11264 (Selaginella moellendorffii), 5'ss of exon 3
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccatttttttccttcctttattgccctttatgcttatggttcactcactcactgtgttttgcgaag
 ||     ||||||| ||||| ||  |||| ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||| || || || |   ||   ||   | |  |    |||  ||| ||  | ||||||| ||  ||| |                                             
TCACAGTGTGGAAGATTTTGCAGTGCGAGGGAAAGAGCCCAAGGAGGAAGTCCAAATCTATACCTGGAAGGACGCTACTCTCCGGGAGCTCACAGAGCTGgttagacctttgttc--cttcgttgcgcgtatttctctg-aattttttcattgttttgtccag-----------------------------------------

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|193377631|gb|FK341981.1|FK341981
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|207805526|gb|GD776449.1|GD776449
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|58020613|gb|CX707355.1|CX707355
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|22929929|gb|BU547068.1|BU547068
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|31467784|gb|CD409812.1|CD409812
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|213604465|gb|DB978253.1|DB978253
EST:     TCAGATTTACAAATGGAAGGACGCTGGC-CTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TCAGATTTACACCTGGAAGGACGCT-ACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|193512610|gb|FK471810.1|FK471810
EST:     CTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: CTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|209707164|gb|BW656781.1|BW656781
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|7234436|gb|AW569773.1|AW569773
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|192317009|gb|FK010912.1|FK010912
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|193720076|gb|FK650488.1|FK650488
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|192317010|gb|FK010913.1|FK010913
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|31475122|gb|CD417150.1|CD417150
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|208320939|gb|GE123388.1|GE123388
EST:     AGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: AGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|193473329|gb|FK438696.1|FK438696
EST:     CAGATTTACACCTGGAAGGTACGTCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: CAGATTTACACCTGGAAGG-ACG-CTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|192314096|gb|FK011132.1|FK011132
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|213593874|gb|DB983138.1|DB983138
EST:     TCAGATTTACACCTGGAAGGACGCTGGC-CTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TCAGATTTACACCTGGAAGGACGCT-ACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|192328075|gb|FK020378.1|FK020378
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|209713909|gb|BW681914.1|BW681914
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|151395245|gb|EV265116.1|EV265116
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|209704041|gb|BW673641.1|BW673641
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
EST: gi|58016323|gb|CX703065.1|CX703065
EST:     TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTT                         GTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC
genomic: TTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctc ... ttttgcgaagGTCAAAGAAGTTGCTCCGGCTGCAAGGAGAAGAAACGCCAAACTCTCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATTCCATGGAAGACTTTGCCGTCAGAGGCAAAGAGCCCAAAGACGAGGTTCAGATTTACACCTGGAAGGACGCTACTCTCCGAGAACTCACCGATCTTgtaatttctcaatttgacctaatgtttcgttcttcactccatttttttccttcctttattgccctttatgcttatggttcactcactcactgtgttttgcgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG