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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatatattctatatcttctttcatcggactatttcttttggagtttagtttatgatcaaacttcatgattttctacttag

Basic information

species Glycine max
transcript GLYMA09G08150.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G130440_T02 (Zea mays), 5'ss of exon 11
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata-ttctatatcttctttcatcggactattt--cttttggagttt----agtttatgatcaaacttcatgattttctacttag----------------
|||||| ||||| |||||||||||||| || ||| | || ||| || || || ||||||||| | |||||||| || || |||||||||||||||||||||||||||| ||| |||| | ||| | | | | ||| || || | ||| | || | | || | | | || | | | |
AGGAAACTTTGTGCAACCAACAATTGTGGAAATTACACCTTCTGCACCAGTTGTGAAAGAAGAACTCTTTGGTCCTGTCCTTTATGTTATGAAATTTCAGgtagcatatagttcaatattatgtttttttgtattttttacctgttctaatttctacaattgagaaccactgtgcctaatatcc-atgaggtttgtgtttcctacag

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM5G820733_T02 (Zea mays), 5'ss of exon 3
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata-ttctatatcttctttcatcggactatttcttttggagtttagtt--tatgatcaa--acttcatgattttctacttag--------------------
|||||| ||||| |||||||||||| | || ||| | | ||| || || || ||||||||| | |||||||| || || |||||||||||||||||||||||||||| ||| |||| | ||| | ||||| | | | || || || || | ||| | | | || |
AGGAAACTTTGTGCAACCAACAATTATGGAAATTACACGTTCTGCACCAGTTGTGAAAGAAGAACTCTTTGGTCCTGTCCTTTATGTTATGAAATTTCAGgtagcatatagttcaatattatgtttttttttg-tattttgtatctgttctaatttctacaattgagaactactgtgtctaatatccatgaggtttgtgtttcctacag

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G070514_T02 (Zea mays), 5'ss of exon 4
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata-ttctatatcttctttcatcggactatttcttttggagtttagtt--tatgatcaa--acttcatgattttctacttag--------------------
|||||| ||||| |||||||||||||| || ||| | | ||| || || || ||||||||| | |||||||| || || |||||||||||||||||||||||||||| ||| |||| | ||| | ||||| | | | || || || || | ||| | || | || |
AGGAAACTTTGTGCAACCAACAATTGTGGAAATTACACGTTCTGCACCAGTTGTGAAAGAAGAACTCTTTGGTCCTGTCCTTTATGTTATGAAATTTCAGgtagcatatagttcaatattatgtttttttttg-tattttgtatctgttctaatttctacaattgagaactactgtatctaatatccatgaggtttgtgtttcctacag

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G382159_T01 (Zea mays), 5'ss of exon 2
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata-ttctatatcttctttcatcggactatttcttttggagtttagtttatg----atcaaacttcatgattttctacttag--------------------
| | | | | | || ||| | | ||| || || || ||||||||| |||||||| || || |||||||||||||||||||||||||||| ||| |||| | ||| | | ||||| | | | || ||| | | |||| | | || || |
AAAATGTGACAAGTATTTTTACCTGGAGGAAATTACACGTTCTGCACCAGTTGTGAAAGAAGAACCCTTTGGTCCTGTCCTTTATGTTATGAAATTTCAGgtagcatatagttcaatattatgttttttttg--tattttgtatctgttctaatttctacaatagagaactactgtgtcttatatccatgaggtttgtgtttcctacag

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 11
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatatattctatatcttctttcatcggactatttcttttggagtttagtttatgatcaaacttcatgattttctacttag------------------
||||||||||| || |||||||| ||||||||||||||| |||| |||||||||| ||||||||||| ||||||||||| ||||| |||||||||||||||| | | || || | | | || || | | | || || ||||||||||| || ||| | || |
GGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGGAAGAATTGTTCGGTCCAGTTCTTTATGTGATGAAATTTCAGgtagtctgttaatgatgtcactctcctcc---ctcttggtggtctatttctcttcctgatcaaactt-atcttttcatgtttggaaactcctctttgtgcag

upper sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 10
lower sequence: Vv09s0002g01010.t01 (Vitis vinifera), 5'ss of exon 9
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatatattctatatcttctttcatcggactatttcttttggagtttagtttatgatcaaacttcatgattttctacttag
||||||||||| | || || |||||||||||||||||| |||| ||| || |||||||||||||||| ||||||||| |||||||| || ||| |||||| | | || || | || | | || || | | | ||| | | | | | || ||
GGGAAATTTTGTGCGGCCCACCATTGTTGAGATTTCTCCAAATGCAGATGTTGTGAAAGAAGAATTGTTTGTTCCAGTTCTTTATGTTATCAAGTTTACGgtagcctcttcatgattcaagtattagttta--tacatgtattcacactttctcattccttaaaactaa--actctttatgcag

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|207768693|gb|GD740504.1|GD740504
EST:     GTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGAT
genomic: GTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGAT
EST: gi|58019812|gb|CX706554.1|CX706554
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTAGGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|57575444|gb|CX548419.1|CX548419
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|254336948|gb|GR843127.1|GR843127
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|208261117|gb|GE060363.1|GE060363
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTCGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|58022816|gb|CX709557.1|CX709557
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|208163845|gb|GD961511.1|GD961511
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|254336949|gb|GR843128.1|GR843128
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|19452651|gb|BM954061.1|BM954061
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAA
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAA
EST: gi|58022682|gb|CX709423.1|CX709423
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTAGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatatattctatatcttctttcatcggactatttcttttggagtttagtttatgatcaaacttcatgattttctacttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG