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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcagcacaaaaacgagcatgcacatgtacacttgg...

Basic information

species Glycine max
transcript GLYMA07G00630.2
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcag----cacaaaaacgagcatgcacatgtacacttgg-
|  ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || ||||  || ||||| ||| ||||||||||| |||||||||   |  |  |  ||||  ||   ||  |   | ||  | |    ||  | |  ||  |  | ||    ||   ||| || || |  |   |  |  ||  
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttg---ttctctgtgttcttgctggacaact--gtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa

upper sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 11
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcagcacaaa---aacgagcatgcacatgtacacttgg
|| | |||||||| || || ||||| |||||||| || |||||| ||||||||||||| ||||||||||  || ||| |  |  |||| ||||| || | ||| | |    |         |  |   || | ||||  ||    |  | | |||     |  ||  | || ||    |||  || | ||||| || ||   |
TTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGAAgttagtacacctgaaaccaacccgtgctcactataattcttg-attgtcttaaatttgtaaaggaataacaaaattctaacatgctttcacattta-acacag

upper sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 27
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattg-----gctttctctctaagcagtttaat-atttatggtacccttaatactatactgatcagcacaaaaacgagcatgcacatgtacacttgg--
|  | ||||||||||||||||||||||| ||||| || |||||||| ||||| || || ||||| || |  || ||||| ||| | || |||||  |||||| |  |    |||     | | | |  || |    |||| | |   |   ||    || |    |     ||           ||   |     | |  | |||   
TGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAAGgtataaacatgttgcacatgatgttttcctcatacttttagtgaaacagaatagttatattgtggtttcagtcgtatggttcgtgatggtttgtttcttgatttgcag

upper sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 29
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcagcacaaaaacgagcatgcacatgtacacttgg--------
|| | ||||| ||||||||||||||||| ||||| || |||||| ||||||||||||| ||||| || |  || ||| | ||||| |||||||| |||||||| | | |    |   |   ||    |   |||  | ||  | ||     ||||  |||| |  |       |  | | |  ||     |||   ||||        
TTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAAGgttagaacttgaagtagtatacttctcgtgattt--tgttcctcgt----ctaattttataatt-tggattttatgatgggt-tgttttcgtatggttgggactgatg

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|16996275|gb|BM085647.1|BM085647
EST:     ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAG                         AGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
genomic: ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattg ... tggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG
EST: gi|33390180|gb|CA853387.1|CA853387
EST:     ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAG                         AGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAGGCTGT
genomic: ACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattg ... tggctttcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAGGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcagcacaaaaacgagcatgcacatgtacacttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA