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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatcaaaaattttgtttttaattggtttttgtttaacctagttctattgtcttaattctaattattcgatttttgttaatttgaattgaacag

Basic information

species Glycine max
transcript GLYMA10G00490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 2
GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatcaaaaattttgtttttaattggtttttgtttaacctagttctattgtcttaattctaattattcgatttttgttaatttgaattgaacag
    ||||| |      |||| || || ||||| ||||||||| | ||||||||||| ||||||||| |||||||||| | |||  | || || || ||||||   |       | || |  ||  |    ||   |||    ||| |   || |  | |||||  |  |  | ||||  |  | ||| |        
TTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGCACTCCACCATGGCTCAAAAGgttcttactt----tcttctccttcgtcttcttccattt---ttagcttccttttactgattct--tcttctgcttttgctctaattgcag-------

upper sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 2
GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgt----ttaaatcaaaaattttgtttt-taattggtt--tttgtttaacctagttcta-ttgtcttaattctaattattcgat-ttttgttaatttgaattgaacag------
 | ||| || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| |||||||||| ||||||| |||||| ||||||||    ||  ||   | ||| |||||| |  |  ||   ||  ||  |  |  |  || || |||  | | | || |||  || ||||  |  ||||||||  |  |      
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag

upper sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaa-atcaa---------aaattttgtttttaattggtttttg---tttaacctagttctattgtcttaattctaattattcgatttttgttaatttgaattgaacag
    ||  | |      |||| ||||| |  ||| |||||||  |||||||||||||||| |||||| ||||||| |||||  | ||  | ||||||||||| | |  ||||         |||||||    |   | || ||| |   |||     | ||   | | |||   |||  | | ||    | |  |  | ||  ||  ||||
CTTGCATCGCAAGCGTCATGGGTACCGACCGGATTACTTCGAAAGGAAGCGCAAGAAAGATGCGCGTGAAGTTCATAAACGGGCGGCCTTCGCCCAGAAGgtatgacgtcaactttctcccaaattttacagtctttggggtttagggttttgttagaattggttagacttgtgtctgttaactcacagtgttctggtgtgggtt--acag

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|26059399|gb|CA802313.1|CA802313
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAAATTATGCTGAAAA
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAG-AAAAATTATGCTGAAAA
EST: gi|11413156|gb|BF425167.1|BF425167
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|20498024|gb|BQ272954.1|BQ272954
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|15813104|gb|BI785379.1|BI785379
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|298179957|gb|HO025172.1|HO025172
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|5606189|gb|AI900287.1|AI900287
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|298178157|gb|HO027540.1|HO027540
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|209725840|gb|BW654703.1|BW654703
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|120530814|gb|EH258947.1|EH258947
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|298182139|gb|HO026314.1|HO026314
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|298189817|gb|HO038220.1|HO038220
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|192329667|gb|FK022933.1|FK022933
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|192333080|gb|FK026409.1|FK026409
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
EST: gi|120530581|gb|EH258714.1|EH258714
EST:     GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAG                         GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG
genomic: GCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatca ... aattgaacagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgtttaaatcaaaaattttgtttttaattggtttttgtttaacctagttctattgtcttaattctaattattcgatttttgttaatttgaattgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG