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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattctagctccaatgaagtatcactagtgattatgagtagagtaatgaacattataatttaatttcttgacatcagttgatttgtatagt...

Basic information

species Glycine max
transcript GLYMA09G36920.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 5'ss of exon 15
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattcta---gctccaatgaagtatcactagtgattatgagtagagtaatgaacattataatttaatttcttgacatcagttgatttgtatagt------------------------
| || ||||| |||||| |  | || || |||   || ||||||||    || || |||||||||||||||||||| |||| |||||| |||||||||||||||||  |  |  ||        ||||| || |   |      | |   |  | |   ||| | | |   |||  |  |  | | |        ||| |  |                        
GGGGGCAAGATTATTGGCAAAATGAGAACATAGTTGAAGAGATGCCATGCTGCCGTCAGATGTTCAACATTTTTCATCCCTTTGATCCTGTAGCATACAGgtttgcagctttcgtacatatattaatgatgttttcatcacttctctttatgtactggagaagactgtc-cttatctgttgcaaagcgaggagcatgtctcatgaatctaagttggcttttatacag

upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G023335_T01 (Zea mays), 5'ss of exon 17
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctaca--attctagctccaatgaagtatcactagtgattatgagtagagtaatgaacattataatt------taatttcttgacatcagttgatttgtatagt--------------------------------------------------------------------------------------
 ||| | ||| |||||| |  |  | || ||||  || ||||||||    || |||||||||||||| |||||||| || | |||||| ||||||||||||||||   |    ||  || |    |    |||   | | || | ||   |   ||    |||    || |      | |   | ||| ||     ||| ||  ||                                                                                        
AAGGGCGAGATTATTGGAAAGATAAGAACATAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGATCCTGTAGCATACAGgtttgtagcttccttacagttttgttttcttatgtttggagagtttgtaaaacatataccacagcggaactaaacaatgacaacctgatatgtaaagatgtgcttaacctttttttcttgcactggaagacagtgtacttatctgtcgcatagtgaggaatatgtcatatgaatctaggtgggcttttatacag

upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G318860_T02 (Zea mays), 5'ss of exon 15
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattcta-gctccaatgaagtatcac-tagtgattatgagtagagtaatgaacattataatttaatttcttgacatcagt-tgatttgtatagt
 ||| ||||| |||||| |  |  | ||  |||  || ||||||||    || |||||||||||||| |||||||| || | ||| || ||||||||||||||||      |  ||  ||    |    | |||  |   ||   |  ||| |  |   || |  | ||   || |     |   || | |||| || |    
AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttttcttatctcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaa---

upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G318860_T01 (Zea mays), 5'ss of exon 15
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattcta-gctccaatgaagtatcactagtgatta-tgagtagagtaatgaacattataatttaatttcttgacatcagt-tgatttgtatagt------------------------------------------------------------------------------------------------
 ||| ||||| |||||| |  |  | ||  |||  || ||||||||    || |||||||||||||| |||||||| || | ||| || ||||||||||||||||      |  ||  ||    |    | |||    ||   | |  ||| |  |   || |  | ||   || |     |   || | |||| || | ||                                                                                                 
AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttttcttatctcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaaagatgcgcttaacctttgctaaatttagatagtgtttttgttgcactggaagacagtgtacttatattgcatagtgaggaatatgtcatatgaatctag

upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G31480.1 (Arabidopsis thaliana), 5'ss of exon 16
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattctagctccaatgaagtatcactagtgattatgagtagagtaatgaacattataattt--aatttcttgacatcagttga---tttgtatagt----
  ||  |||| || |||||  |||| |||   |  || |||||||| |||||||| |  |||||||| || ||||||||||||||||| || ||||| ||||| |     ||   |  |  ||     | |  |||||   |   |     ||  |    |   |  |||  || |   | ||  ||  | |   ||||| |       
AGGGAAAAGATTACTGGGAAGAGGAGAATGCTATTGAAGAGATGCCAGCTTGTCGTCGAATGTTCAATATATTTCACCCCTATGATCCTGTTGCATATAGgttagtcttcatgg-aaataaaacagcttgtagctagtttatgatatcgctgtctttgttaccttcttttgcaagtgtgtaacgccaactaaacttttgtttcacgcag

upper sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S74_64V6.1 (Physcomitrella patens), 5'ss of exon 13
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattctagctccaatgaagta-tcactagtgattatgagtagag--taatgaacattataatttaatttcttgacatcagttg-atttgtatagt----
 |||    || || ||| |  | |||   ||    || || ||||| || || || |   |  | || |||||||||||||||||||| |||||||| ||||  || |    ||| |     |||  | | |   ||   ||| |||  |||   |  |  ||  | |  |  || |      ||     |  |   ||||  |    
CAGGGACGGAGTACTGGCAAGATGAAGGCATTGATGAAGAAATGCCAGCCTGCCGCCTTTTACTGAATATTTTTCACCCCTATGATCCAGTAGCATATAGgtaagcaa----tcttgtcgtgatgtcgaacttgataagaattctgaagagaaactgctcgaccatgtgctgcaagtgtcactcactgtctctacccgtatgattcag

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|8402460|gb|BE058094.1|BE058094
EST:     TGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAG                         GATAGAGCCACTTGTGTGCAAAGAATACATCAGCCAACGGCCTGTTTTGAT
genomic: TGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctaca ... ttcaccaaagGATAGAGCCACTTGTGTGCAAAGAATACATCAGCCAACGGCCTGTTTTGAT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattctagctccaatgaagtatcactagtgattatgagtagagtaatgaacattataatttaatttcttgacatcagttgatttgtatagt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG