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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA

Basic information

species Glycine max
transcript GLYMA02G26480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
----taaaatcttgcacaaattattctcataattctgaa-ataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
     | |||| | | |     || |||  |||  | |  |  |   |      | |   || ||||||   | ||||  | |  | || ||  ||||| |||||| |||||  ||||||||||||| |||||||| || ||| | ||| | |||||||||||||||||||| ||||||||||||||  |||| ||| | || ||
gtacgataatcctcctcct-ccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgat---tgatttggtttgatttgttg--gtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
             |  |   |  |||    ||     |    ||   ||||| |   || || | |   ||     ||                ||| |||||||||  ||||||| ||||| |||||||| || ||| | ||  |||||||||||||||||||||| ||||||||||||||  |||| ||| |||| ||
-----------gtacgtctcttccatctccctcctccatcc-atgcaaacttatagctactgttcatcgatcgtccatgactc----------catgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
-taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
 |   |||     ||  |       |    |||   ||           |    |    | | |||  || | |       ||     |      ||| |||||||||  ||||||| ||||| |||||||| || ||| | ||  |||||||||||||||||||||| ||||||||||||||  |||| ||| |||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
-taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
 |||      ||| ||     ||  ||      ||   || |||     | ||    ||      || |||||    ||    |||  ||||    || ||  | |||  ||   || ||||| |||||||| || ||| ||||| ||||||| ||||||||||||||   |||||||||| || | |||||||| || ||
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaatt-----caattaattggggat---ttggaattgt----tgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
-ta-aaatcttgcacaaattattctcataattctgaaataaatgataataactt-ttttttattgataaataatt--taatat--attctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
 ||    || | | |      | | |  | |  |      |    |  || ||     | ||        | | |  | || |   | ||  || |||  | || ||| |||||  ||||||| ||||| |||||||| || ||| | ||| |||||||||||||||||||||| ||||||||||||||  |||| ||  |||| ||
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgt-ctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014653_T03 (Zea mays), 3'ss of exon 1
---------------taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatatt-ctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
                    ||||     |       |   |    ||||  || |     |       |     ||   |   | |  ||  ||| ||     | |||  || ||| |||||  ||||||| ||||| |||||||| || ||| | ||| |||||||||||||||||||||| ||  |||| |||||  |||| ||| | || ||
gtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgt-gtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCCAGGCCCAACCGCGCCGCCGGGGCTGGGTA

upper sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g02300.t01 (Vitis vinifera), 3'ss of exon 1
taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
       |       |||||| ||||  || ||  ||   |      |         | | |||   || || |      | ||||| |   ||    ||  ||||| ||||||||||||||||||||||| || ||  ||||||| || || || || |||||||||||  ||||||||||| | ||||| || || ||
------gtaattattattattttcatttttttgttatttttttctgaactcccaaaatttggatttttatttaagggggatttggtgat---ttgaacagAGATGGCCTTGTACGGAGAGAAAGAGTGGTACTTCTTTTCGCCGAGAGATCGGAAATATCCGAACGGTTCAAGGCCGAACCGGGCAGCGGGAACAGGGTA

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|22540547|gb|BU090390.1|BU090390
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|6502164|gb|AW203537.1|AW203537
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|11274497|gb|BF324850.1|BF324850
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|16996103|gb|BM085475.1|BM085475
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|15664421|gb|BI701792.1|BI701792
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|37996761|gb|CF808350.1|CF808350
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|26060240|gb|CA803154.1|CA803154
EST:     AATAATCGCCTAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|37995754|gb|CF807343.1|CF807343
EST:     TATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
EST: gi|20075850|gb|BQ094633.1|BQ094633
EST:     AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAG                         GAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC
genomic: AATAATCGCCGAAATCGATCTCTACAAGTACGACCCATGGGACCTTCCAGgtaaattaac ... tgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA
     ttttttttattgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA

- - - cttgcac
- - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg