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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaacttgacagtgattttgatatttccttcacaatagttcagattcttgtttaaatctagcaataaactatgccggtgtatcaccattctaagct...

Basic information

species Glycine max
transcript GLYMA18G11100.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G11100.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g33240.1 (Oryza sativa), 5'ss of exon 5
GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagt------aacttgacagtgattt-tgatatttccttcacaatagttcagattcttgtttaaatctagcaataaact-atgccggtgtatcaccattctaagct-------------------------------------------------------
|||||||||  |  | || ||||||||||| |||||||||||||| |||||| ||       |  |||   ||  ||  |  || | ||||     | |   |  || | ||   | ||| | ||   | | ||||   ||| |     ||| |   |                                                       
GTTGGCTGATCTACAAGATTTCAAGAAAGTGAATGAGATCTATGCCAAATgtaagctcaaaaactttgttcgtccttagtagtactaccttttatttggcctaagtt-tagtgacattcttgaaacgcattcatgctaatgtttatatgttcaatatttttgccgtgatctctatattttgcttctgaagaattttgcaattcttacttgcag

upper sequence: GLYMA18G11100.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0090g00390.t01 (Vitis vinifera), 5'ss of exon 5
GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaacttgacagtgattttgatatttccttcacaatagttcagattcttgtttaaatctagcaataaactatgccggtgtatcaccattctaagct-----
|||||||||||||||||||||||||||||| |||||||||||||| ||||||||||    | | | | |  |   |  |||  | |      || | |   | | || |   ||    | | ||| || |   | |||  || | |||||     
GTTGGCTGACTTGAAGGACTTCAAGAAAGTGAATGAGATCTATGCCAAATgtgagttcaataa-aataaaataactgcttctat-atgtagattgaaaagatgggttgagaata-tggttatcta-gctgtgatttcaatat-caaagctcactt
















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|298191613|gb|HO039092.1|HO039092
EST:     GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAAT                         ACTTCCCTTCACCAGCCCCGGCA
genomic: GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaact ... attgtttcagACTTCCCTTCACCAGCCCCGGCA
EST: gi|298166155|gb|HO009126.1|HO009126
EST:     GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAAT                         ACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTAGCTT
genomic: GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaact ... attgtttcagACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTAGCTT
EST: gi|298179458|gb|HO027929.1|HO027929
EST:     GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAAT                         ACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTAGCTTC
genomic: GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaact ... attgtttcagACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTAGCTTC
EST: gi|298178386|gb|HO024121.1|HO024121
EST:     GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAAT                         ACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTA
genomic: GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaact ... attgtttcagACTTCCCTTCACCAGCCCCGGCACGGTCAACGTATCAAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGCTGACTTGAAGGACTTCAAGAAAGTTAATGAGATCTATGCTAAATgtgagtaacttgacagtgattttgatatttccttcacaatagttcagattcttgtttaaatctagcaataaactatgccggtgtatcaccattctaagct

- - - - - TTGAAG
- - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttcac