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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataacaaatgaacaatctgcttgatattttgatttattaacaaataattactcaggaaagtggggttttattgttggaaccttcaagcttccctg...

Basic information

species Glycine max
transcript GLYMA11G27870.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 17
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 16
GTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataacaaatgaacaatctgcttgatattttgatttattaacaaataattactcaggaaagtggggttttattgttggaaccttcaagcttccctg-----------
|| ||||| ||||| || ||||| |||||  |||| || || ||||| |||||   ||||||||| ||||||||||||||||| ||||  | ||||||||   ||      ||  |  |||  |  | ||   |  ||  |  ||     ||  |        |    |||| || |    |||||  || ||  |             
GTGAATACGCATCTCACCCCACGACCAATACTACTCACTCGGCATGGAGAAAGCATGGATAATGTTAGAGGCAGAATTGGAGGAGATAGCGTAATAAGgt---atgttctctgctctgtctcttccaaatgccg--ttggtttcagccttttttttt------tcttctttttttttgaatacctttcagtttttcgttttgtttgcca

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 16
GTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgt-cagataacaaatgaacaatctgcttgatattttgatttattaaca-aataattactcaggaaagtggggttttattgttggaaccttcaagcttccctg
|| ||||||||||| ||||| || ||||||||||||||  | ||||| || |||| ||||||||| ||||| |||||||| || || |||||| ||||||  | |  | |  |   | |  |  ||||| | ||  ||| ||     ||  ||   |||  ||     |  ||   || | |||   | | | ||  |  
GTTAATACACATCTCACACCCCGACCAATTTTACTTACTAGGCATGGAGAGAGTCGGGATAATGTTAGAGGTAGAATTGGGGGTGACACTGCATTAAGgtatacaatataccttttctagattgttgatttattattttgttggtttaactatctttcaaaaatcatagaattgtctgattgaatgataatgattttc--

upper sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 17
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 5'ss of exon 15
GTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataacaaatgaaca-atctgcttgatattttgatttattaacaaataattactcaggaaagtggggttttattgttg--gaaccttcaagcttccctg
|| ||||| ||| | || ||||| ||||| || ||||| |||||||| |||||| ||||||||||||| ||  | |||||||| ||| ||| | | ||||    |    |         |   |   | | | | ||| | |     ||||||  |  ||    |    || | | || |  |  ||||| |  |      
GTCAATACTCATATCACTCCACGGCCAATATTTCTTACTCGACATGGTGAAAGTGAGGATAATGTGAGGGGTCGTATTGGAGGAGATCCTGTACTTAGgtactttcttgaccttgtgtgttccccccagagtatcattgact---gcataatttttttggtggatttccttctctggtagatgtgccttccaattcttaga

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|51336524|gb|CO980390.1|CO980390
EST:     GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG                         TGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
genomic: GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataac ... gttataacagTGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
EST: gi|51336471|gb|CO980337.1|CO980337
EST:     GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG                         TGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGNNNGCG
genomic: GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataac ... gttataacagTGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
EST: gi|22521914|gb|BU080725.1|BU080725
EST:     GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG                         TGAGGCAGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
genomic: GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataac ... gttataacagTGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
EST: gi|20448750|gb|BQ252874.1|BQ252874
EST:     GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG                         TGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
genomic: GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataac ... gttataacagTGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG
EST: gi|22930234|gb|BU547373.1|BU547373
EST:     GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAG                         TGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAATTTGTTGGAAAGCG
genomic: GAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataac ... gttataacagTGAGGCTGGAGAACTTTATTCAAAGAAGCTTGCCAAGTTTGTTGGAAAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATACACATCTTACACCACGCCCAATTTTACTTACCCGACATGGGGAAAGTCAGGATAATGTGAGAGGCAGAATTGGAGGGGATACTGCAATAAGgtcagataacaaatgaacaatctgcttgatattttgatttattaacaaataattactcaggaaagtggggttttattgttggaaccttcaagcttccctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggggt